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 .
Priority
This application is a 371 of PCT/US2019/063890 11/30/2019, which claims domestic benefit to provisional application 62/773,671 11/30/2018.
Claim Status
The claim set and Applicant’s remarks filed November 07, 2025 have been entered. Claims 6-8, 10, 13-15 and 18-19 are canceled. Thus, claims 1-5, 9, 11-12, 16-17 and 20 are examined on the merits herein.
Claim Interpretation
Claim 1, line 1 recites “a random oligonucleotide”; line 4 recites “a randomly provided single nucleotide”; and line 5 recites “a single-stranded oligonucleotide molecule”.
Because Applicant has recited the article “a” when referring to the synthesized random oligonucleotide, where the synthesis comprises the single nucleotide being added onto the single-stranded oligonucleotide molecule, the Examiner reasonably interprets the phrases “a random oligonucleotide”, “a randomly provided single nucleotide” and “a single-stranded oligonucleotide molecule” to mean any random oligonucleotide, any randomly provided single nucleotide, and any single-stranded oligonucleotide molecule, respectively.
Additionally, the specification states the term “oligonucleotide” refers to a molecule comprising a sequence of nucleotides or nucleotide bases which are linked together by some form of sugar phosphate backbone, see pg. 6, paragraph [0029].
The Examiner also respectfully notes within the meaning of “oligonucleotide” which is discussed above Applicant explicitly recites “a molecule comprising a sequence of nucleotides or nucleotide bases”.
Because Applicant has recited the article “a” when referring to a sequence of nucleotides or nucleotide bases within the definition of the term oligonucleotide, the Examiner reasonably interprets the phrase “a sequence of nucleotides or nucleotide bases” means any sequence of nucleotides or any nucleotide bases.
Furthermore, the Examiner respectfully notes the terms “oligonucleotide” and “nucleotide” are not explicitly defined within the disclosure to exclude any particular type of nitrogenous base that’s comprised within either the recited oligonucleotide or nucleotide within claim 1.
Therefore, based on the recitations of claim 1 and in view of the specification as a whole, the Examiner reasonably considers the broadest reasonable interpretation of the terms “oligonucleotide” and “nucleotide” as recited within claim 1 to mean said “oligonucleotide” and “nucleotide” includes any nitrogenous base, whether they be unmodified (e.g. canonical) nitrogenous bases (e.g. adenine, guanine, cytosine, thymine and uracil) or modified (e.g. non-canonical or analog) nitrogenous bases.
Thus, the Examiner respectfully notes if the prior art teaches a method of synthesizing a random oligonucleotide with any nucleotide comprising any nitrogenous base (e.g. unmodified or modified); the prior art will read on the method recited within claim 1.
Response to Arguments
(I) The rejection of claims 1-3, 16 and 20 under 35 U.S.C. 102(a)(1); and
(II) The rejection of claims 4-5, 9, 11-12 and 17 under 35 U.S.C. 103 are maintained.
Applicant argues:
(A) The methods of the claimed invention do not incorporate any modified nucleobases as described by Fujihara, see Applicant’s remarks, pg. 6, second paragraph from the bottom of the page.
(B) The Examiner is improperly construing the broadest reasonable interpretation of the claim term “nucleotide” to encompass “modified nucleotide” which is improper and not supported by substantial evidence, see Applicant’s remarks, pg. 6, second paragraph from the bottom of the page.
(C) The specification discloses that “nucleotide” refers to A, T, C or G, see Specification at paragraph [0048] and FIG. 2, see Applicant’s remarks, pg. 6, last paragraph of the page.
(D) The only use of the term “modified” relative to nucleotides or oligonucleotides in the specification is by ligating nucleotides to oligonucleotides or oligonucleotides to other oligonucleotides, and not the modification of the purine or pyrimidine bases themselves, see Applicant’s remarks, pg. 7, second paragraph.
(E) The claim term “nucleotide” and the specification would clearly convey to a person of ordinary skill in the art that the term “nucleotide” refers to natural deoxyadenosine, deoxyguanosine, deoxycytidine, or thymidine, rather than the modified nucleotides described by Fujihara, see Applicant’s remarks, pg. 7, third paragraph.
(F) The MPEP does not support the Examiner’s expansive broadest reasonable interpretation of the term “nucleotide” by clearly distinguishing between canonical nucleotides and modified nucleotides, such as those described by Fujihara, see Applicant’s remarks, pg. 7, second paragraph from the bottom of the page.
(G) The claims do not specify modified nucleobases, so these modified nucleotides are not within the scope of the term “nucleotide”, see Applicant’s remarks, pg. 7, second paragraph from the bottom of the page.
(H) A person skilled in the art would reasonably interpret “nucleotide” to refer to the canonical nucleotides: adenosine mono-, di- or tri-phosphate; guanosine mono-, di- or tri-phosphate; cytidine mono-, di- or tri-phosphate; thymidine mono-, di- or tri-phosphate; or uridine mono-, di- or tri-phosphate, see Applicant’s remarks, pg. 7, last paragraph of the page – pg. 8, first paragraph.
(I) The claims, the specification, and the MPEP provide no reason to interpret the term “nucleotide” as encompassing modified nucleotides, see Applicant’s remarks, pg. 8, first paragraph.
(J) Fujihara fails to anticipate the claimed method because this reference is focused on modified nucleosides which is not what is specified in claim 1, see Applicant’s remarks, pg. 8, second paragraph.
With respect to Applicant’s arguments (A)-(J), the Examiner respectfully disagrees and reiterates the Examiner’s interpretation of the terms “oligonucleotide” and “nucleotide” as recited in claim 1 within the Claim Interpretation section above.
Additionally, the Examiner respectfully notes the term oligonucleotide as defined by Applicant within the specification means “a molecule comprising a sequence of nucleotides or nucleotide bases which are linked together by some form of sugar phosphate backbone” as discussed above. However, the Examiner respectfully notes the Applicant does not specify the type of sugar within the “sugar phosphate backbone”, thus the Examiner reasonably interprets the sugar can by any sugar, e.g. a deoxyribose, found in DNA, or a ribose, found in RNA.
Therefore, the Examiner respectfully notes Applicant’s arguments (C) and (E) and Applicant’s argument (H) are inconsistent with each other and are also inconsistent with the Examiner’s interpretation within the previous paragraph.
Moreover, the Examiner respectfully notes Applicant’s argument (H) includes uracil as a nitrogenous base (e.g. uridine) within the nucleotide as discussed above, however the Examiner respectfully notes this argument is inconsistent with the argument that the “nucleotide” refers to A, T, C or G as argued within Applicant’s argument (C) as discussed above.
Furthermore, with particular respect to Applicant’s argument (F) that the MPEP does not support the Examiner’s broadest reasonable interpretation of the term “nucleotide”; the Examiner respectfully notes MPEP 2422(I) refers to disclosing nucleotide sequences in patent applications subject to WIPO ST.25, and therefore refers to standards when disclosing a nucleotide sequence within a patent application and thus is not used to define the term “nucleotide” as argued by Applicant.
Additionally, even if the Examiner did concede that MPEP 2422(I) could be used to define the term “nucleotide”, which the Examiner explicitly does not concede, the Examiner respectively notes Appendix A discloses the symbol “n”, which means “a or g, or c or t/u, unknown, or other” and wherein the origin of the designation of the symbol “n” is from the word “any”; which again the Examiner respectively notes the symbol “n” is used as a standard for disclosing nucleotide sequences within patent applications filed June 30, 2022 and earlier.
Therefore, the Examiner respectfully notes the MPEP does support the Examiner’s interpretation of the term “nucleotide” wherein the nucleotide comprises any nitrogenous base (e.g. unmodified or modified), as the Examiner again respectfully reiterates the MPEP provides guidance for patent applications filed on June 30, 2022 and earlier, wherein said filed patent application that discloses nucleotide sequences may use the symbol “n” to refer to any nucleotide.
Thus, Applicant’s arguments (A)-(J) have been fully considered but are not found persuasive.
(K) The predetermined sequence of Banyai makes the device of Banyai incompatible with the method of claim 1, as a person of ordinary skill in the art when combining the teachings of Fujihara and Banyai would instead arrive at a method for synthesizing modified nucleotides of a predetermined sequence, see Applicant’s remarks, pg. 9, Fujihara and Banyai, fourth paragraph.
(L) The method of Williams requires synthesis of nucleic acid strands according to the sequence of a target nucleic acid, thus the methods disclosed by Williams necessarily cannot be used to synthesize a random nucleotide, see Applicant’s remarks, pg. 9, Fujihara, Banyai and Williams, second paragraph.
With respect to Applicant’s arguments (K)-(L), the Examiner respectfully notes Banyai is only relied upon for its teachings of devices used in oligonucleotide synthesis (e.g. a microwell, required in claim 4; or a microarray, required in claim 5) or in specific reaction conditions during oligonucleotide synthesis (e.g. microfluidics are used, required in claim 11; or directed energy, required in claim 12).
Furthermore, in response to the arguments:
(i) the predetermined sequence makes the device of Banyai incompatible with the method of claim 1, see Argument (K) above; and/or
(ii) the method of Williams cannot be used to synthesize a random nucleotide, see Argument (L) above, the test for obviousness is not whether the features of a secondary reference may be bodily incorporated into the structure of the primary reference; nor is it that the claimed invention must be expressly suggested in any one or all of the references. Rather, the test is what the combined teachings of the references would have suggested to those of ordinary skill in the art. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981).
With respect to argument (i), the Examiner respectfully notes the predetermined sequence of Banyai is not relied upon within the maintained 103 rejections below.
The Examiner also respectfully notes Banyai teaches both the devices and reaction conditions as required in claims 4-5 and 11-12 for use in the synthesis of oligonucleotides of various sizes as discussed in greater detail in the maintained 103 rejections below.
With respect to argument (ii), the Examiner respectfully notes the method of Williams in synthesizing nucleic acid strands from a target nucleic acid is not relied upon as argued by Applicant.
Rather, Williams is relied upon for its teaching of fluorescent labeled Ppi moieties released from nucleotide triphosphates (NTPs) as a polymerase extension product is created; and to have used the teachings of Williams as the fluorescent materials to label the modified oligonucleotide sequence of Fujihara as discussed above.
Thus, Applicant’s arguments (K)-(L) have been fully considered but are not found persuasive.
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.
Claims 1-3, 16 and 20 remain rejected under 35 U.S.C. 102(a)(1) as being anticipated by Fujihara et al. (Published 16 June 2005, US-20050130195-A1, PTO-892 mailed 10/29/2025).
Regarding claims 1-3, 16 and 20, Fujihara teaches a process for producing a functional molecule comprising a forming step which forms a modified nucleotide n-mer (where, n represents an integer) containing a modified nucleoside (e.g. the oligonucleotide, required in claim 1, line 3) and a producing step which produces a modified oligonucleotide sequence by randomly polymerizing the modified nucleotide n-mer (the method for synthesizing a random oligonucleotide, required in claim 1, line 1), see abstract.
Fujihara teaches the modified nucleotide is prepared by introducing a substituent into a nucleoside constructing the nucleic acid, see paragraph [0027].
Fujihara teaches the nucleic acid includes DNA or RNA and the DNA or DNA may have a single-strand structure (e.g. the single-stranded oligonucleotide, required in claim 1, line 5), see paragraph [0030].
Fujihara teaches n in the modified nucleotide n-mer represents an integer, is preferably 2 or more, more preferably 2 to 10, see paragraph [0027].
Fujihara exemplifies the process for synthesizing a modified nucleotide dimer includes the phosphoroamidite method which is preferable (e.g. synthesized by phosphoramidite chemistry, required in claim 1), see paragraph [0046]. The Examiner respectfully notes in the case of the modified nucleotide n-mer is preferably 10 taught by Fujihara above the limitation of “repeatedly adding a randomly provided single nucleotide” as recited in claim 1, line 4 will be met as the Examiner reasonably interprets the limitation recited above in claim 1, line 4 is a physical limitation within the process of synthesizing the random oligonucleotide in view of the modified nucleotide dimer as taught by Fujihara above.
Fujihara teaches the process preferably includes a selecting step, a determining step, and additionally includes other steps properly selected in accordance with a purpose, see paragraph [0023].
Fujihara teaches the selecting step is a step of selecting one having an affinity with the target from the modified oligonucleotide sequence (e.g. identifying unwanted random oligonucleotides, required in claim 16, line 3), see paragraph [0073].
Fujihara teaches the selection method is not specially restricted and may be conducted in 2 or more methods, including density gradient centrifugation, (e.g. selecting random oligonucleotides based on specific sizes of the random oligonucleotides, required in claim 1, last two lines of the claim and screening the random nucleotides by removing the unwanted random oligonucleotides with specific sizes, required in claim 16, lines 4-5), see paragraph [0074].
Fujihara teaches the determining step is a step for amplifying the modified oligonucleotide sequence which has been selected by the selecting step, to determine the base sequence (e.g. determine the sequence of the random oligonucleotide, required in claim 1, line 6), see paragraph [0107].
Fujihara teaches a process for preparing a random polymer pool which includes monomer blocks which are aligned to the previously prepared oligonucleotide random sequence to carry out annealing and a DNA ligase or RNA ligase works to ligate them for preparation of the random polymer pool (e.g. synthesized using an enzymatic process, required in claim 3), see paragraph [0068].
Fujihara teaches the modified oligonucleotide sequence is synthesized by annealing a nucleotide monomer to a nucleotide random sequence and ligating the nucleotide monomer by using at least one of a DNA ligase and a RNA ligase, see pg. 17, left column, claim #14.
Fujihara teaches a reaction product which contains the modified oligonucleotide sequence is obtained as a result of carrying out the producing step and can be used in the selecting step and the like as a random polymer pool containing the modified oligonucleotide sequence (e.g. combining the screened random oligonucleotides at random, required in claim 16, line 6), see paragraph [0061].
The Examiner reasonably interprets the teachings of Fujihara above disclose an additional selecting step for the prepared random polymer pool as discussed above, as the Examiner respectfully notes during the process of preparing the random polymer pool the process includes monomer blocks aligned to the previous oligonucleotide random sequence by annealing with either DNA or RNA ligase as discussed above; as Fujihara explicitly teaches the random polymer pool contains the modified oligonucleotide sequence and explicitly teaches the reaction product (e.g. the random polymer pool containing the modified oligonucleotide) can be used in the selecting step as discussed above.
The Examiner also respectfully notes the Examiner’s interpretation is further supported by the teachings of Fujihara, as Fujihara teaches the process additionally includes other steps properly selected in accordance with a purpose, wherein the Examiner respectfully notes the purpose is to use the prepared random polymer pool after being prepared for producing a functional molecule as taught by Fujihara above.
The Examiner further respectfully notes the selecting step includes density gradient centrifugation as discussed above which meets the limitation of selecting random oligonucleotides based on specific sizes as discussed above as required in the last two lines of claim 1.
With respect to the limitation of “used for molecular cryptography” required in claim 20, the Examiner is reasonably interpreting this limitation to be an intended purpose, e.g. the random oligonucleotides are suitable for molecular cryptography. As such, the intended purpose will be fulfilled as Fujihara teaches the structural limitation of the random oligonucleotide required in claim 20 and thus the intended purpose will be met.
Thus, the teachings of Fujihara above anticipate instant claims 1-3, 16 and 20.
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:
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.
(I) Claims 4-5, 11-12 and 17 remain rejected under 35 U.S.C. 103 as being unpatentable over Fujihara et al. (Published 16 June 2005, US-20050130195-A1, PTO-892 mailed 10/29/2025) as applied to claims 1-3, 16 and 20 above, and further in view of Banyai et al. (Published 31 March 2016, US-20160089651-A1, IDS filed 07/26/2021).
Fujihara addresses claims 1-3, 16 and 20 as written above. Although, Fujihara does not teach (a) within a microwell, required in claim 4; (b) on a microarray, required in claim 5; (c) microfluids are used, required in claim 11; (d) directed energy is used, required in claim 12; and (e) repeating any of steps (d)-(f) within claim 16, required in claim 17.
However, in the same field of endeavor of synthesizing oligonucleotides, Banyai teaches methods and compositions contemplating synthesis of a library of oligonucleotides comprising varying sizes, see paragraph [0430]; wherein in some embodiments related to the method of conducting a set of parallel reactions as described herein, the first or second reaction comprises enzymatic gene synthesis, annealing and ligation reaction, shotgun ligation and co-ligation, see paragraph [0027]; that can be used for the assembly of longer polynucleotides from shorter nucleotides, see paragraph [0462].
With respect to limitations (a) and (b), Banyai teaches a method of depositing droplets to a plurality of microwells, see paragraph [0038]; in some embodiments the first or second reaction comprises microarray-mediated gene synthesis, see paragraph [0027].
With respect to limitation (c), Banyai teaches in some embodiments, a microfluidic device for nucleic acid synthesis is provided, see paragraph [0182]; where a need for methods that can partition and mix liquid reagents in a microfluidic scale for large numbers of individually addressable reactions in parallel; and addresses these needs and provides related advantages as well, see paragraph [0005]. Banyai teaches the difference in the surface energy, or hydrophobicity, of the capping element and the corresponding surface of the microfluidic device can be a parameter to control the portion of the reagents that is retained upon release, see paragraph [0343].
With respect to limitation (d), Banyai teaches it is understood that the methods and compositions can make use of a number of suitable techniques of construction that are well known in the art, such as light directed methods utilizing masks, see paragraph [0434].
With respect to limitation (e), the Examiner reasonably interprets this limitation to be a physical limitation within the synthesis of a random oligonucleotide as recited in line 1 of claim 1. Since Fujihara teaches a process for producing a functional molecule comprising a producing step which produces a modified nucleotide n-mer (where, n represents an integer); wherein “n” in the modified nucleotide n-mer represents an integer, which the Examiner reasonably interprets “an integer” to mean “any integer” greater than 2; and wherein Fujihara exemplifies the modified nucleotide n-mer is preferably 2-10 and is made through either or both of the phosphoroamidite method or through ligation with a DNA or RNA ligase; thereby producing a functional molecule comprising a modified nucleotide n-mer as taught by Fujihara above; the teachings of Fujihara as discussed above will meet the physical limitation of repeating any of the steps as recited in claim 17.
Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the invention was filed to have incorporated limitations (a)-(e) into the method of Fujihara as discussed above as within the scope of the artisan as combining prior art elements according to known methods to yield predictable results as Banyai teaches contemplating synthesis of a library of oligonucleotides comprising varying sizes as discussed above. One of ordinary skill in the art would have been motivated to incorporate limitations (a)-(e) into the method of Fujihara, as Fujihara teaches monomer blocks which are aligned to the previously prepared oligonucleotide random sequence to carry out annealing and a DNA ligase or RNA ligase that works to ligate them for preparing the random polymer pool of Fujihara as discussed above. One of ordinary skill would have had a reasonable expectation of success to incorporate limitations (a)-(e) into the method of Fujihara, as both Fujihara and Banyai are directed to oligonucleotide synthesis as discussed above.
Thus, the claimed invention as a whole would have been prima facie obvious over the combined teachings of the prior art.
(II) Claim 9 remains rejected under 35 U.S.C. 103 as being unpatentable over Fujihara et al. (Published 16 June 2005, US-20050130195-A1, PTO-892 mailed 10/29/2025) and Banyai et al. (Published 31 March 2016, US-20160089651-A1, IDS filed 07/26/2021) as applied to claims 1-5, 11-12, 16-17 and 20 above, and further in view of Williams (Published 02 July 2009, US-20090170074-A1, IDS Filed 07/26/2021).
The combination of Fujihara and Banyai address claims 1-5, 11-12, 16-17 and 20 as written above. Fujihara further teaches the modified oligonucleotide sequence contained in the random polymer pool is preferably labeled with at least one labeling material selected from and including fluorescent materials, see paragraph [0079]. Although, Fujihara does not teach wherein an indicator molecule becomes reactive after a nucleotide is added to the oligonucleotide, required in claim 9.
However, in the same field of endeavor of nucleic acid sequencing by enzymatic synthesis, Williams teaches improved methods for sequencing and genotyping nucleic acid in a single molecule configuration, wherein the method involves single molecule detection of fluorescent labeled Ppi moieties released from NTPs as a polymerase extension product is created, see abstract.
Williams teaches a method for sequencing a plurality of target nucleic acid molecules, the method comprising subjecting the plurality of target nucleic acid molecules to a polymerization reaction including a plurality of types of nucleotides or nucleotide analogs to yield a population of growing nucleic acid strands that are complementary to their respective target nucleic acid molecules, wherein the target nucleic acid molecule and/or a nucleic acid polymerase is attached to a support, where at least one of the types of nucleotides or nucleotide analogs includes a first atomic or molecular tag bonded to a nucleotide or nucleotide analog part released during incorporation; and optically identifying a time sequence of incorporation events, at least one of the incorporation events involving the incorporation of a tagged nucleotide or nucleotide analog into at least one growing nucleic acid strand in the population, where each event involving a tagged nucleotide or nucleotide analog is characterized by a change in a detectable property of the first tag, see page 11, paragraph #73. The polymerase selected for use include T7 DNA polymerase, T5 DNA polymerase, HIV reverse transcriptase, E. coli DNA pol I, T4 DNA polymerase, T7 RNA polymerase, Taq DNA polymerase and E. coli RNA polymerase, see paragraph [0067].
It would have been prima facie obvious to one of ordinary skill in the art before the invention was filed to have incorporated the method of tagged nucleotides as taught by Williams into the combination of Fujihara and Banyai above as combining prior art elements according to known methods to yield predictable results. One of ordinary skill in the art would have been motivated to use the fluorescent labeled Ppi moieties as taught by Williams above as the fluorescent materials to label the modified oligonucleotide sequence of Fujihara as discussed above. One of ordinary skill in the art would have had a reasonable expectation of success to have included the method of tagged nucleotides as taught by Williams into the combination of Fujihara and Banyai, as Banyai teaches triphosphorylated transcripts, such as those generated by T7 RNA polymerase can be "trimmed" to their monophosphorylated analogues before ligation. Trimming can be accomplished by treatment of the transcript pool with RNA 5' pyrophosphohydrolase removing a pyrophosphate group from the 5' end of each RNA, see Banyai, paragraph [0495].
Thus, the claimed invention as a whole would have been prima facie obvious over the combined teachings of the prior art.
Conclusion
No claims are allowed in this action.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JARET J CREWS whose telephone number is (571)270-0962. The examiner can normally be reached Monday-Friday: 9:00am-5:30pm EST.
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/JARET J CREWS/Examiner, Art Unit 1691
/RENEE CLAYTOR/Supervisory Patent Examiner, Art Unit 1691