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 without traverse of Group I in the reply filed on May 14, 2026 is acknowledged. As noted by Applicant in the response of May 14, 2026, all of the currently pending claims read on the elected invention.
Claims 2-8, 10, 13, 19-20, and 22-30 are examined on the merits herein.
Priority
3. All of the pending claims have an effective filing date of June 17, 2020 (i.e., the filing date of Provisional Application Serial No. 63/040,292).
Provisional Application Serial No. 62/933,299, which was filed on November 8, 2019, does not disclose the use of caged nucleotides as required by all of the pending claims.
Information Disclosure Statements
4. Applicant’s submission of an Information Disclosure Statement (IDS) on the following dates is acknowledged: August 25, 2023; November 6, 2023; February 2, 2024; May 6, 2024; September 25, 2024; December 19, 2024; March 27, 2025; June 24, 2025; and May 14, 2026.
One reference on the IDS filed on August 25, 2023 has been lined through as a duplicate citation. All of the other references have been considered.
Drawings
5. The drawings filed on May 24, 2023 are objected to for two reasons.
First, the drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description: 706.
Corrected drawing sheets in compliance with 37 CFR 1.121(d), or amendment to the specification to add the reference character(s) in the description in compliance with 37 CFR 1.121(b) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Second, the drawings are objected to as failing to comply with 37 CFR 1.84(p)(4) because reference character “707” has been used to designate both “photolysis” and “a probe oligonucleotide.” More specifically, Figure 7B and the accompanying description at page 33, last paragraph use reference character “707” is used to designate “a probe oligonucleotide,” but Figures 7C and 7D apparently use reference character “707” to designate “photolysis” (see also page 34, first full paragraph).
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
6. The specification is objected to because the continuity information in the first paragraph should be updated to state that prior-filed Application Serial No. 17/573,126 has issued as US 11,702,698.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
7. 37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, 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 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 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”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 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 statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - This application fails to comply with the requirements of 37 CFR 1.831-1.834 because it does not contain a “Sequence Listing XML” as a separate part of the disclosure. A “Sequence Listing XML” is required because each of Figures 4A, 4B, 5A, 5B, 6A, 6B, and 7A-7D contains an oligonucleotide sequence(s) within the definition set forth in 37 CFR 1.831(a). These figures identify the oligonucleotides with Sequence Identifiers, but a “Sequence Listing XML” has not been filed.
Required response - Applicant must provide:
• A “Sequence Listing XML” part of the disclosure, as described above in item 1. or 2.; together with
o A statement that indicates the basis for the amendment, with specific references to particular parts of the application as originally filed, as required by 37 CFR 1.835(a)(3);
o A statement that the “Sequence Listing XML” includes no new matter as required by 37 CFR 1.835(a)(4)
AND
• A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required incorporation by reference paragraph as required by 37 CFR 1.835(a)(2), consisting of:
o A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
o A copy of the amended specification without markings (clean version); and
o A statement that the substitute specification contains no new matter.
Claim Objections
8. Claim 6 is objected to because “360nm” in line 3 should be replaced with “360 nm”.
Claim Rejections - 35 USC § 112
9. 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 2-8, 10, 13, 19-20, and 22-30 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 2 is indefinite for two reasons.
First, claim 2 is indefinite because it is not clear as to how the recited method steps accomplish the objective set forth in the preamble of “enhancing binding specificity of an analyte binding moiety to a protein in a biological sample.” The caged nucleotides in the capture binding domain of the oligonucleotide portion of the of the analyte binding moiety apparently enhance binding specificity between said capture binding domain and the capture domain in the capture probes (see steps (b) and (c)), but they do not appear to affect binding between the protein analyte and the protein analyte-binding portion of the analyte binding moiety as stated in the preamble. Applicant could address the issue by deleting the preamble from the claim. Alternatively, Applicant could amend the preamble to more accurately describe the binding specificity enhancement resulting from the presence of the caged nucleotides.
Second, claim 2 is indefinite because it is not clear whether step (c) requires releasing the caged moiety from all caged nucleotides in the capture binding domain or if release of the caged moiety in just one of the plurality of caged nucleotides is encompassed.
Claims 3-8, 10, 13, 19-20, and 22-30 are also indefinite since they depend from independent claim 2 and do not correct its indefiniteness issues.
Claims 4-8 are also indefinite for an additional reason. These claims depend from claim 2 and either further limit the step of releasing the caged moiety (claims 4-6) or the structural features of the caged nucleotide (claims 7-8). As noted above with respect to claim 2, it is not clear whether step (c) in claim 2 requires releasing the caged moiety from all caged nucleotides in the capture binding domain or if releasing the caged moiety from just one caged nucleotide is encompassed. As a result, it is not clear whether the additional limitations in claims 4-8 further limit all of the caged nucleotides in the plurality or if they only limit as few as one caged nucleotide in the plurality.
Claim Rejections - 35 USC § 103
10. 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.
11. Claims 2-5, 7, 8, 10, 13, 19, 20, 22-25, 27, and 30 are rejected under 35 U.S.C. 103 as being unpatentable over Zhou et al. (US 2018/0057873 A1; IDS reference) in view of Deiters et al. (US 2010/0099159 A1).
The instant claims are drawn to a method that comprises binding a protein in a biological sample to an analyte binding moiety (e.g., an antibody, antibody fragment, or an aptamer), wherein the analyte binding moiety is associated with an oligonucleotide comprising a capture binding domain. The capture binding domain contains a plurality of caged nucleotides that block binding of the capture binding domain to a complementary portion of a capture probe located on a substrate. The method further comprising releasing the caged moiety from the capture binding domain to allow hybridization of the capture binding domain to the capture probe.
Regarding claim 2, Zhou discloses a method for detecting a protein analyte in a biological sample (see Figs. 5A and 5B and the accompanying description in paras. 12 and 36; see also para. 5 for a broader description of the method shown in Figures 5A & 5B). And more specifically, as can be seen in Figures 5A and 5B and para. 36, the method of Zhou comprises the following steps: (a) contacting a biological sample with a substrate comprising a plurality of capture probes, wherein the capture probes contain a spatial barcode (element 507) and a capture domain (e.g., element 509); and
(b) binding an analyte binding moiety (antibody 506) to the protein to be detected, wherein the analyte binding moiety is associated with an oligonucleotide (element 504) that may include an analyte binding moiety barcode (element 513) and also a capture binding domain (e.g., element 511).
Further regarding claim 2, although the embodiment shown in Figures 5A & 5B and described in para. 36 uses a helper probe (element 502) to facilitate ligation of the capture probe to the antibody-conjugated oligonucleotide (see also para. 36), Zhou also teaches that the antibody-conjugated oligonucleotide may be annealed to the capture probe (see, e.g., para. 5).
Regarding claim 3, Zhou teaches that the method can be used to quantify the amount of an analyte in a biological sample (para. 19).
Regarding claims 10 and 22, Zhou teaches that the method may further comprise determining (i) all or part of the sequence of the oligonucleotide hybridized to the capture probe, or a complement thereof, and (ii) the sequence of the spatial barcode, or a complement thereof, and using the determined sequences to identify the location of the protein in the biological sample (see, e.g., para 5; see also paras. 104-110 for additional discussion of the sequencing step).
Regarding claim 13, Zhou teaches that the analyte binding moiety is an antibody (see, e.g., Figs. 5A & 5B; see also paras. 12 and 36). Zhou additionally teaches that an antibody fragment or an aptamer may be used as the analyte binding moiety (see, e.g., paras. 5 and 34).
Regarding claim 23, Zhou further teaches that the capture probe may contain a primer sequence (see, e.g., para. 36).
Regarding claim 30, Zhou further teaches that the method may include extending the capture probe using the oligonucleotide hybridized thereto as a template, thereby generating a spatially barcoded extension product (see, e.g., para. 5).
Zhou is not anticipatory because the reference does not teach that the capture binding domain in the antibody-conjugated oligonucleotide contains a plurality of caged nucleotides as required by independent claim 2. As a result, Zhou also does not meet the additional requirements set forth in claims 4-8, 19, 20, 24, and 25 concerning the caged nucleotides.
Deiters, though, discloses a variety of caged nucleotides (paras. 4-37 and Examples 1-5 on pages 10-18) and additionally teaches that caging nucleotides can offer “spatial and temporal control of the function of oligonucleotides” (para. 82). The reference also teaches that nucleic acid amplification methods, such as PCR, can benefit from the presence of caged nucleotides in the primers since the caged nucleotides allow one to control when the primers are active (i.e., able to anneal to a complementary sequence) and reduce nonspecific amplification (para. 82; see also Example 6 on pages 18-20, esp. paras. 126-129 and 133).
Further regarding claim 2 and also regarding claims 4 and 5, Deiters also describes using photolysis to remove the caging moiety from caged nucleotides, thereby allowing the oligonucleotide containing the newly uncaged nucleotides to function as intended (see, e.g., paras. 81, 83-84, and 127-129).
Further regarding claims 7, 8, and 25, the caged nucleotides disclosed in Deiters include 6-nitropiperonyloxymethyl (NPOM)-caged thymidine (see, e.g., Example 1 on pages 10-12). Deiters additionally teaches NPOM-caged guanosine in Examples 2 and 3 on pages 12-14 and NPOM-caged deoxyadenosine and NPOM-caged deoxycytidine (Example 5 on pages 15-18).
Further regarding claims 19 and 20, Deiters teaches oligonucleotides containing more than 10% caged nucleotides (see Table 1 on page 19, where primers P4-P7 are taught). Deiters also teaches that up to 30% or up to 50% of the nucleotides in an oligonucleotide may be caged nucleotides (para. 79). These ranges overlap with the range recited in claim 20.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for the ordinary artisan to modify the antibody-conjugated oligonucleotide used in the method of Zhou to contain a plurality of caged nucleotides 2-and then release the caging moiety via photolysis when it is desired to hybridize the antibody-conjugated oligonucleotide to the surface-immobilized capture probe. Deiters provides motivation to do so by teaching that caged nucleotides offer the ability to spatially and temporally control the function of oligonucleotides, including in reactions comprising a hybridization step (i.e., PCR as discussed in Example 6 of Deiters) (paras. 82 and 126-129 and 133). Deiters provides additional motivation by teaching that reduced nonspecific amplification was observed when a PCR was conducted using primers containing caged nucleotides (para. 133). The ordinary artisan would have recognized from these teachings of Deiters that incorporating caged nucleotides into the antibody-conjugated oligonucleotide of Zhou would offer the analogous benefit of reducing nonspecific hybridization via the ability to control when said oligonucleotide is active (i.e., capable of hybridizing to its complementary sequence). The ordinary artisan would have had a reasonable expectation of success in view of the guidance throughout Deiters concerning the synthesis of caged nucleotides and the use of photolysis to release the caging moiety. Thus, the methods of claims 2-5, 7, 8, 10, 13, 19, 22, 23, 25, and 30 are prima facie obvious.
Further regarding claim 20, as noted above, Deiters teaches an overlapping range for the percentage of caged nucleotides in an oligonucleotide (para. 79). As well, no evidence of unexpected results has been presented with respect to the claimed range. This is sufficient to establish a prima facie case of obviousness per MPEP 2144.05 I. Thus, the method of claim 20 is also prima facie obvious.
Further regarding claim 24, it also would have been prima facie obvious for the ordinary artisan to design the antibody-conjugated oligonucleotide suggested by Zhou in view of Deiters such that at least two caged nucleotides are located at the 3’ end of the oligonucleotide. Deiters provides motivation to do so by first teaching that “[T]he number of caging groups and the position of the caged thymidine residues affected DNA hybridization” and going on to teach that placement at or near the 5’ end of an oligonucleotide primer was less effective in blocking hybridization (para. 127). Accordingly, the ordinary artisan seeking to control when the antibody-conjugated oligonucleotide of Zhou hybridizes to the capture probe would have been motivated to place caged nucleotides at the 3’ end to maximize the ability to block hybridization until release of the caging moieties. Thus, the method of claim 24 is also prima facie obvious.
Further regarding claim 27, it also would have been prima facie obvious for the antibody-conjugated oligonucleotide used in the method of Zhou in view of Deiters to contain a polyA sequence as the portion that hybridizes to the capture probe. The ordinary artisan would have recognized that any nucleic acid sequence could be chosen as the sequence that hybridizes to the capture probe, and accordingly, would have been motivated to select a sequence routinely used for capture with a reasonable expectation of success. As well, since Zhou used polyA-poly(dT) binding to capture nucleic acids (paras. 27-28), the ordinary artisan would also have been motivated to use the same binding interaction when analyzing protein analytes as in Figure 5 of Zhou since doing so may allow one to use the same hybridization conditions for protein and mRNA analytes in the sample. Thus, the method of claim 27 is also prima facie obvious.
12. Claim 6 is rejected under 35 U.S.C. 103 as being unpatentable over Zhou et al. (US 2018/0057873 A1; IDS reference) in view of Deiters et al. (US 2010/0099159 A1) and further in view of Rodrigues-Correia et al. (Organic Letters 2013; 15: 5500-5503).
As discussed above, the teachings of Zhou in view of Deiters render obvious the method of claims 2-5, 7, 8, 10, 13, 19, 20, 22-25, 27, and 30.
Regarding claim 6, as discussed above, Deiters teaches using photocleavage to release the caging moiety from the caged nucleotides, but the reference does not teach using light with a wavelength below 360 nm for this purpose.1
Prior to the effective filing date of the claimed invention, though, it would have been prima facie obvious to substitute any or all of the caged nucleotides suggested by Deiters with any other known caged nucleotide (e.g., any of the caged nucleotides shown in Figure 1 of Rodrigues-Correia). The ordinary artisan would have recognized that other caged nucleotides (i.e., the caged nucleotides discussed in Rodrigues-Correia) would show the same ability to block hybridization between the antibody-conjugated oligonucleotide and surface-immobilized capture probe, and accordingly, would have been motivated to substitute one for the other with a reasonable expectation of success, particularly since no evidence of expected results has been presented with respect to the type of caged nucleotide. Then, since the pHP caging moiety disclosed in Rodrigues-Correia requires the use of shorter wavelength light for uncaging (Table 1 on page 5502), the ordinary artisan would have been motivated to perform the uncaging step using a wavelength of light below 360 nm. Lastly, attention is directed to MPEP 2144.06 and 2144.07, where it is noted that, in the absence of unexpected results, it is prima facie obvious to substitute art-recognized equivalents known to be useful for the same purpose or to select a known material based on its suitability for the intended purpose. Thus, the method of claim 6 is prima facie obvious.
13. Claim 26 is rejected under 35 U.S.C. 103 as being unpatentable over Zhou et al. (US 2018/0057873 A1; IDS reference) in view of Deiters et al. (US 2010/0099159 A1) and further in view of Peter et al. (US 2015/0148239 A1).
As discussed above, the teachings of Zhou in view of Deiters render obvious the method of claims 2-5, 7, 8, 10, 13, 19, 20, 22-25, 27, and 30.
Regarding claim 26, Zhou does not teach that the capture probe contains a unique molecular identifier (UMI). Deiters does not remedy this deficiency in Zhou.
Prior to the effective filing date of the claimed invention, though, it would have been prima facie obvious to further include a UMI in the capture probes of Zhou. Peter provides motivation to do so by teaching that such a sequence offers the ability to have “a unique barcode for each individual template molecule” (para. 67), which ultimately allows one to “infer how many individual template molecules were sampled, and how many sequencing reads arose from PCR duplicates” (para. 95; see also para. 79 for further description of the “counters” of Peter, which are UMIs). The ordinary artisan would have had a reasonable expectation of success in view of the guidance provided by Peter (see, e.g., paras. 67, 79, and 95) and also in view of the similarity of the two methods (i.e., the similarity between Figs. 5A & 5B of Zhou and Fig. 7 of Peter). Thus, the method of claim 26 is prima facie obvious.
14. Claims 28 and 29 are rejected under 35 U.S.C. 103 as being unpatentable over Zhou et al. (US 2018/0057873 A1; IDS reference) in view of Deiters et al. (US 2010/0099159 A1) and further in view of Ryazantsev et al. (Biochemistry (Moscow) 2016; 81: 1754-1770).
As discussed above, the teachings of Zhou in view of Deiters render obvious the method of claims 2-5, 7, 8, 10, 13, 19, 20, 22-25, 27, and 30.
Regarding claim 28, the teachings of Zhou in view of Deiters do not teach or suggest that the protein analyte is an antibody.
Regarding claim 29, Zhou teaches that the analyte binding moiety (i.e., the antibody in Fig. 5A) may be conjugated to the oligonucleotide (504) using “any known chemistry” (para. 35), but the reference does not specify that a cleavable linker is used for the conjugation. Deiters does not remedy this deficiency in Zhou.
Prior to the effective filing date of the claimed invention, though, it would have been prima facie obvious for the ordinary artisan to use the method suggested by Zhou in view of Deiters to detect antibody analytes. Ryazantsev provides motivation to do so in section 7 of the table on page 1764 and also at page 1765, column 2 by teaching that antibodies are a desirable target for detection via immunoPCR, which is similar to the method of Zhou in that immunoPCR involves binding an oligonucleotide-tagged antibody to a protein analyte followed by amplification of the oligonucleotide tag (see, e.g., Fig. 1 of Ryazantsev). The ordinary artisan would have had a reasonable expectation of success in view of the similarities between the method of Zhou and immunoPCR and also since Zhou imposes no limits on the type of protein analytes that can be detected. Thus, the method of claim 28 is prima facie obvious.
It also would have been prima facie obvious to use a cleavable linker to conjugate the oligonucleotide to the analyte binding moiety (antibody) when practicing the method suggested by Zhou in view of Deiters. As noted above, Zhou teaches that “any known chemistry” may be used to attach the oligonucleotide to the antibody. Then, since Ryazantsev teaches that cleavable linkers were known to be suitable for this purpose (see, e.g., page 1757, col. 2 – page 1759, col. 1; see also page 1760, col. 1), the ordinary artisan would have had motivation and a reasonable expectation of success in using this “known chemistry” for the intended purpose of conjugating an oligonucleotide to an antibody in the method of Zhou in view of Deiters. See also MPEP 2144.07, which notes that it is prima facie obvious to select a known material or method based on its suitability for the intended purpose in the absence of unexpected results. In this case, no evidence of unexpected results has been presented. Thus, the method of claim 29 is also prima facie obvious.
Conclusion
15. No claims are currently allowable.
Schnall-Levin et al. (WO 2020/047004 A2) is cited as a reference of interest for its disclosure in Figure 10 and pages 76-77, where an antibody-conjugated oligonucleotide is hybridized to an immobilized oligonucleotide containing a spatial barcode. As with the Zhou reference cited above, Schnall-Levin does not teach the use of caged nucleotides.
Yang et al. (Molecules 2021; 26: 1481) is also cited as a reference of interest for its review of caged nucleotides.
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.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Gary Benzion can be reached at 571-272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/ANGELA M. BERTAGNA/Primary Examiner, Art Unit 1681
1 It is noted that para. 95 states that irradiation with UV light of 356 nm was used for photocleavage, but this seems to be a clear typographical error since the paragraph gives the epsilon value for 365 nm and the remainder of the reference uses UV light of 365 nm for photocleavage.
Prosecution Insights