DETAILED ACTION
CONTINUED EXAMINATION UNDER 37 CFR 1.114 AFTER FINAL REJECTION
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant’s submission of RCE filed on September 19, 2025 and amendment filed on August 22, 2025 have been entered. The claims pending in this application are claims 22-25, 27, and 30-44. The objection and rejections not reiterated from the previous office action are hereby withdrawn in view of applicant’s amendment filed on August 22, 2025. Claims 23-25, 27, and 30-44 will be examined.
Claim Objections
Claim 23 is objected to because of the following informality: “a polymerase having terminal transcriptase activity” should be “a polymerase having a terminal transcriptase activity”.
Appropriate correction is required.
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.
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 23-25, 27, and 30-44 are rejected under 35 U.S.C. 103 as being unpatentable over
Ko et al., (Journal of Microbiological Methods, 64, 297-304, 2006) in view of Zeiner et al., (US 2013/0123129 A1, priority date: November 11, 2011), Salimullah et al., (Cold Spring Harb. Protoc., 96-110, published on January 1, 2011) and Multiplexed Sequencing with the Illumina Genome Analyzer System (pages 1-3, published in 2010 by Illumina Inc.).
Regarding claims 23-25, 27, 30, 40, 42, and 44, Ko et al., teach a method comprising: adding a nucleic acid sequence (ie., non-polyA RNA linker in Table 1 such as Ribo-1) to a 3’-end of a precursor nucleic acid (ie., one of sRNAs) to produce a template nucleic acid; combining: the template nucleic acid; a primer (ie., Oigo-1 in Figure 1) comprising a domain that hybridizes to the template nucleic acid; a template switch oligonucleotide (ie., Oigo-2 in Figure 1); a polymerase having a terminal transcriptase activity (ie., a reverse transcriptase); and dNTPs, into a reaction mixture under conditions sufficient to produce a complex comprising the template nucleic acid and the template switch oligonucleotide wherein each of the template nucleic acid and the template switch oligonucleotide hybridizes to a single product nucleic acid polymerized from the dNTPs (ie., the first cDNA strand) in a template switching reaction, and amplifying the single product nucleic acid by contacting the single product nucleic acid with a first amplification primer (ie., oligo-4) comprising at least a portion of a sequence present in the primer and a second amplification primer (ie., oligo-3) comprising at least a portion of a sequence present in the template switch oligonucleotide as recited in claim 23 wherein the precursor nucleic acid is a large target nucleic acid of 100 nucleotides or greater in length (ie., 130 to 350 nt), present in a nucleic acid mixture as recited in claim 24, the precursor nucleic acid is a non-polyadenylated nucleic acid present in a nucleic acid mixture as recited in claim 25, said adding a nucleic acid sequence to a 3’-end of a precursor nucleic acid comprises ligating the nucleic acid sequence to the 3’ end the precursor nucleic acid as recited in claim 27, at least one of the primer, the template switch oligonucleotide, the first amplification primer, and the second amplification primer or a combination thereof includes a barcode (ie., a sequence from at least one of the primer, the template switch oligonucleotide, the first amplification primer, and the second amplification primer) as recited in claim 30, the primer further comprises a sequencing platform adapter construct (ie., a sequence from Oligo-1) as recited in claim 40, the template switch oligonucleotide further comprises a sequencing platform adapter construct (ie., a sequence from Oligo-2) as recited in claim 42, and the polymerase is a reverse transcriptase as recited in claim 44 (see abstract in page 297, pages 298-300, Table 1 and Figure 1).
Ko et al., do not disclose fragmenting a nucleic acid to produce a precursor nucleic acid,
amplifying the single product nucleic acid by contacting the single product nucleic acid with a first amplification primer comprising at least a portion of a sequence present in the primer and a second amplification primer comprising at least a portion of a sequence present in the template switch oligonucleotide wherein the first amplification primer comprises a nucleic acid sequence that is not present in the primer, and the second amplification primer comprises a nucleic acid sequence that is not present in the template switch oligonucleotide as recited in claim 23, the first amplification primer comprises a sequencing platform adapter construct as recited in claim 31, the second amplification primer comprises a sequencing platform adapter construct as recited in claim 32, each of the first amplification primer and the second amplification primer comprise a sequencing platform adapter construct as recited in claim 33, the first amplification primer comprises a sequencing platform adapter construct which is not present in the primer as recited in claim 34, the second amplification primer comprises a sequencing platform adapter construct which is not present in the template switch oligonucleotide as recited in claim 35, the first amplification primer and the second amplification primer comprise sequencing platform adapter constructs which are not present in the primer or the template switch oligonucleotide as recited in claim 36, the sequencing platform adapter construct of the first amplification primer comprises a nucleic acid domain selected from the group consisting of: a domain that specifically hybridizes to the surface-attached sequencing platform oligonucleotide, a sequencing primer binding domain, a barcode domain, a barcode sequencing primer binding domain, a molecular identification domain, and combinations thereof as recited in claim 37, and the sequencing platform adapter construct of the second amplification primer comprises a nucleic acid domain selected from the group consisting of: a domain that specifically hybridizes to the surface-attached sequencing platform oligonucleotide, a sequencing primer binding domain, a barcode domain, a barcode sequencing primer binding domain, a molecular identification domain, and combinations thereof as recited in claims 39, 41, and 43.
Since Zeiner et al., teach to produce cleaved RNA fragments by cleaving an initial RNA sample containing a population of different RNA molecules with a divalent cation and a set of DNAzymes that are designed to cleave multiple target RNAs in the initial sample, generating a ligated product by ligating an adaptor to 3’ ends of the cleaved RNA fragments, and make double stranded cDNAs using the ligated product (see paragraph [0002] and claims 1-20), Zeiner et al., disclose fragmenting a nucleic acid (ie., the initial RNA sample) to produce the precursor nucleic acid (ie., the cleaved RNA fragments) as recited in claim 23.
Salimullah et al., teach synthesis of a nanoCAGE cDNA library and sequencing the nanoCAGE cDNA library in Illumina Gene AmpliferIIx system. Since Salimullah et al., teach that the forward oligonucleotide used in the library PCR comprises a portion of a sequence present in the template-switching oligonucleotide and a nucleic acid sequence that is not present in the template-switching oligonucleotide, and the reverse oligonucleotide used in the library PCR comprises a portion of a sequence present in the reverse transcription primer and a nucleic acid sequence that is not present in the reverse transcription primer (see Figure 1, pages 97, 98, 105 and 106), Salimullah et al., disclose amplifying the single product nucleic acid (ie., the first cDNA strand) by contacting the single product nucleic acid with a first amplification primer (ie., the reverse oligonucleotide used in the library PCR) comprising at least a portion of a sequence present in the primer and a second amplification primer (ie., the forward oligonucleotide used in the library PCR) comprising at least a portion of a sequence present in the template-switching oligonucleotide wherein the first amplification primer comprises a nucleic acid sequence that is not present in the primer, and the second amplification primer comprises a nucleic acid sequence that is not present in the template switch oligonucleotide as recited in claim 23, the first amplification primer comprises a sequencing platform adapter construct (ie., an adapter sequence which is not present in the reverse transcription primer) as recited in claim 31, the second amplification primer comprises a sequencing platform adapter construct (ie., an adapter sequence which is not present in the template-switching oligonucleotide) as recited in claim 32, each of the first amplification primer and the second amplification primer comprise a sequencing platform adapter construct as recited in claim 33, the first amplification primer comprises a sequencing platform adapter construct which is not present in the primer as recited in claim 34, the second amplification primer comprises a sequencing platform adapter construct which is not present in the template switch oligonucleotide as recited in claim 35, the first amplification primer and the second amplification primer comprise sequencing platform adapter constructs which are not present in the primer or the template switch oligonucleotide as recited in claim 36, the sequencing platform adapter construct of the first amplification primer comprises a nucleic acid domain (ie., a sequence from an adapter sequence which is not present in the reverse transcription primer) selected from the group consisting of: a domain that specifically hybridizes to the surface-attached sequencing platform oligonucleotide, a sequencing primer binding domain, a barcode domain, a barcode sequencing primer binding domain, a molecular identification domain, and combinations thereof as recited in claim 37, and the sequencing platform adapter construct of the second amplification primer comprises a nucleic acid domain (ie., a sequence from an adapter sequence which is not present in the template-switching oligonucleotide) selected from the group consisting of: a domain that specifically hybridizes to the surface-attached sequencing platform oligonucleotide, a sequencing primer binding domain, a barcode domain, a barcode sequencing primer binding domain, a molecular identification domain, and combinations thereof as recited in claims 39, 41, and 43.
Multiplexed Sequencing with the Illumina Genome Analyzer System teaches advantages of the Illumina Genome Analyzer System “the Genome Analyzer system offers proven, exceptionally high data yields and the largest number of error-free reads. Harnessing this sequencing power in a multiplex fashion increases experimental throughput while reducing time and cost. This is especially useful when targeting genomic sub-regions or studying small genomes” (see page 1)
Therefore, it would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made to have performed the methods recited in claims 23, 31-39, 41 and 43 by fragmenting a nucleic acid to produce a precursor nucleic acid, making a first amplification primer by adding an adapter sequence that is not present in Oligo-1 taught by Ko et al., and is required for sequencing an amplified product in Illumina Gene AmpliferIIx system to 3’ end of Oligo-4 taught by Ko et al., and making a second amplification primer by adding an adapter sequence that is not present in Oligo-2 taught by Ko et al., and is required for sequencing an amplified product in Illumina Gene AmpliferIIx system to 5’ end of Oligo-3 taught by Ko et al., and amplifying the single product nucleic acid (ie., the first cDNA strand) by contacting the single product nucleic acid with the first amplification primer and the second amplification primer such that the first amplification primer and the second amplification primer comprises sequencing platform adapters construct which are not present in the primer or the template switch oligonucleotide, the sequencing platform adapter construct of the first amplification primer comprises a nucleic acid domain (ie., a sequence from the adapter sequence which is not present in the reverse transcription primer) selected from the group consisting of: a domain that specifically hybridizes to the surface-attached sequencing platform oligonucleotide, a sequencing primer binding domain, a barcode domain, a barcode sequencing primer binding domain, a molecular identification domain, and combinations thereof and the sequencing platform adapter construct of the second amplification primer comprises a nucleic acid domain (ie., a sequence from the adapter sequence which is not present in the template-switching oligonucleotide) selected from the group consisting of: a domain that specifically hybridizes to the surface-attached sequencing platform oligonucleotide, a sequencing primer binding domain, a barcode domain, a barcode sequencing primer binding domain, a molecular identification domain, and combinations thereof in view of the prior arts of Ko et al., Zeiner et al., Salimullah et al., and Multiplexed Sequencing with the Illumina Genome Analyzer System. One having ordinary skill in the art would have been motivated to do so because Zeiner et al., teach to produce cleaved RNA fragments by cleaving an initial RNA sample containing a population of different RNA molecules with a divalent cation and a set of DNAzymes that are designed to cleave multiple target RNAs in the initial sample, generating a ligated product by ligating an adaptor to 3’ ends of the cleaved RNA fragments, and make double stranded cDNAs using the ligated product (see paragraph [0002] and claims 1-20), Salimullah et al., teach that the purpose for library PCR the first cDNA strand using a library PCR forward oligonucleotide and a library PCR reverse oligonucleotide is adding adapter sequences to the nanoCAGE libraries for binding to the genome analyzer’s flow cell and for amplification by bridge PCR such that the nanoCAGE libraries would be sequenced using Illumina Gene AmpliferIIx system (see pages 105 and 106), and Multiplexed Sequencing with the Illumina Genome Analyzer System teaches advantages of the Illumina Genome Analyzer System “the Genome Analyzer system offers proven, exceptionally high data yields and the largest number of error-free reads. Harnessing this sequencing power in a multiplex fashion increases experimental throughput while reducing time and cost. This is especially useful when targeting genomic sub-regions or studying small genomes” (see page 1), the simple substitution of one kind of precursor nucleic acid (ie., one of the sRNAs taught by Ko et al.,) from another kind of precursor nucleic acid (ie., one of the cleaved RNA fragments taught by Zeiner et al.,), and the simple substitution of one kind of sequencing method (ie., the sequencing method taught by Ko et al.,) from another kind of sequencing method (ie., the sequencing method using Illumina Gene AmpliferIIx system taught by Salimullah et al.,) during the process of performing the method recited in claim 23, in the absence of convincing evidence to the contrary, would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made since the one of the sRNAs taught by Ko et al., and the one of the cleaved RNA fragments taught by Zeiner et al., are used for the same purpose (ie., making a cDNA), the sequencing method taught by Ko et al., and the sequencing method taught by Salimullah et al., are used for the same purpose (ie., sequencing cDNAs) and the sequencing method using Illumina Gene AmpliferIIx system taught by Salimullah et al., offers proven, exceptionally high data yields and the largest number of error-free reads, and reduces time and cost. One having ordinary skill in the art at the time the invention was made would have a reasonable expectation of success to perform the methods recited in claims 23, 31-39, 41 and 43 by producing a precursor nucleic acid based on fragmenting a nucleic acid, making a first amplification primer by adding an adapter sequence that is not present in Oligo-1 taught by Ko et al., and is required for sequencing an amplified product in Illumina Gene AmpliferIIx system to 3’ end of Oligo-4 taught by Ko et al., and making a second amplification primer by adding an adapter sequence that is not present in Oligo-2 taught by Ko et al., and is required for sequencing an amplified product in Illumina Gene AmpliferIIx system to 5’ end of Oligo-3 taught by Ko et al., and amplifying the single product nucleic acid (ie., the first cDNA strand) by contacting the single product nucleic acid with the first amplification primer and the second amplification primer in view of the prior arts of Ko et al., Zeiner et al., Salimullah et al., and Multiplexed Sequencing with the Illumina Genome Analyzer System in order to perform the method recited in claim 23 using the precursor nucleic acid taught by Zeiner et al., and take the advantages of the Illumina Genome Analyzer System and sequencing the PCR product of the first cDNA strand using the Illumina Gene AmpliferIIx system.
Furthermore, the motivation to make the substitution cited above arises from the expectation that the prior art elements will perform their expected functions to achieve their expected results when combined for their common known purpose. Support for making the obviousness rejection comes from the M.P.E.P. at 2144.06, 2144.07 and 2144.09.
Also note that there is no invention involved in combining old elements is such a manner that these elements perform in combination the same function as set forth in the prior art without giving unobvious or unexpected results. In re Rose 220 F.2d. 459, 105 USPQ 237 (CCPA 1955).
Response to Arguments
In page 3, second paragraph bridging to page 4, last paragraph of applicant’s remarks, applicant argues that “[O]n page 5, first paragraph of the Advisory Action, the Office also asserts ‘the method taught by Ko et al., can be used for ligating an RNA linker to the 3’ end of both unidentified RNAs and RNAs with known sequences. Furthermore, applicant has not indicate why the method taught by Ko et al., cannot be used for ligating an RNA linker to the 3’ end of RNAs with known sequences.’ (AA pg. 5). However, the argument presented in the response to the Final Office Action filed August 22, 2025 was that the skilled artisan would not be motivated to combine the sequence agnostic methods of Ko with the sequence specific methods of Zeiner. Firstly, if the skilled artisan were to use the method of Ko using known RNAs then the ligation of the RNA linker to the 3' end of a known target RNA would be completely unnecessary as they could simply use a target-specific primer directed to the known sequence. Additionally, the usage of Ko's technique for known RNAs would only add further steps and more components, e.g., a ligase, to the reaction and would complicate the method. 2025 was that the skilled artisan would not be motivated to combine the sequence agnostic methods of Ko with the sequence specific methods of Zeiner. Firstly, if the skilled artisan were to use the method of Ko using known RNAs then the ligation of the RNA linker to the 3' end of a known target RNA would be completely unnecessary as they could simply use a target-specific primer directed to the known sequence. Additionally, the usage of Ko's technique for known RNAs would only add further steps and more components, e.g., a ligase, to the reaction and would complicate the method. Accordingly, as stated in the response to the Final Office Action, Applicant submits that the skilled artisan would not use a target-specific fragmentation method with a library preparation method designed for novel target RNAs having unknown sequences. As discussed above, the methods of Ko are specifically designed to generate libraries from novel sequences through the usage of the RNA linker ligated to the novel sequences. The skilled artisan would not know which RNA sequences to target the ‘feet’ of Zeiner's DNAzymes to for fragmentation and thus would not use Zeiner's DNAzymes. If the skilled artisan knew the sequences of the target RNAs, then the skilled artisan would not use Ko methods as this would add further steps and components to a reaction that could simply be done with a sequence-specific primer. Accordingly, the skilled artisan would not be motivated to combine the methods of Ko and Zeiner at least because the target-specific fragmentation methods of Zeiner would not work for the identification of unknown target RNAs. As Salimullah and Illumina do not teach fragmentation or ligation, Salimullah and Illumina fail to remedy the deficiencies of Ko and Zeiner. As such, claims 23-25, 27, 30, 40, 42, and 44 are not obvious over Ko in view of Salimullah and Illumina and further in view of Zeiner at least because the skilled artisan would not be motivated to combine the references as asserted by the Office”.
The above arguments been fully considered but they are not persuasive toward the withdrawal of the rejection.
First, although applicant argues that “if the skilled artisan were to use the method of Ko using known RNAs then the ligation of the RNA linker to the 3' end of a known target RNA would be completely unnecessary as they could simply use a target-specific primer directed to the known sequence. Additionally, the usage of Ko's technique for known RNAs would only add further steps and more components, e.g., a ligase, to the reaction and would complicate the method”, applicant has no evidence to show that one having ordinary skill in the art at the time the invention was made must perform a cDNA synthesis method based on above assumption suggested by applicant. In fact, which method one having ordinary skill in the art at the time the invention was made selects to perform a cDNA synthesis is based on reagents available in his or her laboratory and whether he or she wants to spend extra money to synthesize a target-specific primer. Furthermore, the method taught by Ko et al., can be used for ligating an RNA linker to the 3' end of both unidentified RNAs and RNAs with known sequences.
Second, although applicant argues that “the methods of Ko are specifically designed to generate libraries from novel sequences through the usage of the RNA linker ligated to the novel sequences. The skilled artisan would not know which RNA sequences to target the ‘feet’ of Zeiner's DNAzymes to for fragmentation and thus would not use Zeiner's DNAzymes. If the skilled artisan knew the sequences of the target RNAs, then the skilled artisan would not use Ko methods as this would add further steps and components to a reaction that could simply be done with a sequence-specific primer. Accordingly, the skilled artisan would not be motivated to combine the methods of Ko and Zeiner at least because the target-specific fragmentation methods of Zeiner would not work for the identification of unknown target RNAs. As Salimullah and Illumina do not teach fragmentation or ligation, Salimullah and Illumina fail to remedy the deficiencies of Ko and Zeiner”, one having ordinary skill in the art at the time the invention was made only requires to know partial sequences of RNAs when he or she uses DNAzymes. Furthermore, since the method taught by Ko et al., can be used for ligating an RNA linker to the 3’ end of both unidentified RNAs and RNAs with known sequences and Zeiner et al., teach to produce cleaved RNA fragments by cleaving an initial RNA sample containing a population of different RNA molecules with a divalent cation and a set of DNAzymes that are designed to cleave multiple target RNAs in the initial sample, generating a ligated product by ligating an adaptor to 3’ ends of the cleaved RNA fragments, and make double stranded cDNAs using the ligated product (see paragraph [0002] and claims 1-20), one having ordinary skill in the art in the art at the time the invention was made would have been motivated to substitute one of the sRNAs taught by Ko et al., from one of the cleaved RNA fragments taught by Zeiner et al., during the process of performing the method recited in claim 23. In addition, applicant has no evidence to show that the method taught by Ko et al., cannot be used for ligating an RNA linker to the 3’ end of RNAs with known sequences.
Conclusion
5. Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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.
6. No claim is allowed.
7. Papers related to this application may be submitted to Group 1600 by facsimile transmission. Papers should be faxed to Group 1600 via the PTO Fax Center. The faxing of such papers must conform with the notices published in the Official Gazette, 1096 OG 30 (November 15, 1988), 1156 OG 61 (November 16, 1993), and 1157 OG 94 (December 28, 1993)(See 37 CAR § 1.6(d)). The CM Fax Center number is (571)273-8300.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Frank Lu, Ph.D., whose telephone number is (571)272-0746. The examiner can normally be reached on Monday-Friday from 9 A.M. to 5 P.M.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Dr. Anne Gussow, Ph.D., can be reached on (571)272-6047.
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/FRANK W LU/Primary Examiner, Art Unit 1683
February 6, 2026