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 .
Application Status
This action is written in response to applicant’s correspondence received 02/23/2024. Claims 1-20 are currently pending and are examined herein.
Specification
The disclosure is objected to because of the following informalities:
The abstract contains legal phraseology such as “said”.
Applicant is reminded of the proper language and format for an abstract of the disclosure.
The abstract should be in narrative form and generally limited to a single paragraph on a separate sheet within the range of 50 to 150 words in length. The abstract should describe the disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details.
The language should be clear and concise and should not repeat information given in the title. It should avoid using phrases which can be implied, such as, “The disclosure concerns,” “The disclosure defined by this invention,” “The disclosure describes,” etc. In addition, the form and legal phraseology often used in patent claims, such as “means” and “said,” should be avoided.
Appropriate correction is required.
Drawings
The drawings are objected to because:
37 CFR 1.84(p)(1) states “Reference characters (numerals are preferred), sheet numbers, and view numbers must be plain and legible, and must not be used in association with brackets or inverted commas, or enclosed within outlines, e.g., encircled. They must be oriented in the same direction as the view so as to avoid having to rotate the sheet.”
In the current case, the view number for Figure 4 is not oriented in the same direction as the view.
37 CFR 1.84 (u)(1) states “Partial views intended to form one complete view, on one or several sheets, must be identified by the same number followed by a capital letter.”
In the current case, the view numbers for the partial views for Figure 8 that appear on several sheets are followed by "Cont." instead of a capital letter such as Figure 8A, Figure 8B, etc.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Interpretation
Claim 1 is drawn to a method for generating a double-stranded nucleic acid having a predetermined sequence. Applicant regards “predetermined” as meaning, “a nucleic
acid sequence which is known and identified.” (p. 6 ln 23-24). The term is interpreted accordingly.
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
Claim 1 recites a step of subjecting a reaction product to “enzymatic, physical or chemical means to eliminate” two oligonucleotide loops. MPEP 2181.I describes the 3-prong analysis to determine whether to apply 35 U.S.C. 112(f). In the instant case, the three prongs are met. At prong A, the claim limitation uses the term “means” as a generic placeholder for performing the claimed function. At prong B, the term “means” is modified by the functional language, “to eliminate” the loops. At prong C, the term “means” is not modified by sufficient structure, material or acts for eliminating the loops.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-3, 8-18 and 20 are rejected 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 (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
The claim limitation of claim 1, “means…to eliminate”, invokes 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. The as-filed specification is devoid of adequate structure and equivalents to perform the claimed function as recited in claim 1. For example, the specification states that, “any means suitable to suppress by-products and the single-stranded oligonucleotide loops of the closed double-stranded nucleic acid are encompassed” (p. 13 ln 5-15). This definition does not provide any specific structure in such a way that one skilled in the art would understand what structure will perform the function of eliminating the oligonucleotide loops. The specification provides some examples, such as CeIV to induce DNA phosphodiester bond hydrolysis or lanthanide III to induce RNA phosphodiester bond hydrolysis for chemical means; photocleavage of a light-sensitive nucleotide as physical means; or exonucleases/nucleases/endonucleases as enzymatic means (p. 13 ln 15-25). However, these examples are structurally diverse moieties, and they are not linked by a common structure which correlates with a shared function of eliminating the oligonucleotide loops.
Therefore, the claim is indefinite and is rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph. Those claims identified in the rejection but not specifically addressed are rejected for failing to remedy the indefiniteness therein.
Claims 4-7 and 19 are excluded from this rejection because they limit the means for eliminating the oligonucleotide loops to a specific class of structures, i.e., a nuclease.
Applicant may:
(a) Amend the claim so that the claim limitation will no longer be interpreted as a limitation under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph;
(b) Amend the written description of the specification such that it expressly recites what structure, material, or acts perform the entire claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(c) Amend the written description of the specification such that it clearly links the structure, material, or acts disclosed therein to the function recited in the claim, without introducing any new matter (35 U.S.C. 132(a)).
If applicant is of the opinion that the written description of the specification already implicitly or inherently discloses the corresponding structure, material, or acts and clearly links them to the function so that one of ordinary skill in the art would recognize what structure, material, or acts perform the claimed function, applicant should clarify the record by either:
(a) Amending the written description of the specification such that it expressly recites the corresponding structure, material, or acts for performing the claimed function and clearly links or associates the structure, material, or acts to the claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(b) Stating on the record what the corresponding structure, material, or acts, which are implicitly or inherently set forth in the written description of the specification, perform the claimed function. For more information, see 37 CFR 1.75(d) and MPEP §§ 608.01(o) and 2181.
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. As described above, the disclosure does not provide adequate structure to perform the claimed function of eliminating the oligonucleotide loops. The specification does not demonstrate that the applicant has made an invention that achieves the claimed function(s) because the invention is not described with sufficient detail such that one of ordinary skill in the art can reasonably conclude that the inventor had possession of the claimed invention.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1 and 4 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by New England Biolabs (NEB) (Instruction Manual: NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 2. New England Biolabs. Version 1 published 11/17. Version 3 published 6/24.).
Please note: the public availability date of version 3.0 of the prior art reference is 6/24. However, as shown in the revision history on page 14, the first version of the document was released in November 2017, and subsequent revisions only changed the format, color balance information, adaptor and index sequence sections, the addition of a new logo to the header and footer, and an updated legal footnote. Therefore, absent evidence to the contrary, it is assumed that the information regarding the library preparation process depicted on page 2 is unchanged from the version published 11/17, and was publicly available as of that date.
Regarding claim 1, NEB teaches a method for generating a double-stranded nucleic acid comprising providing a plurality of single-stranded oligonucleotides, a first hairpin-forming oligonucleotide comprising a single-stranded overhang, and a second hairpin-forming oligonucleotide comprising a single-stranded overhang, the sequence of each single-stranded oligonucleotide being at least partially complementary with the sequence of the single-stranded overhang of the first or second hairpin-forming oligonucleotide (p. 2, Figure 1, “Workflow”; note that two single-stranded oligonucleotides in step one have “A” overhangs, and are shown as being ligated to one hairpin NEBNext Adaptor on each end, each adaptor having a “T” overhang).
NEB further teaches reacting the above components with a ligase (see Figure 1, the adaptor ligation step) to form a closed double-stranded nucleic acid with two single-stranded oligonucleotide loops in a reaction medium (Figure 1, step 2), and subjecting the product of that step to a nuclease to eliminate the two oligonucleotide loops (Figure 1, step 3, USER enzyme, “a combination of UDG and Endo VIII”, p. 2).
NEB teaches that the double-stranded nucleic acid has (i.e., comprises) a predetermined sequence in two aspects. In one aspect, NEB teaches that the adaptor itself has a predetermined sequence, which remains in the double-stranded product (see Figure 1 and the adaptor sequence on p. 2). In another aspect, NEB teaches that the adaptors , “Functionally Validated: Each set of reagents is functionally validated together through construction and sequencing of genomic DNA libraries on the Illumina platform.”. In other words, the method was used to generate and validate known, identified sequences from a known, identified genome.
Regarding claim 4, insofar as NEB identifies the USER enzyme as comprising ENDO VIII, i.e., an endonuclease, it teaches subjecting the reaction product of step b to a nuclease.
Claim Rejections - 35 USC § 103
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:
Determining the scope and contents of the prior art.
Ascertaining the differences between the prior art and the claims at issue.
Resolving the level of ordinary skill in the pertinent art.
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.
Claim 1, 3-4, 8-13, 15-18 and 20 are rejected under 35 U.S.C. 103 as being unpatentable over U.S. Patent No. 8,092,991 B2 to Schatz (hereinafter ‘Schatz’).
Regarding claim 1:
Schatz teaches a method for generating a double-stranded nucleic acid:
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In the above figure, please note the double-stranded section marked as “part of nucleic acid to be manufactured”, which is flanked by restriction enzyme recognition sites for eventual excision from the hairpin loop structures such that the loops may be eliminated from the double-stranded reaction product.
Schatz teaches that the sequence of the nucleic acid is predetermined (i.e., a DNA construct with optimized properties, e.g., high level protein expression) (col 1 ln 5-20):
The present invention is related to methods for the manufacture of a nucleic acid molecule and methods for the ligation of oligonucleotides.
De novo generation of nucleic acid molecules is increasingly used in biopharmaceutical research to replace the often quite complex cloning procedures necessary to produce
desired DNA constructs with optimised properties, e.g. high level protein expression in suitable in vivo or in vitro systems.
Schatz teaches that the method comprises a step of providing a plurality of single-stranded oligonucleotides and two hairpin-forming oligonucleotides comprising single-stranded overhangs, the sequence of each single-stranded oligonucleotide being at least partially complementary with the sequence of at least one other single-stranded oligonucleotide of said plurality and with the sequence of the single-stranded overhang of the first or second hairpin-forming oligonucleotide. Please Fig. 6 above, which shows the resulting structure after the method has been performed, in which partially complementary single-stranded oligonucleotides are annealed to one another and have been reacted with the hairpin-forming oligonucleotides with a ligase to form a closed double-stranded nucleic acid with two single-stranded oligonucleotide loops. See also the steps outlined in column 4, which describe providing a first partially double-stranded oligonucleotide comprising a first and second single-stranded overhang (i.e., the single-stranded oligonucleotides in duplex form); providing an at least partially double-stranded oligonucleotide with an overhang (i.e., the hairpin oligonucleotide); and ligating the first and second oligonucleotides together. Figures 7-13 also illustrate various embodiments of the method, in which various ligation, digestion, and purification steps may be taken to produce a double-stranded oligonucleotide of whatever length and sequence is required.
It is relevant to note that Schatz refers to the hairpin loop oligonucleotides as “capping” oligonucleotides. Schaltz teaches that these capping oligonucleotides meet, “a need in the art…to prevent false ligations to improve the yield of correct ligations”, because the capping oligonucleotides, “…are specifically designed to cap the ends of unreacted side products so as to prevent their further ligation to a correctly formed intermediate” (col 37 ln 30-40). Schaltz further confirms that the capping oligonucleotides may be eliminated by including a recognition site for a type IIS restriction enzyme (col 38 ln 5-15).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of producing a double-stranded nucleic acid as taught by Schatz by selecting from the various alternatives depending on the exact double stranded nucleic acid product required. Schatz teaches a general method of producing a double-stranded product via rounds of ligation and digestion, using hairpin loop oligonucleotides and single-stranded oligonucleotides with various combinations of complementary overhangs as building blocks to generate double-stranded DNA products of a known sequence for recombinant nucleic acid applications. Thus in regard to the limitations of the claims, where the prior art teaches methods of producing double-stranded nucleic acids via ligation of hairpin loop oligonucleotides and a plurality of single-stranded oligonucleotides and subsequent removal of the hairpin loops, a person of ordinary skill has good reason to pursue the known options within his or her technical grasp for optimization of the methods for their specific application. If this leads to the anticipated success, it is likely the product not of innovation but of ordinary skill and common sense to provide routine optimization.
Regarding claim 3, Schatz teaches wherein the ligase is a T4 ligase (Example 1, cols 48-49).
Regarding claim 4, Schatz teaches subjecting the reaction product of step b (the dumbbell product shown in Figure 6) to a restriction endonuclease to digest the loops (see above).
Regarding claims 8, 10 and 12, Schatz teaches, “To build up a double-stranded nucleic acid, its sequence is first broken down into smaller fragments (usually between 6 and 30 base pairs each.” (col 3 ln 10-15). Schatz further notes that, “de novo generation of nucleic acid molecules is increasingly used in biopharmaceutical research…to produce DNA constructs”, and that these constructs (double-stranded DNA molecules), “typically consist of more than one hundred up to several thousand base pairs” (col 1 ln 10-25). While Schatz does not explicitly teach that the plurality of single-stranded oligonucleotides comprises from 3 to 100 single-stranded oligonucleotides, Schatz does teach that the fragments (single-stranded oligonucleotides which are used as building blocks to create the larger construct) are usually between 6 and 30 base pairs each, and discloses that the method steps may be repeated iteratively and as necessary to obtain a double-stranded DNA molecule of the required length (see e.g., col 4). Based on common sense and sound scientific reasoning, the number of fragments needed to perform the method will depend on the size of the desired product. A product of, for example, 200 base pairs would require approximately 6 30-nt fragments, while a product of 3,000 base pairs would need 100 30-nt fragments, both of which lie within the claimed range and are consistent with Schatz’s description of the typical sizes of DNA constructs for biopharmaceutical applications.
Regarding claim 9, Schatz teaches wherein the sequence of each single-stranded oligonucleotide of said plurality comprises two segments, each segment being complementary with a segment of the sequence of another single-stranded oligonucleotide of said plurality (see above, particularly Figure 6).
Regarding claim 11, Schatz teaches wherein the single-stranded overhang of the first or second hairpin-forming oligonucleotides comprises from 5 to 35 nucleotides (col 4 ln 60-67):
the single-stranded overhang has a length from about 5 to 20 nucleotides, from about 10 to 20 nucleotides, from about 15 to 18 nucleotides, from about 5 to 10 nucleotides and from about 6 to 8 nucleotides, depending on the nature of the nucleotides.
Regarding claim 13, Schatz teaches generating multiple double-stranded nucleic acids which are fragments of a greater double-stranded polynucleotide and linking them together according to a predetermined order by use of a ligase (see e.g. cols 9-10, which describe the production of multiple ligation products comprising fragments of the nucleic acid to be manufactured in steps a-d, followed by cutting the products and combining them in steps e-i).
Regarding claims 15 and 16, Schatz teaches wherein at any of the steps, it is obvious that the product may be purified by elimination of impurities such as starting materials, unligated products, etc. (col 45 ln. 5-20).
Regarding claim 17, Schatz teaches, “error correction procedures must be employed in order to obtain a 100% error-free construct” (col 1 ln 41-43).
.Regarding claim 18, Schatz teaches that the resulting DNA molecule is purified (see e.g. col 16 ln 25-26).
Regarding claim 20, Schatz teaches that the, “length of the second overhang is…selected from the group comprising lengths from about 5 to 20 nucleotides” (col 17 ln 34-35). For clarity, Schatz states that, “the second overhang is used to attach the molecule as well as ligation products thereof to a solid support in a specific and reversible fashion”. Figure 6 shows that it is the hairpin oligonucleotide which is attached to the support, and to which the overhang is annealed. Lastly, Schatz states that, “Both perfect matches and single mismatches between the overhangs of the capping oligonucleotides and the intermediate to be capped are within the scope of the present invention.” (col 37 ln 50-55). In summary, Schatz’s second overhang is equivalent to the segment of one of the instant single-stranded oligonucleotides which is partially complementary to the single-stranded overhang of the hairpin oligonucleotide, and the intermediates formed by the annealing of single-stranded oligonucleotides into double-stranded fragments of the larger DNA molecule; this overhang, according to Schatz, can be 5 to 20 nucleotides long; and the complementary overhang of the hairpin oligonucleotide may be a perfect or single mismatch to the second overhang. Logically, this indicates that the hairpin oligonucleotide’s overhang must be the same length as the second overhang, i.e. 5-20 nucleotides, for a perfect match, or may be one nucleotide shorter such that it has no more than one mismatch.
Claim 2 is rejected under 35 U.S.C. 103 as being unpatentable over Schatz, as applied to claims 1, 3-4, 8-13, 15-18 and 20, further in view of BiteSize Bio (T4 DNA Ligase: The Only Ligase You’ll Ever Need? Published February 27, 2020. Accessed via the Wayback Machine at web.archive.org/web/20200511084312/https://bitesizebio.com/46482/t4-dna-ligase-the-only-ligase-youll-ever-need/).
Schatz renders obvious the invention of claim 1, from which the instantly rejected claim depends, as described above.
Schatz does not teach wherein step b (the ligation step) is performed with at least two different ligases.
However, Schatz does teach that accuracy and error detection and correction is important in DNA assembly, as discussed in the previous rejection.
BiteSize Bio teaches that different ligases are suitable for different applications. For example, they state that, “T4 ligase can ligate mismatches in DNA nicks”, whereas, “the higher fidelity of Taq DNA ligases reduces the incidences of mismatched recombinant DNA. But note that this enzyme can only ligate nicks and not blunt or cohesive ends. The selective ligation of nicks by Taq polymerase makes it the perfect solution for techniques where only nicks are to be ligated and end ligation needs to be suppressed, such as some DNA assembly methods.”.
It would have been prima facie obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to have modified the method as taught by Schatz by using two different ligases, as taught by BiteSize Bio. The ordinary artisan would have been motivated by their combined teachings to use high fidelity ligases to assemble recombinant DNA, but would also have recognized that the high fidelity ligases had their own disadvantages, such as an inability to ligate blunt or cohesive ends. The ordinary artisan would have recognized that by using different ligases to address these strength and weaknesses, it would have been possible to optimize the method to obtain efficient, high fidelity ligation.
Claims 5 and 6 are rejected under 35 U.S.C. 103 as being unpatentable over Schatz, as applied to claims 1, 3-4, 8-13, 15-18 and 20, further in view of Bang (Bang et al. Gene synthesis by circular assembly amplification. Nature Methods volume 5, pages37–39 (2008)).
Schatz renders obvious the invention of claim 1, from which the instantly rejected claims depend, as described above.
Schatz does not teach simultaneously subject the reaction product of step b with a nuclease to eliminate the hairpin loops and an exonuclease to remove unassembled single-stranded oligonucleotides.
However, Schatz does teach removing single-stranded and intermediate moieties, and further that it is important to reduce errors in manufactured DNA molecules, as discussed previously.
Regarding claim 5, Bang teaches simultaneous exonuclease and endonuclease digestion to remove single-stranded oligonucleotides and error-containing constructs (p. 37)
We developed a one-cycle gene synthesis method that substantially improves synthesis quality. This approach uses three different tiers of selection (Fig. 1). First, single-stranded oligonucleotides are assembled into circular molecules under a highly stringent annealing condition (70 °C) such that most error-containing oligonucleotides do not anneal (tier one). By subsequently subjecting the ligation mixture to exonuclease treatment we select for circular molecules with the desired sequence (tier two). Finally, by using a mismatch-cleaving endonuclease we convert circular DNA containing residual errors to a linear form that is degraded by exonucleases still present in the solution (tier three).
Regarding claim 6, Bang teaches using a cocktail of exonuclease III and lambda exonucleases (p. 38, left, 1st para).
It would have been prima facie obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of synthesizing double-stranded DNA via a circular (dumbbell) intermediate, as taught by Schatz, to include the one-cycle gene synthesis method as taught by Bang. The ordinary artisan would have been motivated by Schatz to seek out methods of removing unligated products and to remove error-containing products. The ordinary artisan would further have been motivated to use Bang’s method due to its relative simplicity and ability to improve the quality of the resulting product.
Claims 7 and 19 are rejected under 35 U.S.C. 103 as being unpatentable over Schatz, as applied to claims 1, 3-4, 8-13, 15-18 and 20, further in view of Kabotyanski (Kabotyanski et al. Hairpin opening by single-strand-specific nucleases. Nucleic Acids Research, 1995, Vol. 23, No. 19 3872-3881.).
Schatz renders obvious the invention of claims 1 and 4, from which the instantly rejected claims depend, as described above. Specifically, Schatz renders obvious a method of making double-stranded DNA via ligation of circular/dumbbell intermediates and hairpin capping oligonucleotides, then digesting the hairpin oligonucleotides with an endonuclease (restriction enzyme), as discussed above.
Schatz does not teach wherein the endonuclease for digesting the single-stranded loops of the hairpin oligonucleotides is a single-stranded specific, nor that it is nuclease P1, S1, or ming bean nuclease.
Kabotyanski teaches that all three nucleases are single-strand-specific endonucleases capable of introducing nicks near hairpin loops (p. 3872, last para).
It would have been prima facie obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to have modified the method as taught by Schatz, including digesting the hairpin loops with an endonuclease, by using any of the loop-nicking endonucleases taught by Kabotyanski. As a matter of common sense and sound scientific reasoning, the ordinary artisan would have been motivated to use endonucleases which would cleave the hairpin loops specifically and leave the rest of the construct intact, and to use those disclosed by Kabotyanski based on their confirmed suitability for that purpose.
Claim 14 is rejected under 35 U.S.C. 103 as being unpatentable over Schatz, as applied to claims 1, 3-4, 8-13, 15-18 and 20, further in view of Ahern (Biochemical Reagents Kits Offer Scientists Good Return on Investment. The Scientist, Vol:9, #15, pg 20, July 24, 1995.).
Schatz renders obvious the invention of claim 1, from which the instantly rejected claims depend, as described above.
Schatz does not teach a kit for implementation of the method.
Ahern teaches that, “More researchers are buying premade reagents and kits because they are convenient and they save time…Rather than browsing through catalogs and buying individual chemicals from one or several suppliers, investigators can instead purchase a kit that supplies all of the necessary reagents for a particular research application and even provides them with detailed instructions to follow.” (p. 5/8).
It would have been prima facie obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to have included the components necessary to implement the method taught by Schatz in a kit, as taught by Ahern. The ordinary artisan would have been motivated to do so based on Ahern’s teachings that a kit would have been attractive to end users due to its convenience and time savings.
Conclusion
No claims are allowed at this time.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AMANDA M ZAHORIK whose telephone number is (703)756-1433. The examiner can normally be reached M-F 8:00-16:00 EST.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Neil Hammell can be reached on (571) 270-5919. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/AMANDA M ZAHORIK/Examiner, Art Unit 1636
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