Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
DETAILED ACTION
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office Action.
Status of Claims
Claims 1, 3, 8-13, 22, 24, 25 and 27-35 are currently pending. Claims 1, 3, 24, 25, 27, 34 and 35 have been amended by Applicants’ amendment filed 10-17-2025. Claim 23 has been canceled by Applicants’ amendment filed 10-17-2025. No claims have been added by Applicants’ amendment filed 10-17-2025.
Applicant's election with traverse of Group I, claims 1-7, directed to a method of solid-phase synthesis of polymers; and the election of Species without traverse as follows:
Species (A): wherein linkers comprise single-stranded oligonucleotide linkers (instant claims 2 and 4), in the reply filed on January 6, 2022 was previously acknowledged.
Claims 8-20 were previously withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on January 6, 2020.
Claims 5-7 were previously withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected species, there being no allowable generic or linking claim.
The restriction requirement was deemed proper and was made final.
The claims will be examined insofar as they read on the elected species.
A complete reply to the final rejection must include cancellation of nonelected claims or other appropriate action (37 CFR 1.144) See MPEP § 821.01.
Therefore, claims 1, 3, 22, 24, 25 and 27-35 are under consideration to which the following grounds of rejection are applicable.
Priority
The present application filed January 6, 2020.
Interview Summary
Applicant contacted the Examiner to set up an interview, where such telephonic interview was conducted between the Examiner and Applicant’s representative Benjamin Keim on August 22, 2025. Applicant and the Examiner discussed the rejections of record; as well as, proposed amendments to the claims. Additionally, Applicant questioned whether the references taught the limitation of: ‘spatially selective, sequence-dependent orthogonal cleavage in a single reaction vessel,’ wherein this limitation is not recited in claim 1 of the claims filed October 17, 2025.
Withdrawn Objections/Rejections
Applicants’ amendment and arguments filed October 17, 2025 are acknowledged and have been fully considered. The Examiner has re-weighed all the evidence of record. Any rejection and/or objection not specifically addressed below are herein withdrawn.
Maintained Objections/Rejections
Claim Interpretation: the term “thereby achieving orthogonal cleavage in a single reaction vessel” in claim 1 is not given patentable weight because it simply expresses the intended result of a process step positively recited (See, MPEP 2111.04(I)).
The term “the polymer strands are removed from the solid substrate” in claim 34 is interpreted to encompass removal of polymer strands that are attached to the solid substrate and/or removal of polymer strands that are not attached to the solid substrate.
Claim Rejections - 35 USC § 112(b)
The rejection of claims 1, 3, 22, 24, 25 and 27-35 is maintained under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claim 1 is indefinite for the recitation of the term “thereby achieving orthogonal cleavage in a single reaction vessel” such as recited in claim 1, lines 12-13 because the term is not recited in the as-filed Specification and original claims; and no “single reaction vessel” is recited in any of the process steps including claims 1(a) and 1(b), such that the origin, identity and/or use of such a “single reaction vessel” is completely unclear. The as-filed Specification mentions a single reaction vessel once regarding step-by-step solid-phase synthesis (paragraph [0004]), while “orthogonal cleavage” is taught twice, once regarding different groups of linkers 1402-1412 and once with regard to denaturation conditions (paragraphs [0145]-[0146]). However, “orthogonal cleavage” it is not taught in the as-filed Specification with respect to a single reaction vessel. Additionally, the term “thereby” is defined as referring to particular means, or as a result or consequence of contacting the linkers with a cleavage agent with an enzyme (e.g., orthogonal cleavage) as evidenced by Merriam-Webster Dictionary (pg. 1) and Cambridge English Dictionary (pg. 1). Instant claim 1 recites the use of ‘solid phase synthesis’ and a ‘solid substrate’, but there is no indication that a single reaction vessel was used in the process as recited and, thus, the metes and bounds of the claim cannot be determined.
Claim 1 indefinite for the recitation of the term “the regenerated first linkers” such as recited in claim 1, line 27. There is insufficient antecedent basis for the term “the regenerated first linkers” in the claim.
Claim 3 is indefinite for the recitation of the term “prior to (b)” and “wherein the first restriction endonuclease only cleaves double-stranded oligonucleotides” such as recited in claim 3, lines 1-2 and 7-8 because claim 1(b) recites the cleavage of single-stranded first linkers using the ‘first restriction endonuclease’, such that it is completely unclear how claim 1(b) is carried out if “the first restriction endonuclease only cleaves double-stranded oligonucleotides” as recited in claim 3 and, thus, the metes and bounds of the claim cannot be determined.
Claim 24 is indefinite for the recitation of the term “the first regenerated linkers” such as recited in claim 24, line 2. There is insufficient antecedent basis for the term “the first regenerated linkers” in the claim because claim 1, line 20 recites the term “regenerated first linkers.”
Claim 24 is indefinite for the recitation of the term “another round of synthesis” such as recited in claim 24, lines 2-3. There is insufficient antecedent basis for the term “another round of synthesis” in the claim. Moreover, claim 24 depends from claim 1, wherein claim 1 does not recite any ‘rounds of synthesis’ and, thus, the metes and bounds of the claim cannot be determined.
Claim 25 is indefinite for the recitation of the term “storing the solid substrate with the first regenerated linkers and the second regenerated linkers attached thereto” such as recited in claim 25, lines 1-3. There is insufficient antecedent basis for the terms “the first regenerated linkers” and “the second regenerated linkers” in the claim because claim 1, lines 28-29 recites the term “regenerated first linkers.” Moreover, claim 25 depends from claim 1, wherein claim 1 does not recite the presence or regeneration of ‘second linkers’ attached to the solid substrate and, thus, the metes and bounds of the claim cannot be determined.
Claim 27 is indefinite for the recitation of the term “the first linkers” such as recited in claim 27, line 2. There is insufficient antecedent basis for the term “the first linkers” in the claim because claim 1, lines 20 and 27 recites the term “regenerated first linkers”. As noted in claim 1(c), the solid support comprises regenerated first linkers and second linkers.
Claim 31 is indefinite for the recitation of the term “the corresponding portions of the first linkers” such as recited in claim 31, line 4. There is insufficient antecedent basis for the term “the corresponding portions of the first linkers” in the claim.
Claims 22 and 28-35 are indefinite insofar as they ultimately depend from instant claim 1.
Claim Rejections - 35 USC § 112(d)
The rejection of claim 31 is maintained under 35 U.S.C. 112(d) as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 31 recites (in part): “such that regenerated portions of the regenerated first linkers have a different sequence than the corresponding portions of the first linkers while maintaining the first recognition site” such as recited in claim 31, lines 3-5 because claim 31 depends from instant claims 1 and 29, wherein claims 1 and 29 do not recite any ‘corresponding portions’ of the first linkers. Thus, claim 31 is an improper dependent claims for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Applicant may cancel the claim, amend the claim to place the claim in proper dependent form, rewrite the claim in independent form, or present a sufficient showing that the dependent claim complies with the statutory requirements.
Claim Rejections - 35 USC § 103
The rejection of claims 1, 3, 22, 24, 25 and 27-33 is maintained, and claims 34 and 35 are newly rejected, under 35 U.S.C. 103 as being unpatentable over Efcavitch et al. (hereinafter “Efcavitch”) (US Patent Application Publication No. 20190275492, published September 12, 2019; effective filing date October 17, 2013; of record) in view of Tsavachidou et al. (hereinafter “Tsavachidou”) (US Patent Application Publication No. 2018073057, published March 15, 2018; effective filing date May 13, 2016; of record) as evidenced by Tsavachidou et al. (hereinafter “Tsavachidou ‘465”) (International Application WO2015167972, published November 5, 2015; of record); and Gaublomme et al. (hereinafter “Gaublomme”) (US Patent Application Publication 20180320224, published November 8, 2018).
Regarding claims 1, 3, 22, 24, 25, 27, 28, 29 (in part) and 30-35, Efcavitch teaches methods for nucleic acid synthesis including synthesizing polynucleotides such as DNA and RNA using renewable initiators coupled to a solid support, wherein specific sequences of polynucleotides can be synthesized de novo, base by base, in an aqueous environment, without the use of a nucleic acid template (interpreted as solid-phase synthesis with monomers; adding monomers to free ends; including a template for regeneration, claims 1, 24 and 27) (Abstract; and paragraph [0004], lines 1-3). Efcavitch teaches that methods of the invention are directed to template-independent synthesis of polynucleotides by using a nucleotidyl transferase enzyme to incorporate nucleotide analogs coupled to an inhibitor by a cleavable linker (interpreted as cleavable linkers, claim 1) (paragraph [0004]). Efcavitch teaches that a removable terminating group can be linked to the base portion of the nucleic acid and/or to the 3' hydroxyl of the nucleic acid, such that deblocking of the terminating group and/or the 3' blocking group, creates a new active site that is a substrate for the enzyme; and that with subsequent addition of a new nucleotide or nucleotide analog, the oligonucleotide is extended (interpreted as extending the first linker to create an overhang; adding monomers; additional strands; extending the first truncated linker with nucleotides that are complementary to overhangs; and regeneration template, claims 1, 24 and 27-29) (paragraph [0005], lines 10-16). Efcavitch teaches that upon cleavage of the linker, a natural polynucleotide is released from the solid support, such that once the sequence is complete, the support is cleaved away, or the 3' moiety is contacted with a releasing agent, leaving a polynucleotide essentially equivalent to that found in nature (interpreted as a first linker and a second linker attached to a solid substate at a first location and a second location) (paragraph [0007]). Efcavitch teaches that the macromolecules are linked to nucleotide analogs using any of a variety of linkers (interpreted as a first linkers and second linkers, claims 1 and 27) (paragraph [0008]). Efcavitch teaches that linkers can, for example, include photocleavable, nucleophilic, or electrophilic cleavage sites, such that in photocleavable linkers, cleavage is activated by a particular wavelength of light, may include benzoin, nitroveratryl, phenacyl, pivaloyl, sisyl, 2-hydroxy-cinamyl, coumarin-4-yl-methyl, or 2-nitrobenzyl based linkers (interpreted as recognition sites, claims 1 and 27) (paragraph [0046]). Efcavitch teaches the synthesis of nucleotide analogs having the formula NTP-linker-initiator, wherein NTP is a nucleotide triphosphate (i.e., a dNTP or an rNTP), the linker is a cleavable linker between the pyridine or pyrimidine of the base, and the inhibitor is a group that prevents the enzyme from incorporating subsequent nucleotides, such that at each step, a new nucleotide analog is incorporated into the growing polynucleotide chain, where upon the enzyme is blocked from adding an additional nucleotide by the inhibitor group; and once the enzyme has stopped, the excess nucleotide analogs are removed from the growing chain, the inhibitor can be cleaved from the NTP, and new nucleotide analogs can be introduced in order to add the next nucleotide to the chain (interpreted as solid phase synthesis using monomers, claims 1 and 27) (paragraph [0055], lines 1-12). Efcavitch teaches in Figure 22 the incorporation of a reusable 3’ moiety into a nucleic acid coupled to a solid support, growth of the nucleic acid using TdT, and release the de novo oligonucleotide (interpreted as single strand oligonucleotides; contacting linkers with a linker cleavage agent; releasing a polymer strand; interpreting the reusable moiety as forming a truncated linker attached to the solid support; and regenerating linkers, claims 1 and 27) (paragraph [0045]; and Figure 22). Figure 22 is shown below:
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Efcavitch teaches that by repeating the steps sequentially, it is possible to quickly construct nucleotide sequences of a desired length and sequence, wherein advantages of using nucleotidyl transferases for polynucleotide synthesis include: (1) 3'-extension activity using single strand (ss) initiating primers in a template-independent polymerization, (2) the ability to extend primers in a highly efficient manner resulting in the addition of thousands of nucleotides, and (3) the acceptance of a wide variety of modified and substituted NTPs as efficient substrates (interpreted as solid phase synthesis; cleavage; encompassing first linkers and second linkers with different sequences; forming a truncated linker attached to the solid support; regenerating the linker; and same nucleotide sequence having the same chemical and structural identity, claims 1 and 27) (paragraph [0055], lines 12-21). Efcavitch teaches that full length sequences can undergo extension to append any element which will enable selective capture, isolation or enrichment (interpreted as extension reactions; adding additional polymer strands; and purifying strands removed from the solid substrate, claims 1, 24 and 35) (paragraph [0113], lines 15-17). Efcavitch teaches in Figure 26 illustrates an exemplary resin regeneration cycle (paragraph [0049]; and Figure 26). Figure 26 is shown below:
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Efcavitch teaches nucleotide analogs having the formula NTP-linker-inhibitor for synthesis of polynucleotides, wherein a linker can be any molecular moiety that links the inhibitor to the NTP, wherein linkers can be cleaved including by adjusting the pH of the surrounding environment; they can be cleaved by an enzyme that is activated at a given temperature, but inactivated at another temperature, and/or the linkers can include disulfide bonds; the linkers can include photocleavable, nucleophilic, or electrophilic cleavage sites, photo-cleavable linkers, wherein cleavage is activated by a particular wave length of light, including benzoin, nitroveratryl, phenacyl, pivaloyl, sisyl, 2-hydroxy-cinamyl, coumarin-4-yl-methyl, or 2-nitrobenzyl based linkers (interpreted as a first linkers and second linkers that are different, claim 1) (paragraphs [0060]-[0061]). Efcavitch teaches that examples of nucleophilic cleavage sites include fluoride ion cleavable silicon-oxygen bonds or esters which can be cleaved in a basic solution; and that electrophilically-cleaved linkers can include acid induced cleavage sites which can comprise trityl, tert-butyloxycarbonyl groups, acetal groups, and p-alkoxybenzyl esters, amides, and a cysteine residue as shown in Figure 15 (interpreted as different first and second linkers at different locations on a solid substrate, claim 1) (paragraph [0062]; and Figure 15). Efcavitch teaches that nucleic acid initiator will include a 3' moiety that will release the synthesized oligonucleotide when in the presence of a releasing agent, wherein this feature is illustrated in Figure 22 where a nucleic acid initiator (5'-initiator-) is shown coupled to a solid state support (open circle) and a releasable 3' moiety (open star), such that the initiator is a single-stranded oligonucleotide, such as a dimer, trimer, tetramer, pentamer, hexamer, septamer, or octamer; and that because the 3' moiety attached to the initiator is a substrate for the enzyme (e.g., a TdT, e.g., a modified TdT), the enzyme can add additional nucleotides or nucleotide analogs in a stepwise fashion, such that with each addition, the length of the synthesized oligonucleotide increases; and that once the oligonucleotide synthesis is complete, a releasing agent can be introduced to cause the 3' moiety to decouple from the nucleic acid initiator, where in some embodiments, the 3' moiety is a ribonucleotide, such as an A, C, G, or U ribonucleotide (interpreted as an single stranded oligonucleotides, claims 1 and 27) (paragraph [0101], lines 1-18). Efcavitch teaches that the 3' moiety can be an abasic deoxyribose, an abasic ribose, and/or a non-nucleoside 5'-monophosphate; and the releasing agent can include a basic solution or a metal ion; a concentrated NH4OH solution having a pH greater than 8, (i.e., greater than pH 8.5, i.e., greater than pH 9.0, greater than pH 9.5); and/or the releasing agent will be an enzyme, such as a type II restriction nuclease, such that the enzyme will uniquely interact with the nucleic acid sequence of the initiator, and lyse the synthesized oligonucleotide from the initiator, leaving behind the initiator, wherein the initiator is a hexamer and the 3’ moiety is a ribonucleotide (interpreted as releasing agents; a restriction endonuclease; and generating a truncated linker, claims 1 and 27) (paragraph [0101], lines 22-28; and [0102], lines 1-2). Efcavitch teaches that the solid substrate is then washed and/or neutralized to prepare the initiator and 3' moiety for fabrication of a new oligonucleotide, wherein the terminal ribonucleotide is regenerated prior to oligonucleotide synthesis with the use of a phosphatase or the 3' phosphatase activity of T 4 polynucleotide kinase (interpreted as regenerating the truncated linker; and interpreting a new oligonucleotide as extending the truncated linkers, claims 1 and 27) (paragraph [0102]). Efcavitch teaches that solid supports suitable for use with the methods of the invention may include glass and silica supports, including beads, slides, pegs, or wells; and that the support can be tethered to another structure, such as a polymer well plate or pipette tip; wherein the solid support can have additional magnetic properties; and/or it can be a silica coated polymer, thereby allowing the formation of a variety of structural shapes that lend themselves to automated processing (interpreted as a coating as handles or linkers; and glass, silicon, metal or plastic, claim 22) (paragraph [0103]). Efcavitch teaches that multiple different cleavage sites can be installed throughout a strand during synthesis, such that upon digestion, a complex library of the strands located between the cleavage sites can be released from the resin (interpreted as first linkers and second linkers having different sequences; and cleaving a first linker without cleaving the second linker, claims 1 and 27) (paragraph [0112]), wherein it is known that a solid support can comprise oligonucleotides for capturing proteins and oligonucleotide for capturing mRNA, wherein the first and second oligonucleotides comprise different cleavable linkers as evidenced by Gaublomme (paragraph [0015], lines 1-8). Efcavitch teaches in Figure 23 that the resultant initiator can be used for further extension reactions as described to generate the desired sequence (interpreted as generating the same sequence; and extension reaction, claims 1 and 27) (paragraph [0107]; and Figure 23). Efcavitch teaches in Figure 27 that 5'-surface-immobilized sequences are terminated with a short poly-A tract; and extension to produce a terminal 3'-poly-U site of sufficient length will allow a hairpin to fold under appropriate conditions, so that the elements of the initiator preceding the poly-A stretch can be replicated using a template-dependent polymerase; and the sequence can then be extended with a new homopolymer tract to leave a free 3'-terminus; and that upon completion of the write steps, the hairpin linker can then be digested with the USER enzyme to release the data strand, while leaving the template initiator to be regenerated with a 3'-dephosphorylation step, poly-U addition, and recopying of the template strand (interpreted as contacting the linkers with complement strands that hybridize with the linker; template strand; and adding additional monomers to the 3’ end, claims 3, 24, 28 and 29) (paragraph [0114]; and Figure 27). Figure 27 is shown below:
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Efcavitch teaches that multiple different cleavage sites can be installed throughout a strand during synthesis (interpreted as cleavage at recognition sites to generate truncated linkers; and regenerating linkers that remain attached to the solid support, claim 1) (paragraph [0112], lines 1-2). Efcavitch teaches that the nucleic acid initiator comprises an index element, the method further comprising: extending a 3' end of the nucleic acid initiator with complementary nucleotide analogs to a 3' sequence of the nucleic acid initiator to synthesize the first oligonucleotide under appropriate conditions to permit hairpin formation; extending the first oligonucleotide after hairpin formation using the index element as a template (interpreted as extending the first truncated linker with nucleotides that are complementary to overhangs; linker replacement strands; extending; and regeneration template, claims 1 and 27-29) (pg. 25, col 1, claim 14). Efcavitch teaches that various reagents can be stored in separate reservoirs within the inkjet printing device and the inkjet printing device can deliver droplets of various reagents to various discrete locations including, for example, different reaction chambers or wells within a chip (interpreted as storing the regenerated linkers for later use, claim 25) (paragraph [0102], lines 12-15). Efcavitch teaches that the solid support and nucleic acid initiator including the 3' moiety will be reusable, thereby allowing the initiator coupled to the solid support to be used again and again for the rapid synthesis of oligonucleotides (interpreted as storing the regenerated linkers for later use, claim 25) (paragraph [0103], lines 1-5). Efcavitch teaches in Figure 19, the steps of exposing an oligonucleotide to a nucleotide analog, washing, exposing an oligonucleotide to a 3’ exonuclease, washing and cleaving the linker (interpreted as following (b), washing the solid substrate, claim 34) (Figure 19). Efcavitch teaches that after the nucleotide extension step, the reactants are washed away from the solid support prior to removal of the inhibitor by cleaving the linker, and then new reactants are added, allowing the cycle to start anew; and that after the 3’ exonuclease exposure, the enzyme can be washed away before carrying on with the inhibitor cleavage step (interpreted as following (b), washing the solid substrate, claim 34) (paragraph, [0096], lines 15-18; and [0097], last 3 lines). Efcavitch teaches that solid supports suitable for use with the methods of the invention may include glass and silica supports, including beads, slides, pegs, or wells, wherein the support can be tethered to another structure, such as a polymer well plate or pipette tip; the solid support can have additional magnetic properties, thus allowing the support to be manipulated or removed from a location using magnets, wherein the solid support can be a silica coated polymer, thereby allowing the formation of a variety of structural shapes that lend themselves to automated processing (interpreted as purifying the strands removed from the substrate, claim 35) (paragraph [0103]). Efcavitch teaches the invention can make use of an initiator sequence that is a substrate for nucleotidyl transferase, wherein the initiator is attached to a solid support and serves as a recognition site for the enzyme, such that the formed oligonucleotide being cleavable from the initiator (paragraph [0056]).
Efcavitch does not specifically exemplify specific restriction endonucleases; or contacting regeneration templates with a ligase (instant claim 29, in part).
Regarding claim 29 (in part), Tsavachidou teaches methods for constructing consecutively connected and optionally truncated copies of nucleic acid molecules are disclosed, wherein the consecutively connected copies of nucleic acid molecules can be used to perform sequencing of the same nucleic acid molecules several times, improving overall accuracy of sequencing, such that sequencing of truncated copies of nucleic acid molecules can be used to deduce the sequences of nucleic acid molecules from assembling short sequenced segments; and that connected copies of nucleic acid molecules can be constructed by first attaching hairpin adaptors to the nucleic acid molecules, and then using strand displacing polymerases to generate complementary strands of the nucleic acid molecule strands connected by the hairpin adaptors (interpreted as truncated nucleic acids; and complementary sequences, claims 1 and 27) (Abstract). Tsavachidou teaches methods for constructing consecutively connected and progressively truncated copies of nucleic acid molecules (paragraph [0007]). Tsavachidou teaches that such progressively truncated copies are useful because they can be sequenced, along with their associated origin and copy identifiers, using short-read sequencing technologies, and can be aligned to the reference genome in the proper order, according to information stored in the sequences of their associated origin and copy identifiers (interpreted as truncation; and storing, claims 1 and 27) (paragraph [0027]). Tsavachidou teaches that the term “nucleic acid molecule” refers to at least two nucleotides covalently linked together, wherein a nucleic acid molecules can be a polynucleotide or an oligonucleotide including DNA or RNA (interpreted as oligonucleotides and polynucleotides, claims 1 and 27) (paragraph [0033]). Tsavachidou teaches that a "nucleic acid molecule" that participates in reactions, or is said to be exposed to conditions or subjected to processes (or other equivalent phrase) to cause a reaction or event to occur, comprises the nucleic acid molecule and everything associated with it (sometimes referred to as "parts" or "surroundings") including incorporated nucleotides, attached adaptors, hybridized primers or strands, etc., that are associated (e.g., bound, hybridized, attached, incorporated, ligated, etc.) with the nucleic acid molecule prior to or during a method described herein, are or become part of the nucleic acid molecule, and are comprised in the term "nucleic acid molecule" (interpreted as ssDNA, template strands, regenerated strands; oligonucleotides; and under conditions, claims 1 and 27) (paragraph [0037]). Tsavachidou teaches that the nucleic acid molecules are anchored to a surface prior to hybridization to primers or ligation to adaptors, wherein the nucleic acid molecules are hybridized to primers first or ligated to adaptors first and then anchored to the surface; the primers (or adaptors) are anchored to a surface, and nucleic acid molecules hybridize to the primers or attach to the adaptors; the primer is hybridized to the nucleic acid molecule prior to providing nucleotides for the polymerization reaction; and/or the primer is hybridized to the nucleic acid molecule while the nucleotides are being provided (interpreted as truncated linkers; hybridizing; ligating; nucleotides, claims 1 and 27) (paragraph [0066]). Tsavachidou teaches that while diverse nucleic acid molecules can be each anchored to and processed in a separate substrate or in a separate synthesis channel, multiple nucleic acid molecules can also be analyzed on a single substrate (e.g. in a single microfluidic channel), such that nucleic acid molecules can be bound to different locations on the substrate (e.g. at different locations along the flow path of the channel) (interpreted as encompassing different first and second linkers in different locations on a solid support, claims 1 and 27) (paragraph [0068]). Tsavachidou teaches that the poly-A tail facilitates hybridization of the nucleic acid molecule to poly-dT primer molecules anchored to a surface, such that nucleic acid molecule tailing can be carried out with a variety of dNTPs (or heterogeneous combinations), such as dATP, wherein dATP can be used because TdT adds dATP with predictable kinetics useful to synthesize a 50-70 nucleotide tail; and RNA can be labeled with poly-A polymerase enzyme and ATP (interpreted as a template; adding nucleotides; replacement strands, etc., claim 28) (paragraph [0074]). Tsavachidou teaches that copies of a nucleic acid molecule are truncated by using restriction endonucleases that can cut into a region of unknown sequence, the region being located away from their recognition site, wherein enzymes such as MmeI or EcoP15 can be used; and that EcoP15I is a type III restriction enzyme that recognizes the sequence motif CAGCAG and cleave double-stranded DNA molecule 27 base pairs downstream of the CAGCAG motif, such that the cut site contains a 2 base 5’-overhang that can be end repaired to give a 27 base blunt ended duplex (interpreted as a restriction endonuclease; a restriction enzyme; truncation; recognition site; and creating overhangs, claims 1 and 27) (paragraph [0079]). Tsavachidou teaches that adaptors can comprise one or more cleavable features or other modifications, wherein adaptors may or may not be anchored to a surface and/or be linked to one or more enzymes or other molecules, wherein adaptor 102 comprises a cleavable feature (interpreted as encompassing different first and second linkers in different locations on a solid support) (paragraphs [0038]; and [0098]). Adaptor 102 is shown below:
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Tsavachidou teaches that adaptors and nucleic acid constructs can be attached to nucleic acid molecules by using ligation, wherein several types of ligases are suitable and used in embodiments (interpreted as ligation; and encompassing contacting truncated nucleotides with a ligase to hybridize, claim 29) (paragraph [0094]). Tsavachidou teaches that overhangs can be filled or chewed back to yield blunt ends, in the event that blunt ligation is desired; and that a polymerase such as Taq is used to create a single-base 3'-end overhang comprising adenine, suitable for TA ligation to an adaptor (interpreted as an overhang; and regeneration of templates, claims 1 and 27) (paragraph [0132]). Tsavachidou teaches that after completing the construction of the truncated copies, restriction enzymes can be used to release each of the copies for further processing, where in Figure 3, restriction enzymes recognize and cut restriction sites within adaptor sequences, releasing double-stranded segments 301, 302, 303, 304 and 305, wherein 301 comprises the original nucleic acid molecule, preceded by the origin identifier 320, wherein 302 comprises a full-length copy of the nucleic acid molecule, and a copy of the origin identifier 320 (paragraph [0134]). Tsavachidou teaches a cleavable feature can be one or more cleavable nucleotides that can lead to the creation of a nick or a gap by using appropriate reagents (e.g. RNases), wherein cleavable nucleotides and appropriate reagents for cleavage are described in PCT/US2015/027686 (WO2015167972), which is included herein in its entirety) (paragraph [0099]), wherein it is known that constructing a ligation product includes using template-dependent polymerization to construct a segment of cleavable nucleotides reaching the end of the template strand of the nucleic acid molecule, using Taq polymerase to create an overhang suitable for ligation, and using Taq polymerase to create an overhang suitable for ligation, and using template-dependent polymerization to fully complement the template strand of the nucleic acid molecule as evidenced by Tsavachidou ‘972 (pg. 23, lines 715-722; and pg. 26, lines 799-804). Tsavachidou teaches that a nucleic acid molecule is subjected to incubation with restriction endonuclease molecules that recognize a restriction site, wherein the restriction endonuclease is EcoP15I; and step (h) produces truncated nucleic acid molecule copy 221, wherein the truncated copy can have a blunt end or an end with an overhang, depending on the enzyme that performs the cutting (interpreted as generating an overhang, claims 1 and 27) (paragraph [0121]). Tsavachidou teaches that DNA polymerase is able to continuously perform incorporation of nucleotides using the same primer, for a substantial length without dissociating from either the extended primer or the template strand or both the extended primer and the template strand (interpreted as extending a primer using a template strand, claims 1 and 27) (paragraph [0092]). Tsavachidou teaches that suitable enzymatic, chemical, or photochemical cleavage reactions can be used to cleave nucleic acid molecules including those described by, but not limited to Barnes et al. (WO 07/010251) and Rigatti and Ost (US7754429) incorporated herein by reference (interpreted as linkers cleavable by different methods, claim 1) (paragraph [0061]). Tsavachidou teaches hairpin and other adaptors can comprise one or more restriction enzyme binding sites and/or cleavage sites, where restriction enzymes include AatII, AccII, Acc651…XmnI, or ZraI (interpreted as cleavage of spatially distinct, sequence-defined linkers including first linkers and second linkers that are different, claim 1) (paragraph [0080]).
“It is prima facie obvious to combine prior art elements according to known methods to yield predictable results; the court held that, "…a conclusion that a claim would have been obvious is that all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination would have yielded nothing more than predictable results to one of ordinary skill in the art. KSR International Co. v. Teleflex Inc., 550 U.S. ___, ___, 82 USPQ2d 1385, 1395 (2007); Sakraida v. AG Pro, Inc., 425 U.S. 273, 282, 189 USPQ 449, 453 (1976); Anderson’s-Black Rock, Inc. v. Pavement Salvage Co., 396 U.S. 57, 62-63, 163 USPQ 673, 675 (1969); Great Atlantic & P. Tea Co. v. Supermarket Equipment Corp., 340 U.S. 147, 152, 87 USPQ 303, 306 (1950)”. Therefore, in view of the benefits of constructing connected copies of nucleic acid molecules that are consecutively connected and progressively truncated as exemplified by Tsavachidou, it would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of creating solid supports that are reusable after the release of the nascent oligonucleotide including for the production of custom polynucleotides as disclosed by Efcavitch to include the methods of attaching nucleic acid constructs and/or adaptors to nucleic acid molecules as taught by Tsavachidou, with a reasonable expectation of success in increasing the efficiency of producing multiple oligonucleotides of interest; in efficiently producing reusable solid supports comprising polynucleotides bound to selectively cleavable linkers; in constructing consecutively connected nucleic acids that can be simultaneously sequenced to increase optical signals and/or electronic signals and, thus, increase detection sensitivity; and/or in efficiently and cost effectively regenerating reusable supports and reusable nucleic acid initiators to rapidly synthesize different polymer strands that can be selectively separated from the solid support for downstream reaction and/or analysis such as for data storage and/or sequencing.
Thus, in view of the foregoing, the claimed invention, as a whole, would have been obvious to one of ordinary skill in the art at the time the invention was made. Therefore, the claims are properly rejected under 35 USC §103 as obvious over the art.
Response to Arguments
Applicant’s arguments filed October 17, 2025 have been fully considered but they are not persuasive. Applicants essentially asserts: (a) the references fail to teach two spatially distinct, sequence-defined surface linkers and their selective cleavage by a single restriction enzyme (Applicant Remarks, pg. 10, last full paragraph through pg. 11, second full paragraph); (b) Efcavitch employes a universal initiator that is the same at all locations; and Efcavitch repeatedly emphasizes the benefits of using the same initiator (Applicant Remarks, pg. 11, last full paragraph through pg. 12, first full paragraph); (c) Efcavitch' s "linkers" (paragraphs [0008], and [0055]) are not substrate linkers but are chemical moieties connecting an inhibitor group to a nucleotide analog (NTP-Linker-Inhibitor); and nothing in Efcavitch teaches these linkers as surface-attached oligonucleotide initiators (Applicant Remarks, pg. 12, second full paragraph); (d) when Efcavitch mentions "multiple different cleavage sites" in paragraph [0112], this refers to installing cleavable bonds "throughout a strand during synthesis" - meaning within the growing oligonucleotide product, and not different recognition sequences in the surface-attached initiators (Applicant Remarks, pg. 12, third and fourth full paragraphs); (e) Tsavachidou nowhere teaches the concept that motivated claim 1 innovation: achieving orthogonal cleavage where a single restriction enzyme selectively cleaves one population of surface- attached linkers while leaving another population intact in a single reaction vessel (Applicant Remarks, pg. 13, second full paragraph); (f) the cited references do not teach or suggest the hybridization-extension technique for regenerating linkers including truncated linkers, hybridization of templates, creation of an overhang, and enzymatic extension (Applicant Remarks, pg. 14, Section B through pg. 16, Section B); and (g) the cited references do not provide a motivation to combine with a reasonable expectation of success; and the proposed modification would require substantial modification of both systems including engineering a linker that could stably hybridize with a separate regeneration template (Applicant Remarks, pg. 16, last partial paragraph through pg. 19, first partial paragraph).
Regarding (a), although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26USPQ2d 1057 (Fed. Cir. 1993). Moreover, it is noted that none of the references has to teach each and every claim limitation. If they did, this would have been anticipation and not an obviousness-type rejection. One cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986).Additionally, MPEP 2112.01(I) indicates that,
where the claimed and prior art products are identical or substantially identical in structure or composition, or are produced by identical or substantially identical processes, a prima facie case of either anticipation or obviousness has been established. In re Best, 562 F.2d 1252, 1255, 195 USPQ 430, 433 (CCPA 1977). "When the PTO shows a sound basis for believing that the products of the applicant and the prior art are the same, the applicant has the burden of showing that they are not." In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990) (underline added).
Applicant’s assertion that the references fail to teach two spatially distinct, sequence-defined surface linkers and their selective cleavage by a single restriction enzyme, is not found persuasive. As an initial matter, instant claim 1 does not recite the term “two spatially distinct, sequence-defined surface linkers and their selective cleavage by a single restriction enzyme is a single restriction enzyme.” Moreover, claim 1 does not recite the presence of ‘a single restriction enzyme.’ Instead, claim 1, lines 11-12 recites:
“a first linker cleavage agent that comprises a first restriction endonuclease,” where the term “comprising” is open-ended and does not exclude additional, unrecited elements or method steps, including additional enzymes or additional linker cleavage agents.
The Examiner contends that the combined references of Efcavitch and Tsavachidou teach all of the limitations of the claims. To that end -
Efcavitch teaches:
Synthesizing polynucleotides such as DNA and RNA using renewable initiators coupled to a solid support, wherein specific sequences of polynucleotides can be synthesized de novo, base by base, in an aqueous environment, without the use of a nucleic acid template (interpreted as spatially distinct polynucleotides, claim 1) (Abstract; and paragraph [0004]).
A variety of macromolecules are linked to nucleotide analogs using a variety of linkers including cleavable linkers (interpreted as linkers).
The initiator is attached to a solid support and serves as a recognition site for the enzyme, the formed oligonucleotide being cleavable from the initiator (paragraph [0056]).
Installing multiple different cleavage sites can be installed throughout a strand during synthesis, wherein it is known that structurally different and spatially separated oligonucleotides on a solid support can comprise different cleavable linkers as evidenced by Gaublomme (interpreted as sequence-defined linkers including first linkers and second linkers that are different, claim 1) (paragraph [0112], lines 1-2).
A complex library of the strands located between the cleavage sites can be released from the resin (interpreted as cleaving different linkers; and orthogonal cleavage, claim 1) (paragraph [0112], lines 3-4).
Nucleotide analogs having the formula NTP-linker-inhibitor for synthesis of polynucleotides, wherein a linker can be any molecular moiety that links the inhibitor to the NTP, wherein linkers can be cleaved by:
adjusting the pH;
an enzyme that is activated at a given temperature, but inactivated at another temperature;
the linkers can include disulfide bonds;
the linkers can include photocleavable linkers;
nucleophilic linkers; and
electrophilic cleavage sites.
(interpreted as spatially distinct, sequence-defined linkers including first linkers and second linkers that are different, claim 1) (paragraphs [0060]-[0061]).
Upon cleavage of the linker, a natural polynucleotide is released from the solid support (interpreted as cleaving spatially distinct, sequence-defined linkers including first linkers and second linkers that are different, claim 1) (paragraph [0007]).
After cleavage of the synthesized sequence, the resin can then be used in another cycle of cleavage site installation, synthesis, product removal, and regeneration, where Figure 26 provides an overview of an exemplary regeneration cycle (interpreted as regeneration of truncated linkers, claim 1) (paragraph [0110]). Figure 26 is shown below:
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Tsavachidou teaches:
Multiple nucleic acid molecules can also be analyzed on a single substrate (e.g. in a single microfluidic channel), such that nucleic acid molecules such as polynucleotides or oligonucleotides can be bound to different locations on the substrate (interpreted as encompassing different polynucleotides including first linker and second linkers in different locations on a solid support).
Using a restriction endonuclease that recognizes a specific sequence within the adaptor and cleaves only one of the strands (interpreted as spatially distinct, sequence-defined linkers including first linkers and second linkers that are different, claim 1) (paragraph [0073]).
Hairpin and other adaptors can comprise one or more restriction enzyme binding sites and/or cleavage sites including for restriction enzymes including, but not limited to AatII, Acc651,,,XmnI, or ZraI (interpreted as cleavage of spatially distinct, sequence-defined linkers including first linkers and second linkers that are different, claim 1) (paragraph [0080]).
Adaptors can comprise one or more cleavable features or other modifications, wherein adaptors may or may not be anchored to a surface and/or be linked to one or more enzymes or other molecules, wherein adaptor 102 comprises a cleavable feature (interpreted as encompassing different first and second linkers in different locations on a solid support) (paragraphs [0038]; and [0098]). Adaptor 102 is shown below:
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Suitable enzymatic, chemical, or photochemical cleavage reactions can be used to cleave nucleic acid molecules including those described by, but not limited to, Barnes et al (WO 07/010251) and Rigatti and Ost (US7754429) incorporated herein by reference (interpreted as linkers cleavable by different methods, claim 1) (paragraph [0061]).
The combined references of Efcavitch and Tsavachidou teach all of the limitations of the claims including generating polymer strands, and contacting first linkers and second linkers with a linker cleavage agent comprising a first restriction endonuclease, which cleaves the first linkers without cleaving the second linkers. Thus, the claims remain rejected for the reasons of record.
Regarding (b), please see the discussion supra regarding the Examiner’s response to Applicant’s arguments; and the teachings of the combined references. Moreover, MPEP 2123(I) states:
“The use of patents as references is not limited to what the patentees describe as their own inventions or to the problems with which they are concerned. They are part of the literature of the art, relevant for all they contain.” In re Heck, 699 F.2d 1331, 1332-33, 216 USPQ 1038, 1039 (Fed. Cir. 1983) (quoting In re Lemelson, 397 F.2d 1006, 1009, 158 USPQ 275, 277 (CCPA 1968)).
A reference may be relied upon for all that it would have reasonably suggested to one having ordinary skill in the art, including nonpreferred embodiments. Merck & Co. v.Biocraft Labs., Inc. 874 F.2d 804, 10 USPQ2d 1843 (Fed. Cir. 1989), cert. denied, 493 U.S. 975 (1989). See also Upsher-Smith Labs. v. Pamlab, LLC, 412 F.3d 1319, 1323, 75 USPQ2d 1213, 1215 (Fed. Cir. 2005) (reference disclosing optional inclusion of a particular component teaches compositions that both do and do not contain that component); Celeritas Technologies Ltd. v. Rockwell International Corp., 150 F.3d 1354, 1361, 47 USPQ2d 1516, 1522-23 (Fed. Cir. 1998)
Applicant’s assertion that Efcavitch employes a universal initiator that is the same at all locations; and Efcavitch repeatedly emphasizes the benefits of using the same initiator, is not found persuasive. As noted in MPEP 2123(I), a reference may be relied upon for all that it would have reasonably suggested to one having ordinary skill in the art, including nonpreferred embodiments. Although, Efcavitch teaches that the initiator is preferably a universal initiators for the enzyme (paragraph [0056]), Efcavitch also teaches:
“renewable initiators coupled to the solid support” (Abstract);
“De novo synthesis begins with a nucleic acid initiator that is bound to the solid support” (paragraph [0005]);
“the nucleic acid initiator comprises a 3' moiety that is a substrate for the enzyme. A releasing agent is used to decouple the 3' moiety, thereby releasing the oligonucleotide. The 3' moiety, the nucleic acid initiator, and the solid support are reusable after the release of the nascent oligonucleotide” (paragraph [0006]);
“The bioreactor may include a solid support having a nucleic acid initiator and a cleavable 3’ moiety” (paragraph [0007]);
“the initiator bound to the solid support consists of short, single strand DNA sequence that is either a short piece of the user defined sequence or a universal initiator” (paragraph [0053]);
“the initiator is attached to a solid support and serves as a recognition site for the enzyme” (paragraph [0056]);
“a ribonucleotide initiator” (paragraph [0086]); and that
“the initiator is a single-stranded oligonucleotide” (paragraph [0101]).
Thus, consistent with MPEP 2123(I), Efcavitch clearly teaches that the initiators are not limited to “universal initiators” as suggested by Applicant. Additionally, Efcavitch teaches installing multiple different cleavage sites throughout a strand during synthesis; and that nucleotide analogs have the formula NTP-linker-inhibitor, wherein the linker is a cleavable linker, which can be any molecular moiety that links the inhibitor to the NTP. The combined references of Efcavitch and Tsavachidou teach all of the limitations of the claims. Thus, the claims remain rejected for the reasons of record.
Regarding (c) and (d), please see the discussion supra regarding the Examiner’s response to Applicant’s arguments; and the teachings of the combined references. Applicant’s assertion that: (i) nothing in Efcavitch teaches these linkers as surface-attached oligonucleotide initiators; and (ii) Efcavitch refers to installing cleavable bonds "throughout a strand during synthesis" - meaning within the growing oligonucleotide product, and not different recognition sequences in the surface-attached initiators, is not found persuasive. As an initial matter, instant claim 1 does not recite that the first linkers and second linkers are directly attached to the solid substrate. Thus, the linkers taught by Efcavitch can be directly and/or indirectly attached to the solid substrate including via the cleavable initiator and/or the cleavable linkers within the NTP-linker-inhibitor strand (See also, Efcavitch, Figures 13, 20, 22 and 26).
Additionally, please see the teachings of Efcavitch supra with respect to the cleavable initiators, first linkers, and second linkers. Moreover, Efcavitch teaches in claim 17:
The method of claim 8 further comprising: before contacting the nucleic acid initiator with a releasing agent, incorporating a second sequence-specific cleavage element on a 3' end of the first oligonucleotide to create a second nucleic acid initiator and exposing the second nucleic acid initiator, attached to the first oligonucleotide, to nucleotide analogs in the presence of a polymerase to create a second oligonucleotide, wherein contacting the nucleic acid initiator and the second nucleic acid initiator with the releasing agent cleaves the sequence-specific cleavage element and the second sequence-specific cleavage element and release the first oligonucleotide and the second oligonucleotide from the nucleic acid initiator and the second nucleic acid initiator.
Efcavitch clearly teaches that initiators, and NTP-linker-inhibitors, where each strand can have installed therein different cleavable bonds. Figure 13 shows a TdT mediated polynucleotide synthetic cycle including: (a) incorporation of a NTP analog comprising a cleavable terminator, dN*TP-OH (each of which can comprise a different nucleotide in the cleavable terminator). Figure 13 is shown below:
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The combined references of Efcavitch and Tsavachidou teach all of the limitations of the claims. Thus, the claims remain rejected for the reasons of record.
Regarding (e), please see the discussion supra regarding the Examiner’s response to Applicant’s arguments; and the teachings of the combined references. Applicant’s assertion that Tsavachidou nowhere teaches the concept that motivated claim 1’s innovation: achieving orthogonal cleavage where a single restriction enzyme selectively cleaves one population of surface-attached linkers while leaving another population intact in a single reaction vessel, is not found persuasive. As an initial matter, instant claim 1 does not recite:
the use of “a single restriction enzyme that selectively cleaves one population of surface-attached linkers.”
any particular location of the first linker and second linker on the solid support.
orthogonal cleavage or the presence or use of a single reaction vessel
Instant claim 1 recites that the second linker is at a different location from the location of the first linker. Under the broadest reasonable interpretation of the claim language, this can include a first linker and a second linker on the same strand; as well as, a first linker and a second linker, each attached to a different feature on the solid support. Moreover, instant claim 1 teaches:
“contacting both the first linker and the second linker with a first linker cleavage agent that comprises a first restriction endonuclease, thereby achieves orthogonal cleavage in a single reaction vessel” (underline added) (claim 1, lines 11-13).
Thus, instant claim 1 recites that orthogonal cleavage in a single reaction vessel is achieved by contacting the first linker and the second linker with a first linker cleavage agent comprising a first restriction endonuclease, which is taught by the combined references of Efcavitch and Tsavachidou.
Assuming arguendo that claim 1 recites the limitation of orthogonal cleavage in a single reaction vessel, it is noted that: (i) cleaving different linkers using distinct enzymatic methods to selectively cleave the different linker molecules is orthogonal cleavage; and (ii) Efcavitch and Tsavachidou teach a variety of different single reaction vessels that overlap with the reaction vessels taught in the as-filed Specification. Additionally, it is noted that:
There are no working examples in the instant as-filed Specification that illustrate a solid substrate and step-by-step synthesis and/or orthogonal cleavage in a ‘single reaction vessel’ (as-filed Specification, paragraph [0004]).
There is no teaching in the as-filed Specification as to the identity of the “single reaction vessel” (e.g., a solid-phase peptide synthesizer, a single flask comprising beads, a single test tube, one or more wells of a well-plate, a slide, etc.).
The as-filed Specification teaches in Figure 7 a flow diagram showing an illustrative process for the solid-phase polymer synthesis; while Figure 14 shows a patterned substrate.
To that end, Efcavitch teaches the use of a DNA synthesizer, one or more bioreactors, and that solid supports include slides, wells, well plates, etc. Tsavachidou teaches planar arrays or matrices, planar supports, microfluidic devices, a microfluidic synthesis channel, microwells, microparticles, plates, spheres, beads, membranes, slides, etc. As discussed supra, the combined references of Efcavitch and Tsavachidou teach all of the limitations of the claims, such that the references achieve orthogonal cleavage in a single reaction vessel. Thus, the claims remain rejected for the reasons of record.
Regarding (f), please see the discussion supra regarding the Examiner’s response to Applicant’s arguments; and the teachings of the combined references. Applicant’s assertion that the cited references do not teach or suggest the hybridization-extension technique for regenerating linkers including truncated linkers, hybridization of templates, creation of an overhang, and enzymatic extension, is not found persuasive. The Examiner contends that the combined references teach all of the limitation of the claims. To that end -
Efcavitch teaches:
After cleavage of the synthesized sequence, the resin can then be used in repeated cycles of cleavage site installation, synthesis, product removal, and resin regeneration as well as, index strand regeneration (interpreted as synthesizing a truncated linker; and generating an overhang), wherein the linkers of Figure 26 remain tethered to a bead, and the linkers of Figure 27 are tethered to a solid support. Figure 26 below shows a regeneration cycle:
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wherein 5’-surface-immobilized sequences terminated with a short poly-A tract, extension to produce a terminal 3’-poly-U site, replicating the initiator preceding the poly-A stretch using a template and template-dependent polymerase, extending the sequence with a new homopolymer tract to leave a free 3’-terminus, regenerating the template initiator with a 3’-phosphorylatoin step, poly-U addition, and recopying the template strand (interpreted as contacting truncated linkers with regeneration templates and using template dependent polymerase; creating overhangs; and extending the truncated linkers to have the same nucleotide sequence).
The solid support and nucleic acid initiator including the 3' moiety will be reusable, thereby allowing the initiator coupled to the solid support to be used again and again for the rapid synthesis of oligonucleotides (interpreted as a solid support for regenerating oligonucleotide linkers and polymers; and linkers are tethered to the solid support).
Methods for constructing consecutively connected and optionally truncated copies of nucleic acid molecules including regeneration of segment 208 in step (c), regeneration of segment 215 in step (f), regeneration of the long hairpin construct in step (g), and regeneration of the full length of the nicking endonuclease recognition site (interpreted as first linkers and second linkers; truncation; and regeneration to have the same nucleotide sequence).
The resultant initiator can be used for further extension reactions to generate the desired sequence; TdT extension process including dNTP incorporation onto a resin; cleavage site installation can be used immediately after each cycle of enzymatic extension; and full length sequences can undergo extension to append any element which will enable selective capture, isolation or enrichment (interpreted as extension reactions for regenerating linkers).
Tsavachidou teaches:
Truncation can be done by using restriction endonucleases that can cut into a region of unknown sequence, said region being located away from their recognition site. Enzymes such as Mmel or Eco Pl 5 can be used. EcoPl SI is a type III restriction enzyme that recognizes the sequence motif CAGCAG and cleaves the double stranded DNA molecule 27 base pairs downstream of the CAGCAG motif. The cut site contains a 2 base 5'-overhang that can be end repaired to give a 27 base blunt ended duplex (interpreted as creating an overhang).
During step (c), the nucleic acid molecule and its surroundings are exposed to conditions to cause nucleotide incorporation, and to a template-dependent polymerization reaction solution comprising nucleotides and polymerase molecules comprising strand-displacing activity. The polymerization reaction in step (c): (i) regenerates segment 208 which is the part of the adaptor following the exposed 3' end at nick 250, (ii) produces a segment complementary to 202, (iii) produces a segment 210 that is complementary to segment 206 of the hairpin adaptor, loop 207 of the hairpin adaptor, and segment 205 of the hairpin adaptor, (iv) produces segment 251 which is complementary to 201, and (v) produces a segment complementary to segment 209, segment 209 having the same sequence (interpreted as regenerating the first linkers having the same nucleotide sequence).
In order to initiate construction of a copy of a nucleic acid molecule, an extendable 3' end is formed in the nucleic acid molecule, or in an adaptor ligated to the nucleic acid molecule. One way is to denature the nucleic acid molecule linked to the adaptor and hybridize a primer that is complementary to a specific sequence within the adaptor. Another way is to create a nick in the nucleic acid molecule by using a restriction endonuclease that recognizes a specific sequence within the adaptor and cleaves only one of the strands (interpreted as extending the truncated linker; creating an overhang; hybridizing a template; extending the truncated linker; and denaturing).
Polymerization (extension by polymerization) can be template-dependent or template-independent. In template-dependent polymerization, the produced strand is complementary to another strand which serves as a template during the polymerization reaction, whereas in template independent polymerization, addition of nucleotides to a strand does not depend on complementarity.
The term "template strand" refers to the strand of a nucleic acid molecule that serves as a guide for nucleotide incorporation into the nucleic acid molecule comprising an extendable 3' end, in the event that the nucleic acid molecule is subjected to a template-dependent polymerization reaction. The template strand guides nucleotide incorporation via base-pair complementarity, so that the newly formed strand is complementary to the template strand.
Primers (or adaptors) are anchored to a surface, and nucleic acid molecules hybridize to the primers or attach to the adaptors, wherein the primer is hybridized to the nucleic acid molecule prior to providing nucleotides for the polymerization reaction and/or the primer is hybridized to the nucleic acid molecule while the nucleotides are being provided.
The combined references of Efcavitch and Tsavachidou teach all of the limitations of the claims including contacting truncated linkers with regeneration templates; creating overhangs; and extending the truncated linkers to have the same nucleotide sequence. Thus, the claims remain rejected for the reasons of record.
Regarding (g), please see the discussion supra regarding the Examiner’s response to Applicant’s arguments; and the teachings of the combined references. MPEP 2143.01(V) states that if a proposed modification would render the prior art invention being modified unsatisfactory for its intended purpose, then there is no suggestion or motivation to make the proposed modification. In re Gordon, 733 F.2d 900, 221 USPQ 1125 (Fed. Cir. 1984); while MPEP 2143.01(VI) states that if the proposed modification or combination of the prior art would change the principle of operation of the prior art invention being modified, then the teachings of the references are not sufficient to render the claims prima facie obvious. In re Ratti, 270 F.2d 810, 813, 123 USPQ 349, 352 (CCPA 1959). Applicant’s assertion that the cited references do not provide a motivation to combine with a reasonable expectation of success; and the proposed modification would require substantial modification of both systems including engineering a linker that could stably hybridize with a separate regeneration template, is not found persuasive. MPEP 2144(I) states that:
“[T]he rationale to modify or combine the prior art does not have to be expressly stated in the prior art; the rationale may be expressly or impliedly contained in the prior art or it may be reasoned from knowledge generally available to one of ordinary skill in the art, established scientific principles, or legal precedent established by prior case law. In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988); In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992). See also In re Kotzab, 217 F.3d 1365, 1370, 55 USPQ2d 1313, 1317 (Fed. Cir. 2000) (setting forth test for implicit teachings); In re Eli Lilly & Co., 902 F.2d 943, 14 USPQ2d 1741 (Fed. Cir. 1990) (discussion of reliance on legal precedent); In re Nilssen, 851 F.2d 1401, 1403, 7 USPQ2d 1500, 1502 (Fed. Cir. 1988) (references do not have to explicitly suggest combining teachings); Ex parte Clapp, 227 USPQ 972 (Bd. Pat. App. & Inter. 1985) (examiner must present convincing line of reasoning supporting rejection); and Ex parte Levengood, 28 USPQ2d 1300 (Bd. Pat. App. & Inter. 1993) (reliance on logic and sound scientific reasoning).
Furthermore, the applicants are reminded that the motivation for combining the teachings of the prior art may be different from applicants’ motivation to make the disclosed compositions. The fact that applicant has recognized another advantage which would flow naturally from following the suggestion of the prior art cannot be the basis for patentability when the differences would otherwise be obvious. See Ex parte Obiaya, 227 USPQ 58, 60 (Bd. Pat. App. & Inter. 1985). The Office has provided motivation to modify the method of creating solid supports that are reusable after the release of the nascent oligonucleotide including for the production of custom polynucleotides as disclosed by Efcavitch to include the methods of attaching nucleic acid constructs and/or adaptors to nucleic acid molecules as taught by Tsavachidou with a reasonable expectation of success in increasing the efficiency of producing multiple oligonucleotides of interest; in efficiently producing reusable solid supports comprising polynucleotides bound to selectively cleavable linkers; and/or in efficiently and cost effectively regenerating reusable supports and reusable nucleic acid initiators.
Regarding Applicant’s argument that the proposed combination would require substantial modification of both systems. As an initial matter, the Examiner did not state that the motivation for combining the prior art references was “obvious to try,” or that the motivation lies in incorporating Tsavachidou’s methods for constructing truncated and connected copies into Efcavitch’s solid-phase polynucleotide synthesis platform as stated by Applicant. The Examiner stated that it would have been prima facie obvious to modify the method of creating solid supports that are reusable after the release of the nascent oligonucleotide including for the production of custom polynucleotides as disclosed by Efcavitch to include the methods of attaching nucleic acid constructs and/or adaptors to nucleic acid molecules as taught by Tsavachidou (e.g., contacting overhangs with adaptor and nucleic acid constructs and a ligase).
Both Efcavitch and Tsavachidou teach the enzymatic cleavage of cleavable features including cleavable nucleotides attached to a solid support; as well as, the regeneration of cleavable features and polynucleotides from truncated nucleic acid molecules. Applicant’s argument is unclear to the Examiner. The Examiner requests that Applicant provide specific details regarding why the method of Tsavachidou (e.g., contacting an overhang and nucleic acid construct with a ligase) would make the methods of synthesizing polynucleotides as taught by Efcavitch unsatisfactory for its intended purpose (e.g., synthesizing polynucleotides using renewable initiators).
The combined references of Efcavitch and Tsavachidou teach all of the limitations of the claims. Thus, the claims remain rejected for the reasons of record.
Claims 1, 3, 22, 24, 25 and 27-35 are rejected under 35 U.S.C. 103 as being unpatentable over Chen et. al. (hereinafter “Chen”) (US Patent Application Publication No. 20220333145, published October 20, 2022; International Application WO2020178604, filed March 9, 2020; effective filing date March 7, 2019) in view of Crameri et. al. (hereinafter “Crameri”) (International Application WO2018011067, published January 18, 2018).
Regarding claims 1, 3, 24 and 27, Chen teaches the synthesis and assembly of oligonucleotides into contiguous strands, wherein the oligonucleotide can be synthesized and assembled in the same device, allowing production of strands longer than can be prepared using base by base synthesis alone (Abstract). Chen teaches the development of a controlled single-stranded DNA synthesis process through TdT would be invaluable to in situ DNA synthesis for gene assembly or hybridization microarrays as it removes the need for an anhydrous environment and allows the use of various polymers incompatible with organic solvents (paragraph [0009], lines 12-19). Chen teaches a plurality of immobilized initiation oligonucleotide sequences, one or more of which contains a cleavage site (interpreted as a first cleavage site and a second cleavage site, claim 1) (paragraph [0014]). Chen teaches that the device operates by synthesizing a large number of oligonucleotides of different sequence, wherein the sequences can be designed such that the ends of the sequences can assemble to form one or more overlapping regions, which can then be used to link together multiple of the synthesized strands into a contiguous sequence (interpreted as synthesizing a first and second polymer strands to linkers, claim 1a) (paragraph [0012]). Chen teaches that the term “initiator sequence” refers to a short oligonucleotide with a free 5’-end or 3’-end which the nucleotide monomers can attach, wherein the initiator sequence can be as short as one based where the strands are produced chemically, wherein the initiator sequence is a DNA initiator sequence or an RNA initiator sequence (interpreted as linkers, claim 1a) (paragraph [0024]). Chen teaches that following Stage 1 assembly, assembled nucleic acids are then introduced to anchor zones by droplet actuation for solid-phase nucleic acid assembly (Stage 2 assembly), where assembly can be effected by the same assembly process used in Stage 1 (interpreted as generating polymer strands through solid-phase synthesis, claim 1a) (paragraph [0214]). Chen teaches a method for preparing a contiguous oligonucleotide sequence of at least 4 n bases in length, the method comprising: (a) taking a device with a plurality of immobilized initiation oligonucleotide sequences, one or more of which contains a cleavage site (interpreted as oligonucleotide linkers with cleavage sites); (b) using the initiation oligonucleotide sequences to synthesize a plurality of immobilized oligonucleotide sequences of at least n bases in length, using cycles of extension of reversibly blocked nucleotide monomers (interpreted as synthesizing first and second polymer strands); (c) selectively cleaving at least four of the immobilized oligonucleotide sequences of least n bases in length into solution while leaving two or more of the immobilized oligonucleotide sequences attached (interpreted as selective cleavage using a first cleavage agent); (d) hybridizing the cleaved and immobilized oligonucleotides to each other, to form splints on at least two of the immobilized oligonucleotide sequences; (e) joining at least one of the cleaved oligonucleotides to at least two of the immobilized oligonucleotide sequences, thereby preparing two discreet contiguous oligonucleotide sequences of at least 2 n bases in length; (f) performing a further cleavage step of selectively cleaving at least one of the immobilized oligonucleotide sequences of least 2 n bases in length into solution whilst leaving one or more of the immobilized oligonucleotide sequences attached; (g) further hybridizing at least one of the cleaved oligonucleotides to the cleaved oligonucleotide sequences of least 2 n bases, to form a splint on at least one of the immobilized oligonucleotide sequences of least 2 n bases; and (h) further joining at least one of the cleaved oligonucleotides of at least 2 n bases to the immobilized oligonucleotide sequences of least 2 n bases, thereby preparing a further contiguous oligonucleotide sequence of at least 4 n bases in length (interpreted as the steps recited in claim 1 including generating polymer strands; contacting first linkers and second linkers with a cleavage agent; regenerating the first truncated linker by extending complementary overhangs; encompassing contacting linker complement strands to form double stranded oligonucleotide sequence; adding additional polymer strands by adding monomers to free ends of regenerated linkers; and a second linker cleavage agent, claims 1a-c, 3, 24 and 27) (pg. 20, claim 1). Chen teaches that the sequence of 10 n bases can be made single-stranded by denaturing the oligonucleotides which served as splints (interpreted as denaturing to produce single-stranded linkers, paragraph [0030], last 3 lines). Chen teaches the use of the term splint is taken to mean a hybridized structure with three strands, wherein the structure has two complementary double stranded portions, where the splinted structure can have single stranded portions at either end, or between the two double stranded portions, such that the single stranded portion can be made double stranded using a nucleic acid polymerase (interpreted as encompassing contacting linker complement strands to form double stranded oligonucleotide sequence, claim 3) (paragraph [0123]). Chen teaches that gapped or ungapped nucleic acid assembly process (e.g., splint ligation or polymerase chain assembly) is then used to covalently link the hybridized nucleic acids together by actuating droplets from reservoirs containing necessary reagents to perform nucleic acid assembly (interpreted as encompassing contacting linker complement strands to form double stranded oligonucleotide sequence; and covalent bond, claims 3 and 29) (paragraph [0213]). Chen teaches that a base recognized by an enzyme, such as a glycosylase, can be removed to generate an a basic site which can be cleaved by chemical or enzymatic means, such that a base sequence can be recognized and cleaved by a restriction enzyme (interpreted as encompassing different restriction endonuclease cleavage sites; cleaving only double-stranded sequences; and restriction endonucleases, claims 1b) (paragraph [0109]). Chen teaches that the final contiguous assembled strands can be removed from the support, where the removal can be performed by: (i) copying/amplification of the strands using non-immobilized primers, such that the strands obtained by primer extension are non-immobilised (e.g., the original strands remain immobilised, and the material is 'released' by producing non-immobilized copies); or (ii) the contiguous oligonucleotide sequence can be released from being immobilized, for example by chemical or enzymatic treatment which cleaves the strands in a defined location, wherein the selective cleavage can be performed using a restriction enzyme specific to a certain double-stranded sequence (interpreted as encompassing different restriction endonuclease cleavage sites; cleaving only double-stranded sequences; encompassing first and second cleavage agents; and restriction endonucleases, claims 1b, 3 and 27) (paragraph [0049]). Chen teaches that DNA was recovered from the beads by removing a uracil present in the initiator with uracil DNA glycosylase (UDG) cleaving the generated abasic site with endonuclease VIII (interpreted as selectively cleaving second linkers, claim 1b) (paragraph [0011]). Chen teaches that initiator strands can contain a cleavage site such as a restriction site or a non-canonical DNA base such as U or 8-oxoG (interpreted as cleaving second linkers, claim 1b) (paragraph [0191]). Chen teaches that the sequences can be joined together, for example using a DNA ligase, thereby extending each of the immobilized 'areas' to a length 3 n (at least 60 bases) of the immobilised sequences n remain unextended for use as splints later in the process, wherein a subset of these extended or remaining unextended areas can be cleaved such as, for example, 40 of the 50 3 n (60 base) sections can be cleaved; and the splints can be length n, so can come from the original pool of 287 fragments of length n, of which 37 remain unused, or can be extended fragments from the pool of 50 fragments of length 3 n (interpreted as cleaving a first linker then cleaving a second linker; a second linker cleavage agent; and storing the first regenerated linkers and the second regenerated linkers with the solid substrate, claims 1, 25 and 27) (paragraph [0197]). Chen teaches that the final product or products should be transferred from the chip to a collection site, collection vessel, or a downstream module such as described above (interpreted singly and in all as a single reaction vessel, claim 1) (paragraph [0209]). Chen teaches nucleic acid synthesis and subsequent assembly can be implemented on a continuous flow microfluidic device including a device consisting of a surface with a plurality of microwells each containing a bead (interpreted as a single reaction vessel, claim 1) (paragraph [0217]). Chen teaches a plurality of bead can contain immobilized oligonucleotides with an orthogonally deglycosylated base (interpreted as orthogonal cleavage, claim 1) (paragraph [0221], lines 12-14). Chen teaches that after assembly from Stage 1 to Stage N, the anchored assembly is cleaved with the aforementioned orthogonal nucleic acid glycosylase, and the assembly is then retrieved by the end-user from the microfluidic device (interpreted as orthogonal cleavage, claim 1) (paragraph [0223]).
Regarding claim 22, Chen teaches that the device can comprise beads including magnetic beads, wherein the beads can be porous; and the device can contain a population of beads onto which the plurality of immobilized initiation oligonucleotide sequences are attached; and a portion of the beads are cleaved to release the oligonucleotide sequences into solution (interpreted as metal, plastic and/or silicon solid substrate, claim 22) (paragraph [0050], lines 1-5). Chen teaches that the segmented electrode DMF platform (DB3-120 from SciBots) was used to perform assembly of cleaved oligonucleotide components onto an immobilized oligonucleotide, wherein the segmented electrodes were covered with a carrier fluid (dodecane) and a glass cover slip (interpreted as a glass solid substrate, claim 22) (paragraph [0232]). Chen teaches that eight cleaved oligonucleotide components (SEQ IDs 2-9) were assembled onto a single NeutrAvidin-bead immobilized oligonucleotide (SEQ ID 10) component to yield a contiguous oligonucleotide sequence (interpreted as plastic or silicon solid substrate, claim 22) (paragraph [0227], lines 1-4).
Regarding claim 25, Chen teaches that the sequences can be joined together, for example using a DNA ligase, thereby extending each of the immobilized 'areas' to a length 3 n (at least 60 bases) of the immobilised sequences n remain unextended for use as splints later in the process, wherein a subset of these extended or remaining unextended areas can be cleaved such as, for example, 40 of the 50 3 n (60 base) sections can be cleaved; and the splints can be length n, so can come from the original pool of 287 fragments of length n, of which 37 remain unused, or can be extended fragments from the pool of 50 fragments of length 3 n (interpreted as cleaving a first linker then cleaving a second linker; and storing the first regenerated linkers and the second regenerated linkers with the solid substrate, claims 1 and 25) (paragraph [0197]).
Regarding claim 29, Chen teaches that the strands can be synthesized using chemical or enzymatic means, wherein the cycles of extension can be performed using a template independent polymerase, such as TdT, where the nucleotide monomers are nucleoside triphosphates. Alternatively, the cycles of extension can be performed using chemical synthesis, where the nucleotide monomers are nucleoside phosphoramidates (interpreted as comprising contacting with a polymerase and nucleotides, claim 28) (paragraphs [0025]; and [0117]). Chen teaches that hybridization between the strands can be designed such that the ends of the stands are adjacent and can be directly linked; or the strands can be prepared with single stranded regions (gaps) which can be filled in by a nucleic acid polymerase (interpreted as comprising contacting with a polymerase and nucleotides, claim 28) (paragraph [0028]). Chen teaches that gapped or ungapped nucleic acid assembly process (e.g., splint ligation or polymerase chain assembly) is then used to covalently link the hybridized nucleic acids together by actuating droplets from reservoirs containing necessary reagents to perform nucleic acid assembly (interpreted as a covalent attachment to first truncated linkers, claims 3 and 29) (paragraph [0213]). Chen teaches that the chemical linkage between chemically ligated DNA components should be read through by polymerases (interpreted as contacting with a polymerase, claim 28) (paragraph [0207]).
Regarding claim 31, Chen teaches hybridizing at least two of the cleaved oligonucleotides to each other, to form a splint, and hybridizing one end of the splint to one of the immobilized oligonucleotide sequences (interpreted as regenerating portion of the first linkers that have a different sequence than the first linkers, claim 31) (paragraph [0077]).
Regarding claim 32, Chen teaches that the chemical linkage between chemically ligated DNA components should be read through by polymerases (interpreting the linkers to be DNA, claim 32) (paragraph [0207]). Chen teaches that the cycles of extension are performed using a polymerase enzyme and the nucleotide triphosphate monomers are nucleoside triphosphates (interpreting linkers to be DNA, claim 32) (paragraph [0113], lines 1-3).
Regarding claim 33, Chen teaches that the initiator sequence is immobilized on a solid support via a reversible interacting moiety, such as a chemically-cleavable linker, an antibody/immunogenic epitope, a biotin/biotin binding protein (such as avidin or streptavidin), or glutathione-GST tag (interpreting the biotin binding protein as the polymer strand comprising a polypeptide, claim 33) (paragraph [0108]).
Regarding claim 34, Chen teaches that a wash solution is introduced to wash all of the addition components off of the surface (interpreted as washing the solid substrate, claim 34) (paragraph [0219]). Chen teaches that selectively eluted beads are pooled into a solution, and the immobilized oligo-nucleotides are cleaved at the aforementioned base capable of being deglycosylated by a deglycosylase (interpreted as washing the solid substrate, claim 34) (paragraph [0221]).
Regarding claim 35, Chen teaches that eight oligonucleotide components cleaved into solution have been assembled onto a single immobilized oligonucleotide component to yield a contiguous oligonucleotide sequence (interpreted as collecting and purifying polymer strands removed from the solid support, claim 35) (paragraph [0226], lines 9-12).
Chen does not specifically exemplify purification of cleaved strands (claim 35, in part).
Regarding claim 35 (in part), Crameri teaches that at the end of the sequential addition of nucleotides the oligo is released from the solid phase support, further deprotection takes place, and then the crude oligonucleotide is further purified by column chromatography (interpreted a purifying released oligonucleotide linkers, claim 35) (pg. 1, lines 14-16). Crameri teaches the term "pool" refers to a group of oligonucleotides that may vary in sequence, can be shorter or longer than the target sequence, and may not have the same sequence as the target sequence. The pool of oligonucleotides may be the product of oligonucleotide synthesis, e.g. solid phase chemical synthesis via phosphoramidite chemistry, used with or without purification pg. 4, lines 31-34). Crameri teaches producing a single stranded oligonucleotide product having at least one modified nucleotide residue, comprising: (a) providing a template oligonucleotide (I) complimentary to the sequence of the product, said template having properties that allow it to be separated from the product; (b) providing a pool of oligonucleotides (II); (c) contacting (I) and (II) in conditions to allow annealing; (d) changing the conditions to separate any impurities, comprising denaturing the annealed template and impurity oligonucleotide strands and separating the impurities; and (e) changing the conditions to separate the product, comprising denaturing the annealed template and product oligonucleotide strands and separating the product, wherein such a process can be used to isolate a single stranded oligonucleotide product from impurities, e.g. as a purification process (interpreted as purifying released strands, claim 35) (pg. 2, lines 9-20). Crameri teaches that the segment oligonucleotides are joined by enzymatic ligation (pg. 8, lines 3-4). Crameri teaches that the solid support material is a streptavidin coated bead. In a further embodiment, the solid support material is part of the reaction vessel itself, e.g. a reaction wall (interpreted as a single reaction vessel, claim 1) (pg. 9, lines 19-20). Crameri teaches that the process is carried out in a column reactor (interpreted as a single reaction vessel, claim 1) (pg. 14, lines 7-8).
“It is prima facie obvious to combine prior art elements according to known methods to yield predictable results; the court held that, "…a conclusion that a claim would have been obvious is that all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination would have yielded nothing more than predictable results to one of ordinary skill in the art. KSR International Co. v. Teleflex Inc., 550 U.S. ___, ___, 82 USPQ2d 1385, 1395 (2007); Sakraida v. AG Pro, Inc., 425 U.S. 273, 282, 189 USPQ 449, 453 (1976); Anderson’s-Black Rock, Inc. v. Pavement Salvage Co., 396 U.S. 57, 62-63, 163 USPQ 673, 675 (1969); Great Atlantic & P. Tea Co. v. Supermarket Equipment Corp., 340 U.S. 147, 152, 87 USPQ 303, 306 (1950)”. Therefore, in view of the benefits of producing oligonucleotides that are suitable for use in the production of chemically modified oligonucleotides as exemplified by Crameri, it would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of preparing contiguous oligonucleotide sequences by joining splinted sequences to immobilized oligonucleotides followed by selective cleavage and denaturation as disclosed by Chen to include the method of purifying cleaved strands as taught by Crameri, with a reasonable expectation of success in increasing oligonucleotide separation efficiency; producing oligonucleotide strands having a high degree of purity; in assembling oligonucleotides into contiguous strands to produce strands that are longer than can be produced using base-by-base synthesis methods; and/or in synthesizing chemically modified oligonucleotides that can be used in therapy, such as in the treatment of diabetes.
Thus, in view of the foregoing, the claimed invention, as a whole, would have been obvious to one of ordinary skill in the art at the time the invention was made. Therefore, the claims are properly rejected under 35 USC §103 as obvious over the art.
Response to Arguments
Applicant’s arguments filed October 17, 2025 have been fully considered but they are not persuasive. Applicants essentially asserts: (a) Chen does not teach orthogonal cleavage in a single reaction vessel (Applicant Remarks, Section A, pg. 20 through pg. 22, first full paragraph); (b) Crameri does not cure Chen’s deficiency regarding the single reaction vessel orthogonal cleavage; and the Office has not identified any specific teaching in Crameri that would lead a person to modify Chen’s spatially separated microwell approach to achieve sequence-based orthogonal cleavage in a single reaction vessel (Applicant Remarks, pg. 22, Section B, second through fourth full paragraphs); (c) Chen teaches away from the claimed single reaction vessel approach (Applicant Remarks, pg. 23, Section C, first through third full paragraphs); and (d) the proposed combination lacks motivation and a reasonable expectation of success (Applicant Remarks, pg. 23, Section D, first full paragraph through pg. 24)
Regarding (a) and (b), please see the discussion supra regarding the Examiner’s response to Applicant’s arguments; and the teachings of the combined references. Applicant’s assertion that Chen does not teach orthogonal cleavage in a single reaction vessel; and Crameri does not cure Chen’s deficiency regarding the single reaction vessel orthogonal cleavage; and the Office has not identified any specific teaching in Crameri that would lead a person to modify Chen’s spatially separated microwell approach to achieve sequence-based orthogonal cleavage in a single reaction vessel, is not found persuasive. As an initial matter, based on the limitations as recited in claim 1, Applicant’s argument regarding a specific teaching in Crameri that would lead a person to modify the microwell approach of Chen to achieve sequence-based orthogonal cleavage in a single reaction vessel is completely unclear to the Examiner. As previously noted supra:
The as-filed Specification and original claims do not teach orthogonal cleavage in a single reaction vessel.
Instant claim 1 does not recite the use of a single reaction vessel or orthogonal cleavage.
The “thereby” clause is not given patentable weight because it simply expresses the intended result of a process step positively recited.
Instant claim 1 recites that ‘contacting both the first linker and the second linker with a first linker cleavage agent that comprises a first restriction endonuclease, thereby achieving orthogonal cleavage in a single reaction vessel’ (See, claim 1, lines 11-13).
It is unclear as to the identity of the single reaction vessel given that the as-filed Specification teaches a flow diagram in Figure 7 showing an illustrative process for the solid-phase polymer synthesis; while Figure 14 shows a patterned substrate.
Because claim 1 does not recite “orthogonal cleavage in a single reaction vessel”, and the “thereby” clause is not given patentable weight, Chen and Crameri are not required to teach those specific limitations. Assuming arguendo that this limitation is recited in claim 1, it is noted that (i) cleaving different linkers using distinct enzymatic methods to selectively cleave the different linker molecules is orthogonal cleavage; and (ii) both references teach a variety of different single reaction vessels that overlap with reaction vessels taught in the as-filed Specification. For example -
Chen teaches:
(i) A method for preparing a contiguous oligonucleotide sequence of at least 4 n bases in length, the method comprising:
(a) taking a device with a plurality of immobilized initiation oligonucleotide sequences, one or more of which contains a cleavage site (interpreted as oligonucleotide linkers with different cleavage sites);
(b) using the initiation oligonucleotide sequences to synthesize a plurality of immobilized oligonucleotide sequences of at least n bases in length, using cycles of extension of reversibly blocked nucleotide monomers (interpreted as synthesizing first and second polymer strands); and
(c) selectively cleaving at least four of the immobilized oligonucleotide sequences of least n bases in length into solution while leaving two or more of the immobilized oligonucleotide sequences attached, wherein the base can be cleaved by a restriction enzyme such as endonuclease VIII (interpreted as contacting first linkers and second linkers with a first cleavage agent comprising a restriction endonuclease, thereby achieving orthogonal cleavage in a single vessel); and
(f) performing a further cleavage step of selectively cleaving at least one of the immobilised oligonucleotide sequences of least 2 n bases in length into solution whilst leaving one or more of the immobilised oligonucleotide sequences attached (interpreted as cleaving a different second cleavage site).
(ii) A surface with a plurality of microwells each containing a bead; and that the final product or products should be transferred from the chip to a collection site, collection vessel, or a downstream module (interpreted singly and in all as a single reaction vessel).
(iii) A plurality of bead can contain immobilized oligonucleotides with an orthogonally deglycosylated base (interpreted as orthogonal cleavage).
(iv) After assembly from Stage 1 to Stage N, the anchored assembly is cleaved with the aforementioned orthogonal nucleic acid glycosylase, and the assembly is then retrieved by the end-user from the microfluidic device (interpreted as orthogonal cleavage, claim 1)
Crameri teaches:
The solid support material is a streptavidin coated bead. In a further embodiment, the solid support material is part of the reaction vessel itself, e.g. a reaction wall (interpreted as a single reaction vessel, claim 1) (pg. 9, lines 19-20).
The process is carried out in a column reactor (interpreted as a single reaction vessel, claim 1).
The combined references of Chen and Crameri teach all of the limitations of the claims and, therefore, the combined references teach “achieving orthogonal cleavage in a single reaction vessel.” Thus, the claims remain rejected for the reasons of record.
Regarding (c), please see the discussion supra regarding the Examiner’s response to Applicant’s arguments; and the teachings of the combined references. Applicant’s assertion that Chen teaches away from the claimed single reaction vessel approach, is not found persuasive. As an initial matter, please see the discussion supra regarding the recitation of “thereby achieving orthogonal cleavage in a single reaction vessel”.
Assuming arguendo that: (a) claim 1 recites a single reaction vessel, (b) that the as-filed Specification teaches a single reaction vessel in combination with orthogonal cleavage, (c) that the single reaction vessel can be identified as having a particular structure, and (d) that the limitation is given patentable weight, Chen and/or Crameri clearly do not teach away from using a single reaction vessel. Note that disclosed examples and preferred embodiments do not constitute a teaching away from a broader disclosure or nonpreferred embodiments. In re Susi, 440 F.2d 442, 169 USPQ 423 (CCPA 1971). "The use of patents as references is not limited to what the patentees describe as their own inventions or to the problems with which they are concerned. They are part of the literature of the art, relevant for all they contain." A reference may be relied upon for all that it would have reasonably suggested to one having ordinary skill the art, including nonpreferred embodiments. See In re Heck, 699 F.2d 1331, 1332-33,216 USPQ 1038, 1039 (Fed. Cir. 1983); In re Lemelson, 397 F.2d 1006, 1009, 158 USPQ 275,277 (CCPA 1968); Merck & Co. v. Biocraft Laboratories, 874 F.2d 804, 10 USPQ2d 1843 (Fed. Cir.), cert. denied, 493 U.S. 975 (1989); and Upsher-Smith Labs. v. Pamlab, LLC, 412 F.3d 1319, 1323, 75 USPQ2d 1213, 1215 (Fed. Cir. 2005). Moreover,
A reference teaches away “when a person of ordinary skill, upon reading the reference, would be discouraged from following the path set out in the reference, or would be led in a direction divergent from the path that was taken” in the claim. Galderma Labs., L.P. v. Tolmar, Inc., 737 F.3d 731, 738 (Fed. Cir. 2013). A reference that “merely expresses a general preference for an alternative invention but does not criticize, discredit, or otherwise discourage investigation into” the claimed invention does not teach away. Id.
Additionally, MPEP 2141.02(VI) states:
"the prior art’s mere disclosure of more than one alternative does not constitute a teaching away from any of these alternatives because such disclosure does not criticize, discredit, or otherwise discourage the solution claimed…." In re Fulton, 391 F.3d 1195, 1201, 73 USPQ2d 1141, 1146 (Fed. Cir. 2004)
MPEP 2123(II) indicates:
“disclosed examples and preferred embodiments do not constitute a teaching away from a broader disclosure or nonpreferred embodiments. In re Susi, 440 F.2d 442, 169 USPQ 423 (CCPA 1971).
"A known or obvious composition does not become patentable simply because it has been described as somewhat inferior to some other product for the same use." In re Gurley, 27 F.3d 551, 554, 31 USPQ2d 1130, 1132 (Fed. Cir. 1994)”
MPEP 2143 (B) states:
that the Federal Circuit’s discussion in ICON also makes clear that if the reference does not teach that a combination is undesirable, then it cannot be said to teach away. An assessment of whether a combination would render the device inoperable must not "ignore the modifications that one skilled in the art would make to a device borrowed from the prior art." Id. at 1382, 83 USPQ2d at 1752.
Neither Chen and/or Crameri teach away from enzymatic cleavage of different first linkers on a solid support including in a single reaction vessel. Clearly, the references do not criticize, discredit, or otherwise discourage investigation into orthogonal cleavage in a single reaction vessel. The combined references of Chen and Crameri teach all of the limitations of the claims. Thus, the claims remain rejected for the reasons of record.
Regarding (d), please see the discussion supra regarding the Examiner’s response to Applicant’s arguments; and the teachings of the combined references. Applicant’s assertion that the proposed combination lacks motivation and a reasonable expectation of success, is not found persuasive. MPEP 2144(I) states that:
“[T]he rationale to modify or combine the prior art does not have to be expressly stated in the prior art; the rationale may be expressly or impliedly contained in the prior art or it may be reasoned from knowledge generally available to one of ordinary skill in the art, established scientific principles, or legal precedent established by prior case law. In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988); In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992). See also In re Kotzab, 217 F.3d 1365, 1370, 55 USPQ2d 1313, 1317 (Fed. Cir. 2000) (setting forth test for implicit teachings); In re Eli Lilly & Co., 902 F.2d 943, 14 USPQ2d 1741 (Fed. Cir. 1990) (discussion of reliance on legal precedent); In re Nilssen, 851 F.2d 1401, 1403, 7 USPQ2d 1500, 1502 (Fed. Cir. 1988) (references do not have to explicitly suggest combining teachings); Ex parte Clapp, 227 USPQ 972 (Bd. Pat. App. & Inter. 1985) (examiner must present convincing line of reasoning supporting rejection); and Ex parte Levengood, 28 USPQ2d 1300 (Bd. Pat. App. & Inter. 1993) (reliance on logic and sound scientific reasoning).
Furthermore, the applicants are reminded that the motivation for combining the teachings of the prior art may be different from applicants’ motivation to make the disclosed compositions. The fact that applicant has recognized another advantage which would flow naturally from following the suggestion of the prior art cannot be the basis for patentability when the differences would otherwise be obvious. See Ex parte Obiaya, 227 USPQ 58, 60 (Bd. Pat. App. & Inter. 1985). The Office has provided motivation to the method of preparing contiguous oligonucleotide sequences by joining splinted sequences to immobilized oligonucleotides followed by selective cleavage and denaturation as disclosed by Chen to include the method of purifying cleaved strands including by isolating a single stranded oligonucleotide product from impurities, such as through column chromatography as taught by Crameri, with a reasonable expectation of success, for example, in producing oligonucleotide strands having a high degree of purity; in increasing oligonucleotide separation efficiency; and/or in synthesizing chemically modified oligonucleotides that can be used in therapy, such as in the treatment of diabetes.
Additionally, methods of purifying oligonucleotide products are well-known, purely conventional and routine in the art such that one of ordinary skill in the art would clearly have a reasonable expectation of success in purifying single-stranded oligonucleotide products. The combined references of Chen and Crameri teach all of the limitations of the claims. Thus, the claims remain rejected for the reasons of record.
Conclusion
Claims 1, 3, 22, 24, 25 and 27-35 remain rejected.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/AMY M BUNKER/Primary Examiner, Art Unit 1684