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 .
Status of the Application
2. Applicant’s response filed on May 26, 2026 is acknowledged.
Claims 1, 19, 23, 26-28, 30, 45-47, 53, 58, 59, 62, 64, and 105 are pending.
Claims 1, 19, 23, 26-28, 30, 45-47, 53, 58, 59, and 62 are under examination.
Claims 64 and 105 remain withdrawn from consideration as being drawn to a non-elected invention.
Response to Arguments
3. Applicant’s arguments filed on May 26, 2026 have been fully considered.
Sequence Listing/Objection to the Specification
The response does not explicitly address the objections concerning the Sequence Listing and specification. The objections have been withdrawn as moot in view of the specification amendment filed with the response.
Claim Objections
The response does not explicitly address the objections to claims 26 and 53. The objections have been withdrawn as moot in view of the amendments to both claims.
Rejection of claims 1, 16, 19, 23-25, 27, 28, 45-47, 50, 53, 58, 59, and 62 under 35 U.S.C. 101
Applicant argues that the rejection should be withdrawn (Remarks, pages 8-11). More specifically, Applicant argues that the rejection fails to demonstrate that the claimed compositions are found in nature and also fails to consider the combination of components that make up the claimed composition as a whole (see, in particular, pages 10-11 of the Remarks). Applicant also argues that the claimed composition “exhibits a functional capability, selective amplification of variant sequences via suppressor displacement, that is not a natural property of isolated nucleic acids or polymerases” (Remarks, page 10). Therefore, Applicant argues, the answer to Step 2A of the subject matter eligibility analysis would be “no,” and the claims would, in fact, qualify as eligible subject matter (Remarks, pages 10-11). Applicant further argues that the claimed compositions have “enhanced specificity for variant sequences and the ability to selectively enrich target nucleic acids across a defined region” and that “[T]hese properties arise from the claimed structural and functional relationships among the components, and not from any individual component alone” (Remarks, page 11). Therefore, Applicant argues, the answer to Step 2B of the eligibility analysis is “yes,” and the claims amount to significantly more than the judicial exceptions (Remarks, page 11).
These arguments have been fully considered, but they were not persuasive.
Initially, it is noted that the examiner agrees that a naturally occurring composition containing the required oligonucleotides and polymerase does not appear to exist. The naturally occurring counterpart analysis, though, does not require identification of a single naturally occurring counterpart containing all of the required components of the composition as Applicant’s arguments in the first full paragraph on page 11 of the Remarks appear to suggest. What is required is to consider the properties of the naturally occurring counterparts together in the composition (i.e., as a whole). Alone, the oligonucleotides in the claimed compositions each perform their naturally occurring function of hybridization to a complementary sequence, and the polymerase also performs its naturally occurring function of catalyzing nucleic acid replication. In combination (i.e., when the composition is considered as a whole), the same naturally occurring functions occur. That is, the oligonucleotides in the composition hybridize to their complementary sequences, and the polymerase functions to catalyze nucleic acid replication.
It is acknowledged that the claimed compositions are used for selective enrichment and amplification, but this does not result from anything other than the naturally occurring functions of the composition components. Put another way, the natural laws governing the kinetics and thermodynamics of nucleic acid hybridization and the naturally occurring properties of the polymerase control the hybridization and displacement reactions discussed in Applicant’s arguments.
It is also noted that the instant situation is not analogous to the example of the modified bacterium discussed in MPEP 2106.04(c)(C)(1). In that case, the modified bacterium had a new functional characteristic, namely the ability to degrade different hydrocarbons compared to the naturally occurring bacterium. In this case, though, there is no changed functional characteristic relative to the naturally occurring counterparts because the oligonucleotides in the claimed composition simply hybridize according to the laws of thermodynamics and kinetics and the polymerase acts as it does in nature to catalyze extension. The facts in this case, therefore, more closely match the discussion in MPEP 2106.04(c)(C)(2), where primers were determined to lack markedly different characteristics from their naturally occurring counterparts. The primers discussed in MPEP 2106.04(c)(C)(2) may have been able to amplify target DNA with a high degree of specificity and sensitivity, analogous to Applicant’s arguments regarding the claimed compositions, but this does not change the fact that this ability is based on the innate ability of nucleic acids to bind to complementary sequences. Therefore, the answer to Step 2A of the eligibility analysis remains “yes.” That is, the claims are still considered to be directed to a judicial exception.
Lastly, in response to Applicant’s arguments regarding Step 2B of the eligibility analysis, it is noted that, in discussing Step 2B, MPEP 2106.05 I states that “An inventive concept ‘cannot be furnished by the unpatentable law of nature (or natural phenomenon or abstract idea) itself.’ Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016).” This section of the MPEP additionally states that the Step 2B analysis requires asking what else is present in the claim besides the judicial exception. In this case, as discussed in the rejection, there are no other elements in the claims other than the judicial exceptions. As a result, the claims necessarily do not contain significantly more than the judicial exception.
Since Applicant’s arguments were not persuasive, the rejection has been maintained with modifications to address the claim amendments and cancellations.
Rejection of claims 23-28, 30, 45-47, 50, 53, 59, and 62 under 35 U.S.C. 112(b)
Applicant argues that the rejection is moot in view of the amendments to claims 23, 27, 28, 46, 47, and 59 and the cancellation of claims 24, 25, and 50 (Remarks, page 12).
This argument was persuasive. The rejection has been withdrawn.
Rejection of claims 16, 24, and 25 under 35 U.S.C. 112(d)
Applicant argues that the rejection should be withdrawn in view of the amendments to claims 1 and 23 and the cancellation of claims 24 and 25 (Remarks, page 12).
This argument was persuasive. The rejection has been withdrawn.
Rejection of claims 1, 16, 19, 23-25, 27, 28, 45-47, 50, 53, 58, 59, and 62 under 35 U.S.C. 103 as being unpatentable over Zhang 1 in view of Zhang 2
Applicant argues that the rejection should be withdrawn for several reasons (Remarks, pages 12-15).
More specifically, Applicant first notes that since Zhang 1 discloses a “primer duplex system” rather than the separate primer required by the claims, the reference fails to teach or suggest the claimed three-component system, which comprises a Forward primer, a Suppressor oligonucleotide, and an Auxiliary oligonucleotide (Remarks, pages 12-13). Applicant then argues that Zhang 2 fails remedy this deficiency in Zhang 1 because the compositions of Zhang 2, in which a primer and blocker oligonucleotide compete for binding to a target nucleic acid, are also fundamentally different from the claimed three-component system (Remarks, page 13). Put another way, Applicant first argues that the references fail to teach or suggest the particular oligonucleotides and relationships between them required by the instant claims, particularly since the references are fundamentally different both from one another and also from the claimed invention (Remarks, pages 13-14). Second, Applicant additionally argues that the proposed modification would render Zhang 1 unsuitable for its intended purpose (Remarks, pages 13-14). Third, Applicant argues that the rejection is the result of impermissible hindsight and fails to provide sound reasoning for combining Zhang 1 and Zhang 2 to arrive at the claimed compositions. Fourth, Applicant argues that a reasonable expectation of success is lacking (Remarks, pages 14-15).
These arguments have been fully considered, but they were not persuasive for the following reasons.
Applicant’s first argument that the references fail to teach or suggest the claimed compositions was unpersuasive because the references do, in fact, suggest the claimed compositions for the reasons set forth in the rejection. Briefly, as discussed in the rejection, Zhang 1 discloses a composition comprising a nucleic acid polymerase, an oligonucleotide that corresponds to the claimed Auxiliary oligonucleotide, and an oligonucleotide that corresponds to the claimed Suppressor oligonucleotide. The composition of Zhang 1 lacks the required Forward primer, but Zhang 2 provides a reason to include such a primer in the compositions of Zhang 1, particularly when the compositions disclosed in, e.g., Figs. 1A and 1B of Zhang 1 are used as probes. More specifically, since Zhang 2 taught that competitive binding between a probe and primer was advantageous in an amplification reaction, the ordinary artisan would have been motivated to design a Forward primer having the claimed features when using the double-stranded probes disclosed in Zhang 1 in an amplification method to obtain the same benefit of improved specificity and sensitivity.
It is acknowledged that the claimed composition contains three oligonucleotides, whereas the compositions of Zhang 1 and Zhang 2 each contain two oligonucleotides. Nevertheless, the combined teachings of the cited references suggest a composition with the required three oligonucleotides for the reasons set forth in the rejection.
Applicant’s argument that the rejection improperly changes the principle of operation of Zhang 1 was also unpersuasive. The rationale set forth in the rejection does not, in fact, alter the principle of operation of Zhang 1 since the double-stranded probes of Zhang 1 would still function as probes. The rejection only proposes adding a forward primer to the embodiment of Zhang 1 in which the double-stranded oligonucleotides disclosed, e.g., in Figs. 1A and 1B of Zhang 1, are used as probes rather than primers to expand the number of methods for using the double-stranded probes of Zhang 1.
Applicant’s argument that the rejection results from impermissible hindsight was also unpersuasive. In response to this argument, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971). In this case, a rationale is set forth in the rejection that is based, not on the disclosure of the instant application, but on the teachings of Zhang 1 and Zhang 2 in combination with the knowledge and abilities possessed by the ordinary artisan. Briefly, as discussed in the rejection, since Zhang 2 taught that competitive binding between a probe and primer was advantageous in an amplification reaction, the ordinary artisan would have been motivated to design a Forward primer having the claimed features when using the double-stranded probes disclosed in Zhang 1 in an amplification method to obtain the same benefit of improved specificity and sensitivity.
Lastly, Applicant’s argument that a reasonable expectation of success is lacking was unpersuasive. The rejection explains in detail as to how the ordinary artisan would have used the teachings of the references in combination with the general knowledge possessed available prior to the effective filing date to arrive at the claimed compositions. It is also noted that no evidence other than attorney arguments has been provided to support the argument that a reasonable expectation of success is lacking. This is not sufficient per the guidance in MPEP 2145.
Since Applicant’s arguments were not persuasive, the rejection has been maintained with modifications to address the claim amendments and cancellations.
Rejection of claims 26 and 30 under 35 U.S.C. 103 as being unpatentable over Zhang 1 in view of Zhang 2 and further in view of Campbell
Applicant argues that the rejection should be withdrawn because Campbell does not remedy the deficiencies in Zhang 1 and Zhang 2 (Remarks, page 15).
This argument was not persuasive because the combination of Zhang 1 and Zhang 2 is not deficient for the reasons set forth above. The rejection has been maintained with minor modifications to address the claim amendments and cancellations.
Claim Interpretation
4. 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
5. Claim 26 is objected to because “each” in line 2 is unnecessary and should be deleted.
Claim Rejections - 35 USC § 101
6. 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, 19, 23, 27, 28, 45-47, 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 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.
Claim 23
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.
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 composition of claim 23 need not possess any structural or functional differences relative to their naturally occurring counterparts. As with claim 1, the judicial exceptions in claim 23 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, claim 23 is directed to a judicial exception without significantly more, and accordingly, are rejected under 35 U.S.C. 101.
Claims 27, 28, 45-47, 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.
Claims 45-47 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 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.2 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, 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, 19, 23, 27, 28, 45-47, 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
7. 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.
Claim 46 is 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 46 has been amended to depend from claim 47. This causes the claim to no longer “contain a reference to a claim previously set forth” as required by the statute. Accordingly, claim 46 is rejected as not complying with 35 U.S.C. 112(d). Applicant could address the issue by canceling claim 46 and presenting a new claim (claim 122) that depends from claim 47.
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
8. 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.
9. 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.
10. Claims 1, 19, 23, 27, 28, 45-47, 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).3
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 any portion of 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). As well, 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.
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 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 claim 23, which depends 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 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 composition of claim 23 is 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.
Further regarding claims 46 and 47, which depend directly or indirectly from claim 45, it also would have been prima facie obvious (i) to modify the Suppressor oligonucleotide of Zhang 1 to contain an Initiation Subsequence at the 3’ end, 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. Zhang 1 does not teach that the Complement Probe, which corresponds to the claimed Suppressor oligonucleotide, contains an Initiation Subsequence (i.e., a sequence that is not complementary to a Target nucleic acid 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).
Lastly, further regarding the amendments to claim 47, as 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 (i.e., an Initiation Complement Subsequence) added to the 3’ end of the Suppressor oligonucleotide to facilitate this binding.
Thus, the compositions of claims 46 and 47 are prima facie obvious.
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).4 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, 19, 23, 27, 28, 45-47, 53, 58, 59, and 62 are prima facie obvious over Zhang 1 in view of Zhang 2.
11. 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).5
As discussed above, the teachings of Zhang 1 in view of Zhang 2 render obvious the compositions of claims 1, 19, 23, 27, 28, 45-47, 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
12. No claims are currently allowable.
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 Angela Bertagna whose telephone number is (571)272-8291. The examiner can normally be reached 8-5, M-F.
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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 It is noted that Figure 2 and para. 58 describe an embodiment in which the Initiation Subsequence is not complementary to the Template. Claims 46 and 47, though, do not require the Initiation Subsequence to not be complementary to the Template nucleic acid. Accordingly, there need not be a structural or functional difference compared to the naturally occurring counterpart.
3 Each of these references was cited in the last Office action.
4 As noted above, the specification defines “stoichiometric ratio” as equivalent to “molar ratio” in para. 83.
5 Zhang 1 and Zhang 2 were cited in the last Office action. Campbell is newly cited.
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