DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
2. Applicant’s election of Group I (claims 1, 16, 19, 23-28, 30, 45-47, 50, 53, 58, 59, and 62) in the reply filed on October 14, 2025 is acknowledged. The reply of October 14, 2025 does not state whether the election is made with or without traverse. Since the response does not include anything that would constitute a traversal (i.e., Applicant did not distinctly and specifically point out any supposed errors in the restriction requirement), the election has been treated as an election without traverse. See MPEP 818.01(a).
Claims 64 and 105 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on October 14, 2025.
Applicant’s request for rejoinder of the nonelected methods claims when the elected product claims are allowable is also acknowledged. The nonelected method claims will be considered for rejoinder in accordance with the guidance set forth in MPEP 821.04.
Priority
3. The effective filing date of the claims under examination is June 26, 2020 (i.e., the filing date of Provisional Application 63/044,634).
Information Disclosure Statement
4. Applicant’s submission of an Information Disclosure Statement (IDS) on January 30, 2024 and on April 4, 2025 is acknowledged.
All of the references cited on the IDSs have been considered.
Drawings
5. The drawings filed on December 27, 2022 are acceptable.
Nucleotide and/or Amino Acid Sequence Disclosures
6. REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency - The Incorporation by Reference paragraph required by 37 CFR 1.821(c)(1) is missing or incomplete. See item 1) a) or 1) b) above. More specifically, the file size of the Sequence Listing must be provided in bytes rather than kilobytes. See 37 CFR 1.823(b)(iii) and MPEP 2422.03 I.
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specification
7. The specification is objected to because, as noted above, the Incorporation by Reference paragraph provides the file size of the Sequence Listing in kilobytes rather than bytes as required by 37 CFR 1.823(b)(iii). See also MPEP 2422.03 I.
Claim Interpretation
8. The specification of the instant application contains explicit (i.e., limiting) definitions for some of the terms used in the claims. These definitions include the following: subsequence = a sequence of at least five contiguous base pairs (p. 25, para. 74).
It is also noted that the specification explicitly states that the term “complementary” is not limited to 100% complementarity and encompasses “substantially complementary” nucleic acids (see pp. 23-24, para. 70).
Further, it is noted that Applicant has defined the term “stoichiometric ratio,” which appears in claim 58, as equivalent to “molar ratio” (p. 27, para. 83).
Claim Objections
9. Claim 26 is objected to because of the following minor informality. Amending the claim to recite “wherein each Forward Primer in the plurality of Forward Primer oligonucleotide species comprises a Universal Forward Adapter subsequence at or near the 5’ end.” This suggestion is made to improve the grammar of the claim.
Claim 53 is objected to because “of the” should be inserted before “Forward Primer” in the last line of the claim to improve the grammar of the claim.
Claim Rejections - 35 USC § 101
10. 35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1, 16, 19, 23-25, 27, 28, 45-47, 50, 53, 58, 59, and 62 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception—specifically, a product of nature—without significantly more.
Claim 1
Claim 1 is drawn to a composition comprising the following components: (i) a template-dependent polymerase; (ii) an Auxiliary oligonucleotide; (iii) a Suppressor oligonucleotide; and (iv) a Forward Primer oligonucleotide. The Suppressor oligonucleotide has a Protected Subsequence that is at least 20 nucleotides in length and reverse complementary to a subsequence of the Auxiliary oligonucleotide. The Suppressor oligonucleotide also contains an Unprotected Subsequence that is at least 7 nucleotides in length and not reverse complementary to the Auxiliary oligonucleotide. The Forward Primer contains a subsequence that is at least 6 nucleotides in length and identical to a subsequence of the Suppressor oligonucleotide.
The claimed composition is drawn to a judicial exception because its components either encompass naturally occurring products or lack markedly different characteristics relative to their naturally occurring counterpart.
More specifically, the template-dependent polymerase in the composition encompasses naturally occurring polymerases (e.g., E. coli DNA polymerase, Taq DNA polymerase, naturally occurring reverse transcriptases (e.g., MMLV-RT or AMV-RT), or naturally occurring RNA polymerases (e.g., T7 or SP6 RNA polymerase)).
Regarding the oligonucleotides recited in the claim (i.e., the Forward Primer, Auxiliary oligonucleotide and Suppressor oligonucleotide), as discussed in MPEP 2106.04(b)(II), products of nature include naturally occurring products and non-naturally occurring products that lack markedly different characteristics from any naturally occurring counterpart. In this case, it is not clear that the oligonucleotides recited claim 1 are found in nature, but said oligonucleotides need not possess any sequence differences or additional structural elements (e.g., a non-naturally occurring detectable label) relative to their naturally occurring counterparts, which are merely naturally occurring nucleic acid sequences.1
See also MPEP 2106.04(c)(II)(A), which discusses how to select the naturally occurring counterpart for a short, single-stranded nucleic acid fragment (e.g., a primer or probe) and states that the appropriate counterpart for such a nucleic acid is the corresponding sense or antisense strand of the naturally occurring sequence. The claimed oligonucleotides also do not have any functional differences relative to the naturally occurring counterpart because both nucleic acids perform the same function of hybridization to a complementary nucleic acid sequence. See also MPEP 2106.04(c)(II)(C)(2), which discusses why primers lack markedly different characteristics. The same reasoning set forth there applies here. Thus, claim 1 is directed to a judicial exception.
The judicial exceptions recited in claim 1 (i.e., the oligonucleotides and the polymerase) are not integrated into a practical application because there are no other limitations in the claim besides the judicial exceptions and the judicial exceptions each perform the same function in the composition (i.e., extension in the case of the polymerase or hybridization in the case of the oligonucleotides) as they do in nature. As well, since the claim only recites the judicial exceptions, the claim does not include additional elements that are sufficient to amount to significantly more than the judicial exceptions.
Thus, the composition of claim 1 is rejected under 35 U.S.C. 101 as being directed to ineligible subject matter.
Claim 16
Claim 16 depends from claim 1 and recites “wherein the Unprotected Subsequence of the Suppressor oligonucleotide is not reverse complementary to any portion of the Auxiliary oligonucleotide.”
This claim is also directed to a judicial exception for the reasons set forth above with respect to claim 1. Briefly, as discussed below, claim 16 does not further limit claim 1 because its limitations are already required by the last three lines in part (b) of claim 1. Therefore, as in claim 1, the Suppressor oligonucleotide in claim 16 need not possess any structural or functional differences relative to its naturally occurring counterpart. As with claim 1, the judicial exception in claim 16 is not integrated into a practical application because no other elements are recited in the claim. And, since the claim only recites the judicial exceptions, the claim does not include additional elements that are sufficient to amount to significantly more than the judicial exceptions. Thus, claim 16 is directed to a judicial exception without significantly more, and accordingly, is rejected under 35 U.S.C. 101.
Claim 19
Claim 19 depends from claim 1 and requires the Suppressor oligonucleotide and/or the Auxiliary oligonucleotide to contain a 3’ modification or DNA sequence that prevents template-dependent polymerase extension.
This claim is also directed to a judicial exception for essentially the reasons set forth above with respect to claim 1. More specifically, the requirement for a 3’ modification or DNA sequence that prevents template-dependent polymerase extension encompasses naturally occurring 3’ modifications, such as bulky base adducts or other naturally occurring modifications that prevent polymerase-mediated extension. As a result, the judicial exceptions in claim 19 still need not possess any structural or functional differences relative to their naturally occurring counterparts. And, as with claim 1, the judicial exception in claim 19 is not integrated into a practical application because no other elements are recited in the claim. Further, since the claim only recites the judicial exceptions, the claim does not include any additional elements that are sufficient to amount to significantly more than the judicial exceptions. Thus, claim 19 is also directed to a judicial exception without significantly more, and accordingly, is rejected under 35 U.S.C. 101.
Claims 23-25
Claim 23 depends from claim 1 and requires the composition to contain a plurality of different Suppressor oligonucleotides, a plurality of different Auxiliary oligonucleotides, and plurality of different Forward Primers. Claims 24 and 25 each depend from claim 23 and further describe the nucleotide sequence requirements of the plurality of different Suppressor oligonucleotides and the plurality of different Forward Primers.
These claims are also directed to a judicial exception for the reasons set forth above with respect to claim 1. Briefly, the additional oligonucleotides in the compositions of claims 23-25 need not possess any structural or functional differences relative to their naturally occurring counterparts. As with claim 1, the judicial exceptions in claims 23-25 are not integrated into a practical application because no other elements are recited in the claims. And, since the claims only recite the judicial exceptions, they do not include additional elements that are sufficient to amount to significantly more than the judicial exceptions. Thus, claims 23-25 are directed to a judicial exception without significantly more, and accordingly, are rejected under 35 U.S.C. 101.
Claims 27, 28, 45-47, 50, and 53
Claims 27 and 28 each depend from claim 1. Claim 27 requires the composition to additionally contain a nucleic acid template molecule. Claim 28 requires the composition to additionally contain a Reverse Primer.2
Claims 45-47 and 50 depend, directly or indirectly, from claim 27, and further define the structural features of the Template molecule.
Claim 53 depends from claim 27 and further defines the nucleotide sequence requirements of the Auxiliary oligonucleotide.
These claims are also directed to a judicial exception for essentially the same reasons set forth above with respect to claim 1. More specifically, the requirement in claims 27 and 28 for the composition to further include a Template nucleic acid and/or a Reverse Primer only requires the composition to contain additional nucleic acid molecules that are not required by the claims to be different, structurally or functionally, from their naturally occurring counterparts. This is the case when the additional nucleic acids are considered alone or in the presence of the other components of the composition. Similarly, claims 45-47, 50, and 53 further define the sequence requirements of the Template nucleic acid or the Auxiliary oligonucleotide, but they do not require these nucleic acids to possess any structural or functional differences relative to their naturally occurring counterparts.3 As a result, these claims merely add more judicial exceptions to the composition and/or further define judicial exceptions already present in the composition in a manner that does not result in a marked difference relative to their naturally occurring counterparts. As with claim 1, the judicial exceptions in these claims are not integrated into a practical application because no other elements are recited in the claims. And, since the claims only recite the judicial exceptions, they do not include additional elements that are sufficient to amount to significantly more than the judicial exceptions. Thus, claims 27, 28, 45-47, 50, and 53 are directed to a judicial exception without significantly more, and accordingly, are rejected under 35 U.S.C. 101.
Claim 58
Claim 58 depends from claim 1 and requires the stoichiometric ratio of the Auxiliary oligonucleotide to the Suppressor oligonucleotide to be between 0.8 and 100.
This claim is also directed to a judicial exception for the reasons set forth above with respect to claim 1. Claim 58 only limits the relative amounts of the Auxiliary and Suppressor oligonucleotides and does not require either oligonucleotide to possess any structural or functional differences relative to the naturally occurring counterpart. As with claim 1, the judicial exceptions in claim 58 are not integrated into a practical application because no other elements are recited in the claim. And, since the claim only recites the judicial exceptions, it does not include additional elements that are sufficient to amount to significantly more than the judicial exceptions. Thus, claim 58 is directed to a judicial exception without significantly more, and accordingly, is rejected under 35 U.S.C. 101.
Claims 59 and 62
Claim 59 depends from claim 1 and requires the Forward Primer, the Suppressor oligonucleotide, and the Auxiliary oligonucleotide to satisfy particular requirements as to their standard free energies of hybridization (DG⁰1, DG⁰2, and DG⁰3, respectively). Claim 62 depends from claim 59 and further limits the permissible difference between DG⁰2 and DG⁰3.
These claims are also directed to a judicial exception for the reasons set forth above with respect to claim 1. More specifically, the additional requirements in claims 59 and 62 do not require the claimed oligonucleotides to possess any structural or functional differences relative to their naturally occurring counterparts. As with claim 1, the judicial exceptions in claims 59 and 62 are not integrated into a practical application because no other elements are recited in the claims. And, since the claims only recite the judicial exceptions, they do not include additional elements that are sufficient to amount to significantly more than the judicial exceptions. Thus, claims 59 and 62 are directed to a judicial exception without significantly more, and accordingly, are rejected under 35 U.S.C. 101.
Thus, the compositions of claim 1, 16, 19, 23-25, 27, 28, 45-47, 50, 53, 58, 59, and 62 are rejected under 35 U.S.C. 101 as being directed to ineligible subject matter.
Claim Rejections - 35 USC § 112
11. 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 23-28, 30, 45-47, 50, 53, 59, and 62 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.
Claim 23 is indefinite because the presence of claims 24 and 25 raises doubts as to its intended scope. Claim 23 depends from claim 1 and requires the composition to contain a plurality of Suppressor oligonucleotide species, a plurality of Auxiliary oligonucleotide species, and a plurality of Forward Primer species. Since claim 1 requires each of these different oligonucleotides to have particular structural features (e.g., the Protected Subsequence recited in part (b) of claim 1), it would ordinarily be assumed that the additional Forward Primers, Auxiliary oligonucleotides, and Suppressor oligonucleotides recited in claim 23 would have to meet these same requirements (e.g., the presence of a Protected Subsequence as recited in part (b) of claim 1). The presence of claims 24 and 25, though, creates doubt as to whether this interpretation of claim 23 is correct since those claims reiterate the structural features set forth in claim 1 with respect to the Suppressor oligonucleotide, Auxiliary oligonucleotide, and Forward Primer. Put another way, either (i) claims 24 and 25 do not further limit claim 23, or (ii) the additional oligonucleotides in claim 23 need not possess the structural features recited in claim 1 for the Auxiliary oligonucleotide, Forward Primer, and Suppressor oligonucleotide. And, if (ii) is correct, it is not clear as to just what structural features the additional oligonucleotides in the composition of claim 23 must possess. As a result, the requirements of claim 23 are not entirely clear, and the claim is rejected as indefinite.
Claims 24-26 are also indefinite by way of their dependency on claim 23.
Claim 27 is indefinite because there is insufficient antecedent basis for “the 3’ subsequence of the Forward Primer oligonucleotide,” which is recited in the last two lines of the claim. More specifically, claim 1 does not recite “a 3’ subsequence of the Forward Primer oligonucleotide.” Consequently, it is unclear whether “the 3’ subsequence” recited in claim 27 merely refers to the 3’ end of the primer or if it refers to a particular subsequence at the 3’ end of the primer.
Claim 28 is indefinite because there is insufficient antecedent basis for “the Template molecule,” which is recited in line 2. Claim 1, from which claim 28 depends, does not recite a Template molecule. As a result of the antecedent basis issue, it is also not clear whether claim 28 was intended to depend from claim 27, which provides antecedent basis for “the Template molecule.”
Claims 30, 45, and 53 are also indefinite by way of their dependency on claim 27 or claim 28.
Claims 46, 47, and 50 are indefinite because the structural features required of an “Initiation Subsequence” in claims 46 and 47 and an “Initiation Complement Subsequence” in claim 50 are unclear. Neither of these terms is routinely used in the art, and the specification does not provide an explicit definition for either term. Figure 2 and the accompanying description in para. 58 gives an example of an Initiation Subsequence and an Initiation Complement Subsequence, but it is not clear that an Initiation Subsequence (and an Initiation Complement Subsequence) are required to have the structural features disclosed in Figure 2 and para. 58. And, if they are not, it is unclear as to what structural features, at minimum, are required of these subsequences. Since the requirements of the claims cannot be clearly determined, they are indefinite.
Claim 46 is also indefinite because there is insufficient antecedent basis for “the Initiation Subsequence,” which is recited in the last line of the claim. None of the claims from which claim 46 directly or indirectly depends recites an Initiation Subsequence.
Claim 59 is also indefinite because there is insufficient antecedent basis for “the Template molecule,” which is recited in line 2. The “and/or” language in line 6 also renders the claim indefinite because it is not clear whether it makes optional any of the three “wherein” clauses recited in the claim or if it only applies to the last two “wherein” clauses.
Claim 62 is also indefinite by way of its dependency on claim 59.
Claim Rejections - 35 USC § 112
12. The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 16, 24, and 25 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 16 depends from claim 1 and recites “wherein the Unprotected Subsequence of the Suppressor oligonucleotide is not reverse complementary to any portion of the Auxiliary oligonucleotide.” This is not further limiting because it is already required by the last three lines of part (b) in claim 1.
Claims 24 and 25 each depend from claim 23 and recite structural requirements concerning the Suppressor and Auxiliary oligonucleotides (claim 24) or the Forward Primer and the Suppressor oligonucleotide (claim 25). As discussed above, the presence of claims 24 and 25 causes the scope of claim 23 to be unclear, but one interpretation is that the additional oligonucleotides recited in claim 23 must possess the structural features set forth in claim 1 for Forward Primer, Auxiliary oligonucleotide, and Suppressor oligonucleotide. If this is the case, claims 24 and 25 are not further limiting because their requirements are already required by claim 23.
Applicant may cancel the claims, amend them to be in proper dependent form, or present a sufficient showing that the dependent claims comply with the statutory requirements.
Claim Rejections - 35 USC § 103
13. 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.
14. 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.
15. Claims 1, 16, 19, 23-25, 27, 28, 45-47, 50, 53, 58, 59, and 62 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (US 2013/0274135 A1; “Zhang 1” below) in view of Zhang et al. (US 2017/0067090 A1; “Zhang 2” below).4
The instant claims are drawn to a composition comprising the following components: (i) a template-dependent polymerase; (ii) an Auxiliary oligonucleotide; (iii) a Suppressor oligonucleotide; and (iv) a Forward Primer oligonucleotide. The Suppressor oligonucleotide has a Protected Subsequence that is at least 20 nucleotides in length and reverse complementary to a subsequence of the Auxiliary oligonucleotide. The Suppressor oligonucleotide also contains an Unprotected Subsequence that is at least 7 nucleotides in length and not reverse complementary to the Auxiliary oligonucleotide. The Forward Primer contains a subsequence that is at least 6 nucleotides in length and identical to a subsequence of the Suppressor oligonucleotide.
An embodiment of the invention is depicted in Figure 1 of the instant application:
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Regarding claim 1, Zhang 1 discloses an oligonucleotide probe composition that comprises oligonucleotides with the structural features of the claimed Auxiliary and Suppressor oligonucleotides (see Figures 1A and 1B (reproduced below), where the shorter “protector strand” corresponds to the claimed Auxiliary oligonucleotide, and the longer “complement probe” strand corresponds to the claimed Suppressor oligonucleotide).
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As can be seen in these figures, the Suppressor oligonucleotide (i.e., the Complement Probe) contains a Protected Subsequence that is at least 20 nucleotides long and reverse complementary to a subsequence of the Auxiliary oligonucleotide. As well, the Suppressor oligonucleotide contains an Unprotected Subsequence (i.e., the toehold region) that is 7 nucleotides in length and not reverse complementary to the Auxiliary oligonucleotide (i.e., the Protector strand).
Further regarding claim 1, the oligonucleotides shown in Figures 1A and 1B of Zhang 1 may be provided in a composition with a polymerase (see, e.g., paras. 22, 68, and 71).
Zhang 1 also teaches that the “Complement Probe” strand in the composition shown in Figure 1B may function as a primer (para. 68) in addition to teaching that the Protector and Complement Probe oligonucleotides in Figures 1A and 1B may each function as probes alone (i.e., not as primers) (para. 8).
Zhang 1 does not teach a Forward Primer that is a separate oligonucleotide as recited in part (c) of claim 1.
Prior to the effective filing date of the claimed invention, though, it would have been prima facie obvious to further include a Forward Primer as recited in claim 1 in the composition of Zhang 1. More specifically, when the compositions of Figures 1A and 1B of Zhang 1 are used as probes (i.e., with the “Complement Probe” strand not functioning as a primer), it would have been prima facie obvious to provide a Forward Primer in the form of a separate oligonucleotide that contains at least part of the complement probe strand. Zhang 2 provides motivation to do so by teaching that a similar composition in which a primer that overlaps with a blocker oligonucleotide offers improved specificity and sensitivity, particularly when the composition is used for allele-specific amplification (Fig. 4 and paras. 8 and 19). The ordinary artisan also would have recognized that this Forward Primer should have a subsequence at least 6 nucleotides in length that is identical to a subsequence of the Suppressor oligonucleotide for two reasons. First, the toehold region in Fig. 1B of Zhang 1 to which the Forward Primer suggested by Zhang 2 would correspond is 7 nucleotides in length, which would have suggested to the ordinary artisan that a Forward Primer should be at least 7 nucleotides in length and identical to the toehold region in the Complement Probe strand of Zhang 1. Second, since Zhang 2 teaches that a useful length for a Forward Primer is ~20 nucleotides with 10 nucleotides of overlap between the primer and blocker probe (Fig. 4), the ordinary artisan would have recognized that when substituting a separate Forward Primer in the composition of Zhang 1 as suggested by Zhang 2, the Forward primer should have the general structural features disclosed in Zhang 2 (i.e., total length of about 20 nucleotides and overlap with the blocker of about 10 nucleotides). Thus, the composition of claim 1 is prima facie obvious over Zhang 1 in view of Zhang 2.
Further regarding claim 16, which depends from claim 1, as can be seen in Figures 1A and 1B of Zhang 1, the Unprotected Subsequence of the Suppressor oligonucleotide (i.e., the toehold region in Figs. 1A-1B of Zhang 1) is not reverse complementary to any portion of the Auxiliary oligonucleotide. Thus, the composition of claim 16 is also prima facie obvious over Zhang 1 in view of Zhang 2.
Further regarding claim 19, which depends from claim 1, Zhang 1 teaches that the Auxiliary oligonucleotide may have a 3’ chemical modification that prevents template-dependent polymerase extension (see, e.g., paras. 15-16, where the Protector strand corresponds to the claimed Auxiliary oligonucleotide). Thus, the composition of claim 19 is also prima facie obvious over Zhang 1 in view of Zhang 2.
Regarding claims 23-25, which depend directly or indirectly from claim 1, Zhang 1 teaches that the partially double-stranded nature of the disclosed oligonucleotides “means that…they are amenable to highly multiplexed replication…reactions” (para. 9). See also paras. 34, 66, 208, and, especially, para. 238, where Zhang 1 teaches multiplexed PCR designed to amplify many different target nucleic acids in a single reaction. These teachings of Zhang 1 clearly suggest a composition that contains a plurality of oligonucleotides with the structural features set forth in Figures 1A and 1B (i.e., a plurality of Suppressor oligonucleotides, each containing a Protected Subsequence as recited in claim 24 and a plurality of corresponding Auxiliary oligonucleotides). Then, combining the teachings of Zhang 1 with Zhang 2, the ordinary artisan also would have recognized that such compositions should include a plurality of Forward Primers, with each different Forward Primer having the general structural features set forth in claim 1 and corresponding to a particular Suppressor oligonucleotide. Thus, the compositions of claims 23-25 are also prima facie obvious over Zhang 1 in view of Zhang 2.
Regarding claims 27 and 28, which each depend from claim 1, Zhang 1 teaches that the disclosed compositions are to be used in an amplification reaction (see, e.g., paras. 8, 22, 32, 63, 206, and 208). This clearly suggests inclusion of a nucleic acid Template molecule in the composition. Further, the ordinary artisan would have recognized that for the Forward Primer in the composition to be effective, the nucleic acid Template molecule should contain “a subsequence that is over 90% homologous to the reverse complement of the 3’ subsequence of the Forward Primer” as recited in claim 27. Otherwise, the ordinary artisan would have recognized, the Forward Primer would not be effective in the amplification reaction. Similarly, further regarding claim 28, the ordinary artisan would have recognized that PCR, which is listed in, e.g., para. 208 of Zhang 1, as a suitable amplification method, would require a Reverse Primer to be present in the composition and that the nucleic acid Template molecule should also contain “a subsequence that is over 90% homologous to a 3’ subsequence of the Reverse primer.” Otherwise, the ordinary artisan would have recognized, the Reverse Primer would not be effective in the PCR. Thus, the compositions of claims 27 and 28 are also prima facie obvious over Zhang 1 in view of Zhang 2.
Regarding claim 45, which depends from claim 27, as discussed above, Zhang 1 teaches that the disclosed compositions may be used in amplification reactions such as PCR (see, e.g., paras. 205, 206, and 208). And, as discussed above with respect to claims 27 and 28, the ordinary artisan would have recognized that PCR requires a Forward Primer and a Reverse Primer, and accordingly, would have been motivated to include both in the compositions suggested by Zhang 1 in view of Zhang 2. The ordinary artisan also would have recognized that a suitable nucleic acid Template molecule for use in a PCR contains a Target Subsequence (i.e., a sequence to be amplified) positioned between a Forward Primer-binding Subsequence and a Reverse Primer-homologous Subsequence as recited in claim 45. Otherwise, the ordinary artisan would have recognized, the PCR would not work. Thus, the composition of claim 45 is also prima facie obvious over Zhang 1 in view of Zhang 2.
Regarding claim 46, which depends from claim 45, as discussed in the indefiniteness rejection, it is unclear what, at minimum, is required structurally of “an Initiation Subsequence.” One possible interpretation is that an Initiation Subsequence is a subsequence in the Suppressor oligonucleotide that is not complementary to the nucleic acid Template molecule. Zhang 1 discloses such a subsequence in Figure 15A, where the Toehold Exchange Primer, which corresponds to the claimed Suppressor oligonucleotide has a 5’ Subsequence that is not complementary to the nucleic acid Template molecule. This 5’ Subsequence is considered to be an Initiation Subsequence.
Further regarding claim 46 and also regarding claim 47, each of which depends from claim 45, it would have been prima facie obvious (i) to modify the Suppressor oligonucleotide of Zhang 1 to contain an Initiation Subsequence at the 3’ end, wherein the Initiation Subsequence is not complementary to the Target Subsequence, and (ii) for the Target Subsequence to be at least 70% identical to the reverse complement of the portion of the Suppressor oligonucleotide Protected Subsequence that does not include the Initiation Subsequence. As discussed above, the structural requirements of an Initiation Subsequence are unclear, but one possible interpretation is that an Initiation Subsequence is a sequence that is not complementary to a Target nucleic acid sequence (see Fig. 2 of the instant application). Zhang 1 does not teach that the Complement Probe, which corresponds to the claimed Suppressor oligonucleotide, contains such a sequence at its 3’ end, but such a modification would have been prima facie obvious in view of Zhang 2. In particular, Zhang 2 teaches that a Blocker oligonucleotide may have a 3’ Subsequence that is not complementary to a Target nucleic acid to be amplified, and that the purpose of this 3’ Subsequence is to prevent enzymatic extension of the Blocker (see Fig. 8 and paras. 32 and 101). The ordinary artisan would have recognized that when the Complement Probe of Zhang 1 is intended to only function as a probe (i.e., not as a primer), it would be desirable to prevent its extension by a polymerase used in the intended amplification reaction. Accordingly, the ordinary artisan would have been motivated to modify the Complement Probe with a 3’ Initiation Subsequence as taught in Zhang 2 and would have had a reasonable expectation of success since oligonucleotide synthesis was routine and conventional.
Further as to (ii) above, the ordinary artisan also would have recognized that the Target Subsequence should be at least 70% identical to the reverse complement of the portion of the Suppressor oligonucleotide Protected Subsequence that does not include the Initiation Subsequence because this would be necessary for the Target Subsequence to successfully compete with the Auxiliary oligonucleotide (i.e., Protector strand) for binding the Suppressor oligonucleotide (i.e., Complement Probe) in Zhang 1 (see, e.g., Fig. 15A, where the Target competes with the Auxiliary oligonucleotide for binding the Suppressor oligonucleotide).
Thus, the compositions of claims 46 and 47 are prima facie obvious over Zhang 1 in view of Zhang 2.
Regarding claim 50, which depends from claim 47, as discussed above, the structural requirements of an Initiation Subsequence are unclear. Therefore, the structural requirements of an Initiation Complement Subsequence are also unclear. As also discussed above, the teachings of Zhang 1 in view of Zhang 2 suggest adding an Initiation Subsequence at the 3’ end of the Complement Probe oligonucleotide in Zhang 1, wherein the Initiation Subsequence is not complementary to the Target Subsequence. Then, since the Auxiliary oligonucleotide (i.e., Protector strand) in Zhang 1 is designed to bind to the Suppressor oligonucleotide (i.e., Complement Probe) in Zhang 1, the ordinary artisan would have recognized that the Auxiliary oligonucleotide should also include at its 5’ end a nucleotide sequence complementary to the Initiation Subsequence added to the 3’ end of the Suppressor oligonucleotide to facilitate this binding. Thus, the composition of claim 50 is prima facie obvious over Zhang 1 in view of Zhang 2.
Regarding claim 53, which depends from claim 27, it also would have been prima facie obvious for the ordinary artisan to design the Auxiliary oligonucleotide in the composition suggested by Zhang 1 in view of Zhang 2 such that it does not contain a subsequence that is more than 30% identical to the reverse complement of the Forward Primer. The ordinary artisan would have recognized that the purpose of the Forward Primer in the composition is to compete with the Suppressor oligonucleotide (i.e., Complement Probe in Zhang 1) for binding to the nucleic acid to be amplified. Therefore, to avoid undesirable binding of the Forward Primer to the Auxiliary oligonucleotide, the ordinary artisan would have recognized that the Auxiliary oligonucleotide should be designed such that it has very limited identity (e.g., less than 30% identity) to the reverse complement of the Forward Primer. Thus, the composition of claim 53 is prima facie obvious over Zhang 1 in view of Zhang 2.
Regarding claim 58, which depends from claim 1, Zhang 1 teaches that the Auxiliary oligonucleotide and the Suppressor oligonucleotide (i.e., the Protector strand and the Complement Probe strand) may be present at a stoichiometric ratio of 1:1 (see, e.g., para. 240).5 See also paras. 243 and 259, where Zhang 1 discloses other amounts for the Auxiliary and Suppressor oligonucleotides that result in a stoichiometric ratio within the claimed range. Thus, the composition of claim 58 is prima facie obvious over Zhang 1 in view of Zhang 2.
Regarding claims 59 and 62, which depend directly or indirectly from claim 1, neither Zhang 1 nor Zhang 2 teaches any of the recited hybridization free energy ranges. Zhang 1 does teach, though, that the standard free energy of hybridization between a primer oligonucleotide and the target nucleic acid to which it hybridizes should be “close to zero,” while the standard free energy of hybridization between a primer and a non-target nucleic acid should be “high enough to make their binding unfavorable by comparison” (para. 10). The ordinary artisan would have understood from these teachings of Zhang 1 that the standard free energies of hybridization between various components in the composition suggested by Zhang 1 in view of Zhang 2 (e.g., between the Forward Primer and the Template molecule; between the Suppressor oligonucleotide and the Template molecule; or between the Suppressor oligonucleotide and the Auxiliary oligonucleotide) are results-effective variables that should be optimized to obtain the best results. As discussed in MPEP 2144.05 II, it is prima facie obvious to optimize results-effective variables in the absence of unexpected results. In this case, no such evidence has been presented. Therefore, the ordinary artisan would have been motivated to perform routine experimentation to optimize the various standard free energies of hybridization between different components in the compositions suggested by Zhang 1 in view of Zhang 2 and would have had a reasonable expectation of success since Zhang 1 describes how to calculate standard free energies of hybridization (see, e.g., paras. 72-79). Thus, the compositions of claims 59 and 62 are prima facie obvious over Zhang 1 in view of Zhang 2.
In view of the foregoing, the compositions of claims 1, 16, 19, 23-25, 27, 28, 45-47, 50, 53, 58, 59, and 62 are prima facie obvious over Zhang 1 in view of Zhang 2.
16. Claims 26 and 30 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (US 2013/0274135 A1; “Zhang 1” below) in view of Zhang et al. (US 2017/0067090 A1; “Zhang 2” below) and further in view of Campbell et al. (Molecular Ecology Resources 2015; 15: 855-867).6
As discussed above, the teachings of Zhang 1 in view of Zhang 2 render obvious the compositions of claims 1, 16, 19, 23-25, 27, 28, 45-47, 50, 53, 58, 59, and 62.
These references do not teach or suggest that each of the Forward Primers in the composition containing a plurality of Forward Primers contains a Universal Forward Adapter subsequence at or near the 5’ end as recited in claim 26, nor do they teach or suggest that each Reverse Primer in the composition contains a Universal Reverse Adapter subsequence at or near the 5’ end as recited in claim 30.
Prior to the effective filing date of the claimed invention, though, it would have been prima facie obvious to modify the Forward and/or Reverse Primers in the compositions suggested by Zhang 1 in view of Zhang 2 to contain a 5’ Universal Adapter subsequence. Campbell provides motivation to do so by teaching that 5’ Universal Adapter subsequences (e.g., sequencing adapters) may be added to amplification primers to facilitate a downstream sequencing step (see, e.g., Fig. 1 on p. 857). The ordinary artisan would have been motivated to obtain the ability to sequence amplification products generated using the compositions suggested by Zhang 1 in view of Zhang 2 since sequencing amplicons was generally desirable. Campbell also provides motivation to incorporate sequencing adapters into the primers by noting that sequencing can be used “to both identify and genotype thousands to millions of SNPs directly from sequencing data” (p. 855, col. 1). This teaching of Campbell would have been relevant to the user of the compositions suggested by Zhang 1 in view of Zhang 2 since Zhang 1 taught that the disclosed compositions could be used for SNP analysis (see, e.g., paras. 8 and 250-251). The ordinary artisan would have had a reasonable expectation of success in view of the guidance provided by Campbell as to adapter design and incorporation of the adapters into primers (pp. 856-858 and Fig. 1). Thus, the compositions of claims 26 and 30 are prima facie obvious in view of the combined teachings of the cited references.
Conclusion
17. No claims are currently allowable.
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/ANGELA M. BERTAGNA/Primary Examiner, Art Unit 1681
1 None of the claims requires the oligonucleotides to have any particular/specific nucleotide sequence.
2 As discussed below, claim 28 lacks proper antecedent basis for “the Template molecule.” The claim may have been intended to depend from claim 27. Nevertheless, it is clear that claims 27 and 28 further require the composition to contain a Template molecule and a Reverse Primer.
3 It is noted that Figure 2 and para. 58 describe an embodiment in which the Initiation Subsequence is not complementary to the Template. As discussed in the indefiniteness rejection, though, the structural requirements of an Initiation Subsequence are not clear, and it is not clear that an Initiation Subsequence is required to not be complementary to the Template as shown in Figure 2. Therefore, it is not clear that an Initiation Subsequence is not complementary to the Template nucleic acid, and as such, indistinguishable structurally and functionally from its naturally occurring counterpart.
4 Each of these references was cited in the last Office action.
5 As noted above, the specification defines “stoichiometric ratio” as equivalent to “molar ratio” in para. 83.
6 Zhang 1 and Zhang 2 were cited in the last Office action. Campbell is newly cited.