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 .
The preliminary amendments dated 2/24/2026 are under consideration.
The amendments and arguments presented in the papers filed 2/24/2026 ("Remarks”) have been thoroughly considered. The issues raised in the Office action dated 8/25/2025 listed below have been reconsidered as indicated.
a) The rejections of claims 3, 4, 5, 6, 7, 9, 10, 12 and 13 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, are withdrawn in view of the amendments and the Remarks (p. 6-7).
b) The rejections of claim(s) 1, 2, 3, 4, 5, 7, 11, 14 and 15 under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Guillou-Bonnici (US 5,744,308) are withdrawn in view of the amendments.
The Examiner’s responses to the Remarks regarding issues not listed above are detailed below in this Office action.
New and modified grounds of rejection necessitated by amendment are detailed below and this action is made FINAL.
Information Disclosure Statement
The listing of references in the specification or the citation of references throughout the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892 or cited on a submitted IDS, they have not been considered.
Drawings
High resolution copies of the drawings may be accessed via PAIR/Patent Center Retrieval using the Supplemental Content tab.
Claim Interpretation
In claim 7, the structure of an “identifier sequence” and/or a “adaptor sequence” is broadly interpreted as encompassing any nucleic acid segment of any sequence and of any length. In the context of claim 7, only one oligonucleotide probe is required, and thus, any nucleic acid segment of the prior art is encompassed by claimed “identifier sequence” and/or “adaptor sequence”.
Claim Rejections - 35 USC § 112
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 4, 16 and 18 is 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 following are new rejections necessitated by the amendments to the claims.
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.
Regarding claim 4, the claim further requires “the hydrolysis comprises hydrolysing a phosphodiester bond in the sugar phosphate backbone in the template in a region that is hybridized to the oligonucleotide probe, thereby introducing a nick in the template” in addition to the “hydrolysis…with an exonuclease” required by amended claim 1. This embodiment constitutes new matter for the reasons provided below.
First, the: 1) use of an exonuclease; and 2) “hydrolysing a phosphodiester bond in the sugar phosphate backbone in the template in a region that is hybridized to the oligonucleotide probe”, e.g. hydrolysing with an endonuclease, were presented as different embodiments in claims 3 and 4, respectively.
Second, the instant specification describes the exonuclease and the endonuclease as alternatives to one another and not specifically used together. On pages 5 and 24, the specification describes a kit for performing the method of the invention that comprises “a 3’->5’ exonuclease or an endonuclease. On page 11, the use of exonucleases and endonucleases can be used in the inventive method, the exonucleases are the preferred embodiment. On page 12, an alternative, second embodiment of hydrolysing the nucleic acid template is made at the sugar phosphate backbone of a nucleic acid strand (e.g. phosphodiester bonds) in the hybridized, double strand region to produce single-stranded "nicks", preferably by using endonuclease. On page 13, the instant specification describes that according to both embodiments, “hydrolysing a 3’ part of the nucleic acid template” thus can mean hydrolysing a nucleotide bond (e.g. by endonuclease) of the nick, or several nucleotide bonds in the 3’ part, e.g. by exonuclease according to the first embodiment. On page 28, the instant specification describes in one particular embodiment the 3’->5’ exonuclease digestion is replaced through a riboendonuclease treatment which introduces “nicks” in an RNA-DNA heteroduplex.
Third, Examples 1, 2, 3, 5, 6, 7 and 9 uses only a single-stranded specific exoribonuclease. Examples 10 and 11 uses only a riboendonuclease. Example 12 compares libraries made using only a single-stranded specific exoribonuclease and libraries made using only a riboendonuclease.
As a whole, the instant specification demonstrates that an exonuclease and an endonuclease are used as alternatives for each other. The instant specification does not disclose the use of both an exonuclease and an endonuclease in a single method.
Thus, claim 4 constitutes new matter.
Claim 16 depends from claim 4 and is rejected for the same reasons.
New claim 18 specifies the template sequence of choice is a poly(T)-sequence of at least 6 consecutive T’s. This constitutes new matter. Original claim 13 and the instant specification describes a poly(T)-sequence of at least 6 consecutive T’s that is part of a oligonucleotide probe (p. 22-23) and that is a complementary sequence to a template. A template comprising poly(T)-sequence of at least 6 consecutive T’s is new matter.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 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.
Claim(s) 13 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Guillou-Bonnici (US 5,744,308; previously cited).
Regarding claim 13, Guillou-Bonnici teaches a set of chimeric oligonucleotides, said set comprising:
an oligonucleotide segment, comprising a sense sequence of a promoter of an RNA polymerase as “transcription promoter”;
an oligonucleotide segment comprising a transcription initiation site for said promoter as an “identifier sequence of at least 4 nucleotides in length” that is recognized by RNase H; and
an oligonucleotide segment that hybridizes with a part of said target sequence. See claim 6; and col. 9, lines 4-15.
Response to the traversal of the 102 rejections
The Remarks do not provide any arguments regarding the 102 rejection over the set of oligonucleotides of claim 13. The arguments focus on the exonuclease element required by the method of amended claim 1. Claim 13 does not require any type of exonuclease. Thus, the arguments over Guillou-Bonnici are not persuasive in the context of claim 13.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 1, 2, 3, 5, 7, 11, 14 and 15 is/are rejected under 35 U.S.C. 103 as being unpatentable over Guillou-Bonnici (US 5,744,308; previously cited) in view of Vincent (The Journal of Biological Chemistry. 2006. 281(40):29769-29775).
The following are new rejections necessitated by the amendments to the claims.
Regarding claims 1 and 3, Guillou-Bonnici teaches a method of generating transcribed acids as depicted in Figure 1, reproduced below with annotations added by the examiner in text boxes:
Guillou-Bonnici teaches providing a nucleic acid template identified with a “(-)” sign. See part labeled “A and B” above in Figure 1.
Guillou-Bonnici teaches hybridizing an oligonucleotide probe comprising “S1”, “I1” and “P1” to the nucleic acid template. The S1 part is complementary to and hybridized with the nucleic acid template. A 5’ part in the form of P1 of the oligonucleotide probe does not hybridize with the template nucleic acid and comprises a transcription promoter sequence. See part labeled “A and B” below in Figure 1.
Guillou-Bonnici teaches hydrolysing the 3’ part of the nucleic acid template that is not hybridized to the oligonucleotide probe and the part hybridized with I1. See part labeled “C” below in Figure 1.
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Guillou-Bonnici teaches extending the nucleic acid template with nucleic acids complementary to the part P1 of the oligonucleotide probe as a template. See part of “D” below in Figure 1.
Guillou-Bonnici teaches transcribing the nucleic acid template with a transcriptase that binds the duplex of the sequence of the transcription promoter in P1 forming nucleic acids identified with a “(+)” sign. See part of “E” above in Figure 1.
Guillou-Bonnici does not specifically teach “hydrolysing a 3' part of the nucleic acid template that resides in 3' direction to a part of the nucleic acid template that hybridizes to the oligonucleotide probe in step b) and wherein said 3' part is not hybridized to the oligonucleotide probe, wherein the hydrolysis is with an exonuclease” or in particular a single-stranded RNA specific exonuclease that catalyses the removal of nucleotides in 3' to 5' direction.
However, Guillou-Bonnici teaches the degradation of the RNA in the RNA:DNA heteroduplex region formed by hybridization allows an end 3' to be created on the beginning molecule. The RNA of the RNA:DNA heteroduplex region is degraded by RNase H activity. However, this degradation can be effected by any other means.
It would have been obvious to the ordinary artisan at the time of filing to look for alternative ways to hydrolyse the 3’ part of the nucleic acid template that is not hybridized to the oligonucleotide probe based on Guillou-Bonnici expressing interest in other means of degrading the 3’ end of the template.
Vincent teaches that exoribonuclease RNase R is able to digest single-stranded 3’ sequences of RNA, including sequence comprised of A residues, U residues or C residues (p. 29772, left column; and Fig. 2). Vincent teaches that poly(A) sequences were of interest because RNAs are often polyadenylated in vivo (p. 29771, right column). Vincent teaches RNase R recognizes and cleaves solely at the 3’ terminal phosphodiester bond even in the absence of a terminal 3’ hydroxyl group (p. 29773, right column).
It would have been prima facie obvious to the ordinary artisan at the time of filing to have substituted the RNase H of Guillou-Bonnici with the RNase R of Vincent. One would have been motivated to do so because RNase R has a strong preference for poly(A) sequences (Fig. 2 of Vincent). For example, when choosing S1 probe and/or I1 sequences that hybridize adjacent to the 3’ poly(A) tail of cellular mRNA, one would be motivated to use RNase R in order to preferentially cleave the poly(A) sequence and generating a 3’ end which can be extended by using the chimera oligonucleotide of Guillou-Bonnici as a template.
Regarding claim 2, Guillou-Bonnici teaches the nucleic acid template is RNA (Figure 1; and col. 10, line 43-45). Regarding claim 5, Guillou-Bonnici teaches the extending of the nucleic acid template is by nucleotide polymerization carried out by a DNA polymerase. See part labeled “C” above in Figure 1.
Regarding claim 7, Guillou-Bonnici teaches I1 as a “first adaptor sequence” between non-complementary part P1 and complementary part S1. See Figure 1 above.
Regarding claim 11, Guillou-Bonnici teaches the method is done in an reaction medium (col. 21, lines 30-35). One would recognize that a reaction medium would be in a “container” of some type.
Regarding claim 14, the term “kit” is broadly interpreted as any collection of reagents used together.
Guillou-Bonnici teaches using oligonucleotide probes with a transcription promoter along with RNase H, DNA and RNA polymerases and transcriptases that initiate at the transcription promoter. See Figure 1; and col. 21, EXAMPLE 6.
For the reasons provided above in the rejection of claims 1 and 3, it would have been prima facie obvious to have replace the RNase H with the RNase R of Vincent.
Regarding claim 15, Guillou-Bonnici further teaches the above elements are used with dNTPS (col. 14, lines 51-64).
Claim(s) 6, 8, 9, 10 and 12 is/are rejected under 35 U.S.C. 103 as being unpatentable over Guillou-Bonnici (US 5,744,308; previously cited) in view of Vincent (The Journal of Biological Chemistry. 2006. 281(40):29769-29775) as applied to claim 1 above, and in further view of Schuster (US 5,169,766; previously cited).
The following are new rejections necessitated by the amendments to the claims.
Regarding claims 6, 8, 9 and 10, Guillou-Bonnici and Vincent renders obvious the elements of claim 1 as described above and as required by claims 6, 8, 9, 10 and 12.
Guillou-Bonnici does not specifically teach the elements of 6, 8, 9 and 10 and 12.
However, Schuster teaches a method of amplifying nucleic acids using in vitro transcription that is in the same technical field as Guillou-Bonnici.
Regarding claim 6, Schuster teaches hybridizing an oligonucleotide probe comprising a 5’ promoter and extending the probe and the template it is hybridized to. See Fig. 1.
Regarding claim 8, Schuster teaches hybridizing a secondary primer to a transcript and extending it using the transcript as a template. See Fig. 1.
Regarding claim 9, Schuster teaches the nucleic acid template is from a cell (col. 13, lines 39-56).
Regarding claim 10, Schuster teaches the RNA is a pool of nucleic acids comprising DNA (col. 13, lines 20-36).
Regarding claim 12, Schuster teaches the RNA is from cells, which would be lysed in order to obtain RNA and inactivating enzymes using EDTA (col. 13, lines 39-56).
It would have been obvious to have modified the method of Guillou-Bonnici and Vincent by incorporating the elements of Schuster. One would have been motivated to modify the oligonucleotide probe of Guillou-Bonnici such that it can be extended to form an additional template to ultimately drive in vitro transcription. Similarly, by hybridizing and extending primers on the resulting transcript allows for further amplification of the target molecular via in vitro transcription.
It would have been obvious to have used the RNA source of Schuster, e.g., a cell, as it a well-known source of RNA for analysis, e.g., a transcriptomics assay.
Claim(s) 17 is/are rejected under 35 U.S.C. 103 as being unpatentable over Guillou-Bonnici (US 5,744,308; previously cited) in view of Vincent (The Journal of Biological Chemistry. 2006. 281(40):29769-29775), and Schuster (US 5,169,766; previously cited) as applied to claim 12 above, and in further view of Motyan (Biomolecules. 2013. 2:923-942).
The following are new rejections necessitated by the amendments to the claims.
Regarding claim 17, Guillou-Bonnici, Vincent and Schuster render obvious the elements of claim 12 as described above and as required by claim 17.
The combination does not teach inactivating enzymes by a proteinase.
However, Motyan demonstrates that it was known that EDTA (p. 930) and/or proteolytic enzymes, such as Proteinase K, may be used to inactive nucleases.
It would have been prima facie obvious to have used either EDTA or Proteinase K to inactive enzymes, such as nucleases, as they are obvious variants that are functionally equivalent as demonstrated by Motyan.
Claim(s) 19 is/are rejected under 35 U.S.C. 103 as being unpatentable over Guillou-Bonnici (US 5,744,308; previously cited) in view of Hashimsony (Cell Reports. 2012. 2:666-673).
The following are new rejections necessitated by the amendments to the claims.
Regarding claim 19, Guillou-Bonnici teaches a set of chimeric oligonucleotides, said set comprising:
an oligonucleotide segment, comprising a sense sequence of a promoter of an RNA polymerase as “transcription promoter”;
an oligonucleotide segment comprising a transcription initiation site for said promoter; and
an oligonucleotide segment that hybridizes with a part of said target sequence. See claim 6; and col. 9, lines 4-15.
Guillou-Bonnici does not specifically teach the identifier sequence is different for at least two oligonucleotide probes of the plurality.
However, Hashimsony teaches an oligonucleotide that is analogous in structure to those of Guillou-Bonnici. Both the oligonucleotides of Hashimsony and Guillou-Bonnici are used for the in vitro transcription/amplification of an RNA molecule.
Hashimonsony teaches the oligonucleotides include a barcode (Fig. 1) as an “identifier sequence” that is used to identify and distinguish between different RNA molecules, e.g., those from different samples (p. 671).
It would have been prima facie obvious to the ordinary artisan at the time of filing to have modified the oligonucleotides of Guillou-Bonnici such that they include barcodes that may be used to distinguish between different RNA molecules. The modification has a reasonable expectation of success as it involves adding an 8 bp sequence to the oligonucleotides of Guillou-Bonnici. Alternatively, the barcode may be incorporated into one of the other structural features of Guillou-Bonnici’s oligonucleotides, e.g., included as part of the I1 sequence.
Conclusion
No claims allowed.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JOSEPH G DAUNER whose telephone number is (571)270-3574. The examiner can normally be reached 7 am EST to 4:30 EST with second Fridays Off.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Winston Shen can be reached at 5712723157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JOSEPH G. DAUNER/Primary Examiner, Art Unit 1682
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