DETAILED ACTION
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 .
Office Action: NOTICE
This is a second non-final rejection, filed in response to Applicant’s arguments (6/11/2026).
Claim Status
Claims 46, 70 and 72 were amended (6/11/2026). Claims 6, 8-10, 13, 16-17, 21-24, 28, 30-31, 33-34, 43-45, 47-6971, 73-76 and 78-102 were previously cancelled (7/7/2023). Claims 1-5, 7, 11-12, 14-15, 18-20, 25-27, 29, 32, 35-42, 46, 70, 72 and 77 are under examination.
Priority
Claims 1-5, 7, 11-12, 14-15, 18-20, 25-27, 29, 32, 35-42, 46, 70, 72 and 77 receive a priority date of 5/5/2020, the effective filing date of US Provisional 63020115.
Objections Withdrawn
Specification:
The objections to the specification due to the use of a trademark are withdrawn in view of
Applicant’s amendments.
Rejections Withdrawn
The rejections to claims 46, 70, 72 and 77 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, are withdrawn in view of Applicant’s amendments of claims 46, 70 and 72 (6/11/2026).
The rejection of claims 1-5, 7, 11-12, 14-15, 18-20, 25-27, 29, 32, 35-42, 46, 70, 72 and 77 are rejected under 35 U.S.C. 102 (a)(1) and (a)(2) as being anticipated by Nesbit et al. (US PGPub 2007/0197538 A1; published 8/23/2007) is withdrawn in view of Applicant’s arguments (6/11/2026). Specifically, the Applicant’s arguments further specify the ordered nucleotide-identification workflow, including selective removal of a first nucleotide while retaining the polymerase and primed-template nucleic acid, followed by delivery and examination of a second nucleotide. Upon reconsideration, Nesbit does not teach these limitations in the arranged manner required by the claim set (6/11/2026).
New Rejections
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-5, 7, 11-12, 14-15, 18-20, 25-27, 29, 32, 35-42, 46, 70, 72 and 77 are rejected under 35 U.S.C. 103 as being unpatentable over Nesbit et al. (US PGPub 2007/0197538 A1; published 8/23/2007), Fuller et al. (“Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array”, PNAS, published 2016) and further in view of Rannou et al. (“Functional interplay of DnaE polymerase, DnaG primase and DnaC helicase within a ternary complex, and primase to polymerase hand-off during lagging strand DNA replication in Bacillus subtilis, Nucleic Acids Research, published 2013).
Regarding claim 1, Nesbit teaches an invention relating to the modulation and/or inhibition of cell signaling, cell proliferation, extracellular matrix production, chemotaxis, the control of abnormal cell growth and cell inflammatory response and more specifically, this invention relates to the use of substituted quinoxaline compounds which exhibit selective inhibition of differentiation, proliferation or mediator release by effectively inhibiting platelet-derived growth factor-receptor (PDGF-R) tyrosine kinase activity and/or Lck tyrosine kinase activity (Abstract). Further, Nesbit teaches that the previously described invention can be applied to cytosine arabinoside-cytarabine commercialized under Cytosar-U which is an antimetabolite specific for cells in the S-phase of the cell cycle, which acts through inhibition of DNA polymerase and cytosine incorporation into DNA and RNA, as well as Daunorubicin, which is also named Cerubidine and Idarubicin or Idamycin which are topoisomerase-II inhibitors, inhibiting DNA and RNA polymerase (Paragraph 49, lines 1-5). Specifically, Nesbit teaches that Topoisomerase II inhibitors include, but are not limited to, epipodophyllotoxins. Epipodophyllotoxins are phase specific anti-neoplastic agents derived from the mandrake plant, where epipodophyllotoxins typically affect cells in the S and G2 phases of the cell cycle by forming a ternary complex with topoisomerase 11 and DNA causing DNA strand breaks (Paragraph 399, lines 1-5).
Nesbit also teaches that in another aspect, the DNA sequence of the invention is integrated within a replicable expression vector, which is understood to mean any nucleic acid comprising a nucleotide sequence of interest and competent to be incorporated into a host cell and to be recombined with and integrated into the host cell genome, or to replicate autonomously as an episome and such vectors include linear nucleic acids, plasmids, phagemids, cosmids and the like which are within the knowledge of a skilled person in the art (Paragraph 366, lines 1-10). Nesbit also teaches that metal salts of compounds of the present invention may be obtained by contacting a hydride, hydroxide, carbonate or similar reactive compound of the chosen metal in an aqueous or organic solvent with the free acid form of the compound where the aqueous solvent employed may be water or it may be a mixture of water with an organic solvent, preferably an alcohol such as methanol or ethanol, a ketone such as acetone, aliphatic ether such as tetrahydrofuran, or an ester such as ethyl acetate (Paragraph 291, lines 1-5).
Regarding claim 2, Nesbit teaches that where the compound of the invention is substituted with an acidic moiety, base addition salts may be formed and are simply a more convenient form for use; and in practice, use of the salt form inherently amounts to use of the free acid form (Paragraph 290, lines 1-5). Specifically, Nesbit teaches that pharmaceutically acceptable salts, including for example alkali and alkaline earth metal salts, within the scope of the invention are those derived from the following bases: sodium hydride, sodium hydroxide, potassium hydroxide, calcium hydroxide, aluminum hydroxide, lithium hydroxide, magnesium hydroxide, zinc hydroxide, ammonia, trimethylammonia, triethylammonia, ethylenediamine, n-methyl-glucamine, lysine, arginine, omithine, choline, N,N'-dibenzylethylenediamine, chloroprocaine, diethanolamine, procaine, n-benzylphenethylamine, diethylamine, piperazine, tris(hydroxymethyl)-aminomethane, tetramethylammonium hydroxide, and the like (Paragraph 290, lines 5-15).
Regarding claim 3, Nesbit teaches that in another aspect, the coating on the stent device can be formed by applying the compound of the invention to at least one surface of the stent device to form a bioactive layer and then applying one or more coats of porous polymeric material over the bioactive layer, such that the porous polymeric material has a thickness adequate to provide a controlled release of the compound (Paragraph 335, lines 1-5).
Regarding claim 4, Nesbit teaches that another aspect of the invention is directed to a pharmaceutical composition comprising a pharmaceutically effective amount of a compound of formula I and a pharmaceutically acceptable carrier or vessel (Paragraph 127, lines 1-3).
Regarding claim 5, Nesbit teaches that metal salts of compounds of the present invention may be obtained by contacting a hydride, hydroxide, carbonate or similar reactive compound of the chosen metal in an aqueous or organic solvent with the free acid form of the compound where the aqueous solvent employed may be water or it may be a mixture of water with an organic solvent, preferably an alcohol such as methanol or ethanol, a ketone such as acetone, aliphatic ether such as tetrahydrofuran, or an ester such as ethyl acetate (Paragraph 291, lines 1-5).
Regarding claims 7 and 11, Nesbit teaches that compositions according to the invention may also be formulated in a manner which resists rapid clearance from the vascular (arterial or venous) wall by convection and/or diffusion, thereby increasing the residence time of the viral particles at the desired site of action where a periadventitial depot comprising a compound according to the invention may be used for sustained release n alternative approach for minimizing washout of a compound according to the invention during percutaneous, transvascular delivery comprises the use of nondiffusible, drug-eluting microparticles (Paragraph 317, lines 1-5). Nesbit also teaches that the microparticles may be comprised of a variety of synthetic polymers, such as polylactide for example, or natural substances, including proteins or polysaccharides. Such microparticles enable strategic manipulation of variables including total dose of drug and kinetics of its release, where microparticles can be injected efficiently into the arterial or venous wall through a porous balloon catheter or a balloon over stent, and are retained in the vascular wall and the periadventitial tissue for at least about two weeks (Paragraph 318, lines 1-15).
Specifically, Nesbit teaches that Topoisomerase II inhibitors include, but are not limited to, epipodophyllotoxins. Epipodophyllotoxins are phase specific anti-neoplastic agents derived from the mandrake plant, where epipodophyllotoxins typically affect cells in the S and G2 phases of the cell cycle by forming a ternary complex with topoisomerase 11 and DNA causing DNA strand breaks (Paragraph 399, lines 1-5). Nesbit teaches that the pharmaceutical compositions for therapeutic treatment are intended for parenteral, topical, oral or local administration and preferably, the pharmaceutical compositions are administered parenterally, e.g., intravenously, subcutaneously, intradermally, or intramuscularly and thus, the invention provides compositions for parenteral administration which comprise a solution of the combination of the PDGF receptor inhibitor and anti-angiogenic chemotherapeutics in an acceptable carrier, preferably an aqueous carrier (these compositions may be sterilized by conventional, well known sterilization techniques, or may be sterile filtered) (Paragraph 429, lines 1-15).
Further, Nesbit teaches acid addition salts of the compounds of this invention which are prepared by reaction of the free base with the appropriate acid, by the application or adaptation of known methods and where for example, the acid addition salts of the compounds of this invention are prepared either by dissolving the free base in aqueous or aqueous-alcohol solution or other suitable solvents containing the appropriate acid and isolating the salt by evaporating the solution, or by reacting the free base and acid in an organic solvent, in which case the salt separates directly or can be obtained by concentration of the solution (Paragraph 288, lines 1-8).
Regarding claim 12, Nesbit teaches that another aspect of the invention is directed to a pharmaceutical composition comprising a pharmaceutically effective amount of a compound of formula I and a pharmaceutically acceptable carrier or vessel (Paragraph 127, lines 1-3).
Regarding claims 14-15, 18-19, Nesbit teaches that the biopharmaceutical of the present invention preferably retains the signal peptide of PDGF-R.beta, however, alternative signal peptides may be used to efficiently initiate or act as primers for the transport of a protein across the membrane of the endoplasmic reticulum and signal sequences have been well characterized in the art and are known typically to contain 16 to 30 amino acid residues, and may contain greater or fewer amino acid residues, where a typical signal peptide consists of three regions: a basic N-terminal region, a central hydrophobic region, and a more polar C-terminal region and the central hydrophobic region contains 4 to 12 hydrophobic residues that anchor the signal peptide across the membrane lipid bilayer during transport of the nascent polypeptide (Paragraph 365, lines 10-20). Further, Nesbit teaches that following initiation, the signal peptide is usually cleaved within the lumen of the endoplasmic reticulum by cellular enzymes known as signal peptidases (Paragraph 365, lines 15-25).
Regarding claim 20, Nesbit teaches that alkylating agents are non-phase anti-cancer specific agents and strong electrophiles and typically, alkylating agents form covalent linkages, by alkylation, to DNA through nucleophilic moieties of the DNA molecule such as phosphate, amino, sulfhydryl, hydroxyl, carboxyl, and imidazole groups. Such alkylation disrupts nucleic acid function leading to cell death (Paragraph 386, lines 1-5).
Regarding claims 25-26, Nesbit teaches that an example of exogenous labelling includes a reaction which is stopped by addition of 150 .mu.l of stopping buffer (100 mM Hepes pH7.5, KF 400 mM, EDTA 133 mM, BSA 1 g/l.) containing a selected anti tyrosine antibody labelled with the Europium cryptate (PY20-K) at 0.8 .mu.g/ml and allophycocyanine-labelled streptavidin (XL665) at 4 .mu.g/ml where the labelling of Streptavidin and anti-tyrosine antibodies were performed by Cis-Bio International (France) and the mixture is counted using a Packard Discovery counter which is able to measure time-resolved homogeneous fluorescence transfer (excitation at 337 nm, readout at 620 nm and 665 nm) where the ratio of the 665 nm signal/620 nm signal is a measure of the phosphorylated tyrosine concentration and the blank is obtained by replacing enzyme by buffer to calculate the specific signal which is the difference between the ratio obtained without inhibitor and the ratio with the blank (Paragraph 606, lines 15-25).
Regarding claims 27 and 29, Nesbit teaches that the previously described invention can be applied to cytosine arabinoside-cytarabine commercialized under Cytosar-U which is an antimetabolite specific for cells in the S-phase of the cell cycle, which acts through inhibition of DNA polymerase and cytosine incorporation into DNA and RNA, as well as Daunorubicin, which is also named Cerubidine and Idarubicin or Idamycin which are topoisomerase-II inhibitors, inhibiting DNA and RNA polymerase (Paragraph 49, lines 1-5). Specifically, Nesbit teaches that Topoisomerase II inhibitors include, but are not limited to, epipodophyllotoxins. Epipodophyllotoxins are phase specific anti-neoplastic agents derived from the mandrake plant, where epipodophyllotoxins typically affect cells in the S and G2 phases of the cell cycle by forming a ternary complex with topoisomerase 11 and DNA causing DNA strand breaks (Paragraph 399, lines 1-5).
Regarding claim 32, Nesbit teaches that an example of exogenous labelling includes a reaction which is stopped by addition of 150 .mu.l of stopping buffer (100 mM Hepes pH7.5, KF 400 mM, EDTA 133 mM, BSA 1 g/l.) containing a selected anti tyrosine antibody labelled with the Europium cryptate (PY20-K) at 0.8 .mu.g/ml and allophycocyanine-labelled streptavidin (XL665) at 4 .mu.g/ml where the labelling of Streptavidin and anti-tyrosine antibodies were performed by Cis-Bio International (France) and the mixture is counted using a Packard Discovery counter which is able to measure time-resolved homogeneous fluorescence transfer (excitation at 337 nm, readout at 620 nm and 665 nm) where the ratio of the 665 nm signal/620 nm signal is a measure of the phosphorylated tyrosine concentration and the blank is obtained by replacing enzyme by buffer to calculate the specific signal which is the difference between the ratio obtained without inhibitor and the ratio with the blank (Paragraph 606, lines 15-25).
Regarding claims 35-41, Nesbit teaches acid addition salts of the compounds of this invention which are prepared by reaction of the free base with the appropriate acid, by the application or adaptation of known methods and where for example, the acid addition salts of the compounds of this invention are prepared either by dissolving the free base in aqueous or aqueous-alcohol solution or other suitable solvents containing the appropriate acid and isolating the salt by evaporating the solution, or by reacting the free base and acid in an organic solvent, in which case the salt separates directly or can be obtained by concentration of the solution (Paragraph 288, lines 1-8). Specifically, Nesbit teaches the porous polymeric material is applied by plasma deposition and representative polymers suitable for plasm deposition include poly(ethylene oxide), poly(ethylene glycol), poly(propylene oxide), and polymers of methane, silicone, tetrafluoroethylene tetramethyldisiloxane, and the like (Paragraph 337, lines 1-5).
Nesbit also teaches that metal salts of compounds of the present invention may be obtained by contacting a hydride, hydroxide, carbonate or similar reactive compound of the chosen metal in an aqueous or organic solvent with the free acid form of the compound where the aqueous solvent employed may be water or it may be a mixture of water with an organic solvent, preferably an alcohol such as methanol or ethanol, a ketone such as acetone, aliphatic ether such as tetrahydrofuran, or an ester such as ethyl acetate (Paragraph 291, lines 1-5).
Nesbit further teaches that also useful in some special instances are monoacrylates such as n-butyl-acrylate, n-butyl methacrylate, 2-ethylhexyl acrylate, lauryl-acrylate, and 2-hydroxy-propyl acrylate where small quantities of amides of (meth)acrylic acid such as N-methylol methacrylamide butyl ether are also suitable, N-vinyl compounds such as N-vinyl pyrrolidone, vinyl esters of aliphatic monocarboxylic acids such as vinyl oleate, vinyl ethers of diols such as butanediol-1,4-divinyl ether and allyl ether and allyl ester are also suitable; also included are other monomers such as the reaction products of di- or polyepoxides such as butanediol-1,4-diglycidyl ether or bisphenol A diglycidyl ether with (meth)acrylic acid (Paragraph 339, lines 1-10).
Regarding claim 42, Nesbit teaches that alkylating agents are non-phase anti-cancer specific agents and strong electrophiles where typically, alkylating agents form covalent linkages, by alkylation, to DNA through nucleophilic moieties of the DNA molecule such as phosphate, amino, sulfhydryl, hydroxyl, carboxyl, and imidazole groups and such alkylation disrupts nucleic acid function leading to cell death (examples of alkylating agents include, but are not limited to, nitrogen mustards such as cyclophosphamide, melphalan, and chlorambucil; alkyl suffonates such as busulfan; nitrosoureas such as carmustine; and triazenes such as dacarbazine) (Paragraph 386, lines 1-5).
Regarding claim 46, Nesbit teaches that the choice of vehicle and the content of active substance in the vehicle are generally determined in accordance with the solubility and chemical properties of the product, the particular mode of administration and the provisions to be observed in pharmaceutical practice; for example, excipients such as lactose, sodium citrate, calcium carbonate, dicalcium phosphate and disintegrating agents such as starch, alginic acids and certain complex silica gels combined with lubricants such as magnesium stearate, sodium lauryl sulfate and talc may be used for preparing tablets, troches, pills, capsules and the like and to prepare a capsule, it is advantageous to use lactose and liquid carrier, such as high molecular weight polyethylene glycols (Paragraph 310, lines 1-10). Nesbit further teaches that another aspect of the invention is directed to a pharmaceutical composition comprising a pharmaceutically effective amount of a compound of formula I and a pharmaceutically acceptable carrier or vessel (Paragraph 127, lines 1-3). Further, Nesbit teaches acid addition salts of the compounds of this invention which are prepared by reaction of the free base with the appropriate acid, by the application or adaptation of known methods and where for example, the acid addition salts of the compounds of this invention are prepared either by dissolving the free base in aqueous or aqueous-alcohol solution or other suitable solvents containing the appropriate acid and isolating the salt by evaporating the solution, or by reacting the free base and acid in an organic solvent, in which case the salt separates directly or can be obtained by concentration of the solution (Paragraph 288, lines 1-8).
Specifically, Nesbit teaches that Topoisomerase II inhibitors include, but are not limited to, epipodophyllotoxins. Epipodophyllotoxins are phase specific anti-neoplastic agents derived from the mandrake plant, where epipodophyllotoxins typically affect cells in the S and G2 phases of the cell cycle by forming a ternary complex with topoisomerase 11 and DNA causing DNA strand breaks (Paragraph 399, lines 1-5). Nesbit teaches that the biopharmaceutical of the present invention preferably retains the signal peptide of PDGF-R.beta, however, alternative signal peptides may be used to efficiently initiate or act as primers for the transport of a protein across the membrane of the endoplasmic reticulum and signal sequences have been well characterized in the art and are known typically to contain 16 to 30 amino acid residues, and may contain greater or fewer amino acid residues, where a typical signal peptide consists of three regions: a basic N-terminal region, a central hydrophobic region, and a more polar C-terminal region and the central hydrophobic region contains 4 to 12 hydrophobic residues that anchor the signal peptide across the membrane lipid bilayer during transport of the nascent polypeptide (Paragraph 365, lines 10-20).
Regarding claim 70, Nesbit teaches that an example of exogenous labelling includes a reaction which is stopped by addition of 150 .mu.l of stopping buffer (100 mM Hepes pH7.5, KF 400 mM, EDTA 133 mM, BSA 1 g/l.) containing a selected anti tyrosine antibody labelled with the Europium cryptate (PY20-K) at 0.8 .mu.g/ml and allophycocyanine-labelled streptavidin (XL665) at 4 .mu.g/ml where the labelling of Streptavidin and anti-tyrosine antibodies were performed by Cis-Bio International (France) and the mixture is counted using a Packard Discovery counter which is able to measure time-resolved homogeneous fluorescence transfer (excitation at 337 nm, readout at 620 nm and 665 nm) where the ratio of the 665 nm signal/620 nm signal is a measure of the phosphorylated tyrosine concentration and the blank is obtained by replacing enzyme by buffer to calculate the specific signal which is the difference between the ratio obtained without inhibitor and the ratio with the blank (Paragraph 606, lines 15-25).
Regarding claim 72, Nesbit teaches that the compound of the present invention is substituted with a basic moiety, acid addition salts are formed and are simply a more convenient form or reversible for use; and in practice, use of the salt form inherently amounts to use of the free base form, where the acids which can be used to prepare the acid addition salts include preferably those which produce, when combined with the free base, pharmaceutically acceptable salts, that is, salts whose anions are non-toxic to the patient in pharmaceutical doses of the salts, so that the beneficial inhibitory effects on PDGF inherent in the free base are not vitiated by side effects ascribable to the anions and although pharmaceutically acceptable salts of said basic compounds are preferred, all acid addition salts are useful as sources of the free base form even if the particular salt, per se, is desired only as an intermediate product as, for example, when the salt is formed only for purposes of purification, and identification, or when it is used as intermediate in preparing a pharmaceutically acceptable salt by ion exchange procedures (Paragraph 287, lines 1-15).
Regarding claim 77, Nesbit also teaches that metal salts of compounds of the present invention may be obtained by contacting a hydride, hydroxide, carbonate or similar reactive compound of the chosen metal in an aqueous or organic solvent with the free acid form of the compound where the aqueous solvent employed may be water or it may be a mixture of water with an organic solvent, preferably an alcohol such as methanol or ethanol, a ketone such as acetone, aliphatic ether such as tetrahydrofuran, or an ester such as ethyl acetate (Paragraph 291, lines 1-5).
Nesbit does not teach or suggest forming and interrogating polymerase-primed template nucleotide ternary complexes and selectively disassociating/removing a bound nucleotide while retaining the polymerase and primed-template nucleic acid.
Fuller teaches a single-molecule sequencing-by-synthesis method in which a DNA polymerase is complexed with primer/template DNA and an incoming complementary tagged nucleotide forms a ternary complex with the polymerase and primer/template (Abstract). Further, Fuller teaches that the four differently tagged nucleotide types produce distinguishable, sequence-specific signals and are sequentially captured and detected, thereby permitting nucleotide identification and continuous sequence determination during the polymerase reaction (Figures 1A-1B; Introduction: Paragraphs 1-5).
Rannou teaches polymerase-containing nucleic-acid systems in which DnaE polymerase interacts with replication proteins during primer synthesis and extension, including formation of a DnaC-DnaG-DnaE ternary complex and transfer of a newly synthesized primer for continued polymerase-mediated synthesis (Abstract). Further, Rannou teaches washing and maintaining the polymerase/protein compounds in aqueous buffers containing glycerol, a polyol, including extensive washing and subsequent storage/dialysis in glycerol-containing buffer (Introduction: Paragraphs 1-3; Materials and Methods). Rannou also teaches sequential use of different polymerases, wherein DnaE initially extends the primer, and nascent primer is subsequently handed off to PolC for continued DNA synthesis (Materials and Methods).
It would have been obvious to one of ordinary skill in the art at the time of the invention to modify the teachings of Nesbit in view of Fuller and Rannou to provide the claimed polymerase-based nucleotide interrogation method. As previously stated, Fuller teaches the missing polymerase-primed template and cognate-nucleotide ternary complex architecture and the sequential detection and identification of different nucleotide cognates during nucleic acid sequencing. Rannou further teaches that polymerase-containing nucleic acid systems may be subjected to aqueous washing conditions, including glycerol-containing buffers, while maintain the polymerase/protein components, and teaches the sequential use and hand-off of nucleic acid substrates between different polymerases. Therefore, a person of ordinary skill in the art, seeking to perform successive nucleotide interrogations using the ternary complexes taught by Fuller, would have recognized the need to remove the previously contacted or bound nucleotide before exposing the retained polymerase/primed-template complex to a different nucleotide cognate, thereby preventing carryover and permitting accurate subsequent nucleotide interrogation. It therefore would have been obvious to employ an aqueous wash containing a polyol/alcohol component, as supported by the solution teachings of Nesbit and the glycerol-containing washing conditions of Rannou, as predictable means of clearing the previously presented nucleotide while maintaining the polymerase-containing nucleic acid system for a subsequent interrogation cycle. Such a modification amounts to the application of known washing/solution conditions to Fuller’s known polymerase ternary-complex sequencing system or their expected function in enabling successive nucleotide-contact cycles. Additionally, a person of ordinary skill in the art would have recognized that successive interrogation with different nucleotide cognates requires clearing residual nucleotide from the preceding interrogation so that the subsequently supplied nucleotide can be evaluated without interference or carryover. Thus, employing a wash between successive nucleotide-contact steps would have been a predictable use of a known technique to accomplish its established function. As such, Rannou’s use of aqueous glycerol-containing buffers in polymerase-containing nucleic acid systems would have provided a reasonable expectation of success that such washing conditions could be employed while maintaining the functional protein/nucleic acid components needed for subsequent interrogation, since the proposed modification merely applies known washing conditions to Fuller’s known polymerase/nucleotide binding system at the point where removal of the previously presented nucleotide is desirable before presentation of a different nucleotide cognate, with no indication in the prior art that such use would have beyond the ordinary skill in the art.
Further consideration for instant claims 46 and 70, Rannou additionally teaches the sequential use of different DNA polymerases, as established above, including extension by one polymerase followed by transfer of the nucleic acid substrate to a second polymerase for continued synthesis. Accordingly, it would have been obvious to employ a second polymerase following extension of the primed-template in the modified method of Nesbit and Fuller in order to continue subsequent polymerase-mediated nucleotide interrogation and synthesis cycles using a polymerase suited to the subsequent step.
Applicant’s Response: The Applicant argues that Nesbit does not disclose the claimed polymerase-primed template-nucleotide ternary complexes or contacting such complexes with the recited solution to dissociate/remove a nucleotide while retaining the polymerase and primed-template nucleic acid. The Applicant further contends that Nesbit’s pharmaceutical, solvent, and unrelated nucleic acid disclosures do not teach the ordered nucleotide-interrogation and sequential nucleotide-delivery workflow now recited in the pending claim set.
Examiner’s Response to Traversal: Applicant’s arguments have been carefully and fully considered and were found partially persuasive, as discussed below.
Specifically, the Applicant’s arguments regarding the prior rejection under 35 USC 102 were found to be persuasive to the extent that Nesbit alone does not disclose each limitation arranged as required by the pending claims. Accordingly, the anticipation rejection over Nesbit has been withdrawn. However, withdrawal of the 102 rejection does not establish patentability over the prior art as a whole, and claims 1-5, 7, 11-12, 14-15, 18-20, 25-27, 29, 32, 35-42, 46, 70, 72 and 77 are presently rejected under 35 USC 103, as shown above.
Although Nesbit does not itself teach the claimed polymerase-primed template cognate-nucleotide ternary complex architecture, Fuller teaches formation of a ternary complex comprising a polymerase, primer/template nucleic acid and cognate nucleotide, together with detection and identification of different nucleotide types during sequential nucleic acid analysis, as previously stated. Rannou further teaches manipulation and washing of polymerase-containing nucleic acid systems using aqueous glycerol-containing buffers, glycerol being a recited polyol, while maintaining protein-containing systems, and further demonstrates the use of different polymerases during successive stages of primer extension, as previously stated. In view of these teachings, one of ordinary skill in the art would have found it obvious to employ the known aqueous/polyol washing conditions in the ternary complex interrogation system taught by Fuller to remove a previously contacted nucleotide before presentation of a different nucleotide cognate, thereby reducing carryover and permitting successive nucleotide interrogation cycles while retaining the polymerase/primed-template complex. With respect to claims 46 and 70, Rannou additionally provides the teaching of employing a second polymerase following extension for continued polymerase-mediated synthesis, as previously stated.
Applicant’s arguments that Nesbit does not individually disclose the claimed ternary-complex sequencing workflow therefore do not overcome the present rejection because the current rejection does not rely upon Nesbit alone for these limitations. Rather, the rejection is based upon the combined teachings of Nesbit, Fuller and Rannou and the predictable application of known washing and polymerase-handling techniques to Fuller’s known nucleotide-interrogation system. Obviousness does not require any one reference to expressly describe the claimed sequence in its entirety; rather, the combined teachings would have suggested using the known wash conditions in Fuller’s sequential nucleotide-interrogation process to achieve the predictable result of clearing a previously contacted nucleotide before the next interrogation steps.
As of note, to potentially overcome the present rejection, Applicant may amend the claims to recite a further structural or functional limitation that distinguishes the claimed selective nucleotide-disassociation process from the combined teachings (i.e., particular wash conditions).
Conclusions
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ELIZABETH ROSE LAFAVE whose telephone number is (703)756-4747. The examiner can normally be reached Compressed Bi-Week: M-F 7:30-4:30.
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/ELIZABETH ROSE LAFAVE/
Examiner, Art Unit 1684
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684
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