DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s arguments and amendments have been thoroughly reviewed and considered. Claims 9 and 14-19 have been canceled. Claims 43-47 are newly added. Claims 1-8, 10-13, 20-22, and 43-47 are pending and are examined on the merits herein.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 2/2/2026 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Response to Applicant’s Amendments
Nucleotide and/or Amino Acid Sequence Disclosures
The Sequence Disclosure and Specification were objected to for not labeling all sequences with sequence identifiers, for not providing a Sequence Listing, and for providing a defective Sequence Incorporation by Reference paragraph. Applicant has provided a new Sequence Listing, and has provided sequence identifiers for the sequences present in the specification. Applicant has also amended the Sequence Incorporation by Reference paragraph. These objections are maintained-in-part, as the Sequence Incorporation by Reference paragraph is still defective. See “Nucleotide and/or Amino Acid Sequence Disclosures” below.
Claim Objections
Claims 5, 12, and 16-17 were objected to for minor informalities. In light of Applicant’s amendments to the claims submitted 2/2/2026, these objections have been withdrawn for all currently pending claims. Claims 16-17 and 19 have been canceled, and so these objections have been rendered moot.
35 USC 112(b) Rejections
Claims 2-5, 16-17, and 19-20 were rejected for various indefiniteness issues. In light of Applicant’s amendments to the claims submitted 2/2/2026, these rejections have been withdrawn for all currently pending claims. Claims 16-17 and 19 have been canceled, and so these rejections have been rendered moot. However, see new grounds of rejection below.
35 USC 112(d) Rejections
Claim 21 was rejected for failing to further limit the subject matter of the claim upon which it depends. In light of Applicant’s amendments to the claims submitted 2/2/2026, this rejection has been withdrawn.
35 USC 103 Rejections
Claims 1-22 were rejected under 35 U.S.C. 103 as being unpatentable over Halbert et al. (US 2016/0003835 A1) and various combinations of references. In light of Applicant’s amendments to the claims submitted 2/2/2026, these rejections have been withdrawn for all currently pending claims. However, see new grounds of rejection and “Response to Applicant’s Arguments” below. Claims 9 and 14-19 have been canceled, and so these rejections have been rendered moot.
Nucleotide and/or Amino Acid Sequence Disclosures
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. Specifically, the Sequence Incorporation by Reference paragraph does not include the date of creation of the file.
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
The disclosure is objected to because of the following informalities: the Sequence Incorporation by Reference paragraph is defective, as noted above.
Appropriate correction is required.
Response to Applicant’s Arguments
Regarding the 35 USC 103 Rejections presented in the Non-Final Rejection, Applicant argues that Halbert does not teach several of the newly amended limitations added to claim 1, particularly first and second primers, aptamers with adapters complementary to those primers, and surface-based amplification.
It is noted that in newly amended claim 1, the second primers must be “orthogonal” to the first primers, which is defined in para. 38 of the instant specification as primers that substantially do not hybridize with one another. Regarding “surface-based amplification,” in newly amended claim 1, Applicant notes in para. 65 that such amplification may be bridge amplification, but does not specifically define the term. See also the 35 USC 112(b) Rejections below.
Halbert teaches that aptamer candidates may contain fixed sequences that are hybridization sites for PCR primers (para. 145), where preferably, the candidates have both a randomized portion and fixed portions necessary for efficient amplification, where the fixed sequences are 5’ and 3’ terminal sequences (para. 146). In para. 298, Halbert teaches that aptamers can also have 5’ leader and 3’ tail sequences that can facilitate primer binding. Example 1 and paras. 444-448 of the reference describe a method in which a target is affixed to a solid substrate along with aptamer candidates that contain 5’ and 3’ primer tails, and during aptamer selection, the aptamers can be amplified via primer binding to said tails. These teachings are considered to read on the claimed primers and adapters, and are incorporated into the rejections below. However, Halbert does not appear to teach that primers are in a well or attached to a substrate before the addition of the aptamers, nor does the reference teach the use of bridge amplification or direct use of the well surface for amplification.
Thus, due to Applicant’s amendments to the claims, new grounds of rejection are provided below. It is noted that the relevant portions of Halbert presented in the Non-Final Rejection are also reiterated below.
Claim Rejections - 35 USC § 112(b)
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 1-8, 10-13, 20-22, and 43-47 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.
As noted above, the term “surface-based amplification” does not have any specific definition in the instant specification. Therefore, this term as it appears in claims 1, 10, 13, and 22 is indefinite, as the term is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. That is, with the use of "surface-based amplification," it is unknown how and by what means a surface must be interacted with during amplification to be considered "surface-based”.
Claims 2-8, 10-13, 20-21, and 43-47 are also rejected due to their dependence on rejection claim 1.
Claims 10 and 12 are similarly also rejected due to the phrase “fluid-based amplification.” This term is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. That is, with the use of "fluid-based amplification," it is unknown how and by what means a fluid must be interacted with during amplification to be considered "fluid-based”.
Claims 11-13 are also rejected due to their dependence on rejected claim 10. Claim 13 is additionally rejected due to its dependence on rejected claim 12.
Claim Interpretation
It is noted that in the instant specification, an aptamer is defined as an oligonucleotide that has a tertiary structure causing that oligonucleotide to be selective for a target, and when an aptamer is selective for a target, this means that the aptamer couples to that particular target and not another target. An “aptamer candidate” is an oligonucleotide that may potentially be selective for a target (para. 51).
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1-3, 6-7, 10-13, 20-22, 43-44, and 47 are rejected under 35 U.S.C. 103 as being unpatentable over Halbert et al. (US 2016/0003835 A1) in view of Feagin et al. (WO 2019/236548 A1).
Halbert teaches methods for aptamer pools that bind to biomarkers of interest (Abstract). The aptamers are nucleic acid molecules having specific binding affinity to molecules through interactions other than classic Watson-Crick base pairing, and specifically can be DNA or RNA (paras. 7 and 21; instant claim 21). This specific binding affinity is considered to be selective as defined by the instant specification (see the “Claim Interpretation” above). This is further evidenced by para. 8 of Halbert, which states, “Aptamers…are capable of specifically binding to selected targets…” Halbert teaches method in which a target is tethered to a substrate and is contacted by a pool of aptamer candidates, and the aptamers which preferentially bind to the tethered target are isolated (paras. 56-57). Figure 13A and para. 125 show that this selection can involve a washing step to remove aptamer oligonucleotides unbound to a target. A similar method is shown in Figure 15B and para. 127. In particular, the method of para. 127 and Figure 15B recites identical interactions of the aptamer and target as in instant claim 1. The reference teaches the use of wells, particularly as substrates (e.g. paras. 27, 60, 101, 103, and 112), and so it would be possible to tether the targets to a well substrate. Halbert also teaches that a plurality of wells may be used (paras. 208 and 421). The wells may act as physical separations and may be used with arrays (para. 208).
Thus, though Halbert does not explicitly teach the use of wells with the target/aptamer methods described above, it would have been prima facie obvious for the ordinary artisan to use a well substrate with these methods of Herbert, attach a target to said well substrate, and then analyze a pool of aptamer candidates to obtain and analyze aptamers as described in instant claim 1. By utilizing wells, aptamer pools could easily be flowed or placed over the attached targets, and the well would provide a relatively easy surface to wash and remove unbound aptamers.
Additionally, the teachings provided above do not explicitly state that the aptamer candidates are provided to the bound targets via a fluid. However, Halbert teaches the use of microfluidic devices with the planar substrates and array-based assays of their invention (para. 229 and 233). Thus, it would also be prima facie obvious to use microfluidics to introduce aptamers candidates into the wells. This would allow for a more efficient introduction process that ensures that each well receives a similar amount and flow of fluid, and thus would ensure that similar amounts of aptamers are introduced into each well. This would reduce user error and create a more efficient methodology.
In methods of identifying the aptamer oligonucleotides, amplification and sequencing of the aptamers can be performed (paras. 39-40 and 55-56). Halbert teaches that aptamer candidates may contain fixed sequences that are hybridization sites for PCR primers (para. 145), where preferably, the candidates have both a randomized portion and fixed portions necessary for efficient amplification, where the fixed sequences are 5’ and 3’ terminal sequences (para. 146). In para. 298, Halbert teaches that aptamers can also have 5’ leader and 3’ tail sequences that can facilitate primer binding. Example 1 and paras. 444-448 of the reference describe a method in which a target is affixed to a solid substrate along with aptamer candidates that contain 5’ and 3’ primer tails, and during aptamer selection, the aptamers can be amplified via primer binding to said tails. Para. 198 also notes specifically that PCR can occur in wells on arrays. These 5’ and 3’ sequences on the aptamers are considered analogous to the claimed first and second adapters of the aptamers.
However, Halbert does not appear to teach that primers are in a well or attached to a substrate before the addition of the aptamers, nor does the reference teach the use of bridge amplification or direct use of the well surface for amplification.
Feagin teaches methods for screening aptamers to find those that have a binding affinity to a target molecule (Abstract). Specifically, the reference teaches the formation of clusters of aptamers on a solid support, where the aptamers can have adapter sequences at each end (para. 59). In para. 60, such cluster generation may be carried out via bridge amplification, where the aptamers are hybridized to short sequences on the solid support that contain sequences complementary to the first and section adapters (i.e. two distinct short sequences, one complementary to the first adapter and another complementary to the second, acting analogously to the claimed primers). Then, amplification and sequencing may occur (para. 61). Para. 63 of the reference notes that these methods may be performed within a flow cell that utilizes wells, where cluster generation creates many aptamers in each well that contain the same sequence. The reference teaches that their aptamer selection methods are efficient (paras. 56 and 72), and notes that performing clustering in wells specifically saves time during sequencing processes (para. 101).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to combine the teachings of Halbert and Feagin to arrive at the invention of instant claim 1. Specifically, both Halbert and Feagin teach aptamers with fixed sequences that can act as primer binding sites. Halbert does not particularly limit the amplification that may be performed in the methods of their invention (e.g. para. 39), and utilizing the bridge amplification teachings for aptamers of Feagin, the ordinary artisan would recognize that by having the primers for amplification attached to the well substrate, this would eliminate the need for the addition of primers later, particularly in free solution, thus simplifying the method. This also allows for amplification of the aptamers to occur on the wells, eliminating the need to capture aptamer candidates and amplify them outside of the wells, which would save on time and equipment. Keeping initial amplification on the wells also provides the efficiency benefits for sequencing described above in Feagin. These reasons would all be motivating to the ordinary artisan. There would be a reasonable expectation of success as the methods of Feagin are specifically noted to work with aptamers of the same structure as in Halbert, and are also stated to specifically work with wells in a flow cell.
Therefore, claims 1 and 21 are prima facie obvious over Halbert in view of Feagin.
Regarding claims 2-3 and 43-44, para. 640 of Halbert teaches that when analytes (i.e. targets of interest) are attached to a substrate, it may be through biotin-streptavidin binding. Para. 338 notes that targets may be attached to substrates through a linker, where said linker may be a biotinylated nucleic acid. Therefore, it would be prima facie obvious that the target of Halbert in view of Feagin could be linked to a biotinylated nucleic acid that binds to a streptavidin coated substrate (i.e. streptavidin coated wells).
Regarding claim 6, it is noted that “detection circuitry” is not defined in the instant specification, and so is considered any technology that is within or attached to the substrate that allows sequencing data to be obtained. In Halbert, Example 17 shows an aptamer selection protocol. In Step 8, aptamers are tested against particular targets (paras. 812-814). Wells are used (para. 815). After the binding of the aptamer to the target and washing steps, sequencing is performed within the wells (para. 825). The sequencing results from the reactions in these wells can then be obtained and analyzed (paras. 823-830). Thus, Halbert teaches that their wells can be capable of use with sequencing technologies. It would therefore be prima facie obvious to use such a well array in the method of Halbert in view of Feagin described above, as this would prevent the need to remove the aptamer/target complex from the wells, cutting down on method steps and resources required.
Regarding claims 7 and 47, as noted above in the rejection of claim 1, Halbert and Feagin teach the use of microfluidic devices. Halbert teaches that such devices can control the flow of fluid, and describes designs of such devices that allow fluid to flow into multiple pluralities of channels and reaction sites (e.g. wells) before isolating each site and performing the desired reaction (para. 235). It would thus be prima facie obvious to design the microfluidic device in the combination of teachings of Halbert in view of Feagin described above using the teachings and already described microfluidic devices of Halbert, as such inventions have established success being used together.
Regarding claims 10-13, Halbert teaches that negative or positive selection of aptamers can be performed (Example 9). The focus of the negative selection is to remove aptamers that bind non-target antigen components of the final assay. The positive selection is to identify aptamers that bind the desired target (para. 494). These selections involve multiple rounds of aptamer recovery and PCR using standard methods (i.e. para. 494). Though Example 9 does not specify that wells are used, para. 351 notes the use of wells with selection methods, and para. 350 notes that multiple rounds of positive selection in particular can provide improved stringency of selection. Thus, the ordinary artisan would be motivated to perform the selection methods described by Halbert in the context of the method of Halbert in view of Feagin described above in the rejection of claim 1 – namely performing multiple rounds of positive selection in the plurality of wells (see para. 350), where aptamers are recovered and undergo PCR between rounds. As the purpose of the selection is to ensure that only aptamers that bind the desired target remain, it would be logical to do this before the bridge amplification of Halbert in view of Feagin, so that only the aptamers that have successfully been through the rounds of positive selection, and thus are most likely to truly be good aptamers for a target, would be used. The aptamer recovering is noted by Halbert to specifically not include the target (i.e. it would involve decoupling the target and the aptamer, para. 349; instant claims 10 and 12-13). As the purpose of this selection is to recover and amplify the aptamers for additional exposure to the target, it would be prima facie obvious for the PCR to occur away from the wells so that targets or other reaction components are not inadvertently amplified, which would affect results. Halbert teaches standard PCR methodologies, and so the ordinary artisan would recognize a thermocycler could be used, for example (instant claim 11).
Regarding claim 20, the instant specification states that spacers “may provide suitable distance between the oligonucleotide subsequence 171", 172", 173", 174" and capture primer adapter 311 or 312 such that capture primer adapter 311 may not inhibit the oligonucleotide subsequence from suitably coupling to target 160. Illustratively, spacer 300 may include 5 or more nucleotides, 10 or more nucleotides, or 15 or more nucleotides,” (para. 68). No specific definition is provided for this term, and there is no specific requirement for the sequences/structure of the spacers. Thus, any nucleic acid sequence can be considered to contain a spacer.
In Halbert, the primer tail adaptors are taught to be 5-10 nucleotides long (para. 444). In Feagin, these adaptor sequences can be 5-40 nucleotides long (para. 59). Thus, these adaptors can themselves can be considered to contain spacer sequences of a minimum amount as exemplified by the instant specification (e.g. 5 nucleotides) and still contain at least 5 nucleotides of adaptor sequence, while still meeting the adaptor requirements of the references. The use of such adaptors in Halbert in view of Feagin would therefore meet the requirements of instant claim 20 in view of the interpretation of spacers provided above.
Regarding claim 22, this claim is a system claim that contains all of the components of instant claim 6, in that there is a well substrate, targets and primers coupled in the well, a fluid of aptamer candidates introduced into the wells, and detection circuitry for sequencing the aptamers, where the structure of each component is stated to be the same as those in claim 6. Claim 22 also specifically notes that to remove aptamers that are not coupled to targets in the wells, a buffer must be used. The use of such a buffer for this purpose is taught by Halbert (e.g. para. 464). Thus, Halbert in view of Feagin teaches the methods of claims 1 and 6 as described above, as well as the additional limitations of claim 22, and so also teaches the system of claim 22.
Claims 4 and 45 are rejected under 35 U.S.C. 103 as being unpatentable over Halbert et al. (US 2016/0003835 A1), in view of Feagin et al. (WO 2019/236548 A1), and further in view of Domenyuk et al. (US 2020/0376022 A1).
Halbert in view of Feagin teaches the methods of claim 2 and 43 as described above, where streptavidin is covalently attached to the substrate (para. 126 and Figure 14). However, Halbert generally teaches that streptavidin may be attached to other components (e.g. a reporter in para. 184). Feagin also teaches the use of labeled/tagged primers and targets (e.g. paras. 9, 41, 67, and 75)
It is noted that regarding claims 4 and 45, if the well-attached first or second primer of Halbert in view of Feagin was attached to the target via biotin/streptavidin binding, the ordinary artisan would recognize that this would mean that the aptamer would be capable of binding to the target and primer sequence at the same time, as these two components would be in close proximity.
Domenyuk teaches methods and compositions for oligonucleotides that bind to targets of interest (Abstract). This can involve the use of aptamers (paras. 7-8 and 16). Figure 2A shows that a target for detection (in this example, a disease vesicle), can be attached to a capture agent bound to a substrate, where the capture agent can be an aptamer (para. 30). The reference teaches that the oligonucleotides of their invention can be modified to alter desired characteristics, where one such listed modification is to include streptavidin on an oligonucleotide (paras. 327-328). Domenyuk also teaches that to recover oligonucleotide probes that are bound to targets in a sample, a capture oligonucleotide can be used, where the captured oligonucleotide may be captured to a substrate (para. 571). The reference also teaches that aptamer candidates can contain biotin moieties, which can be used for capturing/anchoring the aptamers (para. 669).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the teachings of Domenyuk, along with ordinary skill, knowledge, and creativity in the art, to arrive at the inventions of claims 4 and 45. Specifically, Domenyuk teaches that oligonucleotides can be attached to a substrate and can contain a streptavidin moiety on the end, as well as the use of biotin for capturing and anchoring. Halbert in view of Feagin also already teaches primer sequences that are attached to well surfaces and the biotin labeling of targets. As noted above, the ordinary artisan would recognize the benefit of attaching the primer and target to one another, as it would more easily allow for aptamer binding to both components. This would likely increase aptamer binding to appropriate targets, as the adapter on the aptamer would bind with the primer, and would ensure that the aptamer and target are in close proximity. This would increase the accuracy of the aptamer selection process. There would be a reasonable expectation of success as biotin/streptavidin binding is well-known in the art as evidenced by Halbert and Domenyuk, and the primers of Halbert in view of Feagin are already attached to a substrate.
Thus, claims 4 and 45 are prima facie obvious over Halbert, in view of Feagin, and further in view of Domenyuk.
Claims 5 and 46 are rejected under 35 U.S.C. 103 as being unpatentable over Halbert et al. (US 2016/0003835 A1), in view of Feagin et al. (WO 2019/236548 A1), in view of Domenyuk et al. (US 2020/0376022 A1), and further in view of Santala et al. (Journal of Immunological Methods, 2004).
Regarding claims 5 and 46, Halbert, in view of Feagin, and further in view of Domenyuk render obvious the methods of claims 4 and 45, where a primer is bound to streptavidin, and the streptavidin is bound to a biotin-labeled target.
However, none of these references teach that the streptavidin is removed from the oligonucleotide before sequencing occurs. Feagin teaches cleavage of sequences between an aptamer and primer sequence (e.g. para. 64 and 123), but this does not involve moiety cleavage. Halbert and Domenyuk also generally teach cleavable chemical linkages (e.g. Halbert paras. 211 and 612 and Domenyuk paras. 127 and 571).
Santala teaches methods for more efficiently removing targets from substrates (Abstract). Particularly, the reference notes that in washing methods to remove unbound or loosely bound targets from a substrate, the efficiency of the washing may be lowered due to tight moiety binding (page 159, column 2, para. 1). In this reference, streptavidin is linked to a bead via a linker, where the streptavidin then binds to a biotinylated target (Figure 1). Santala teaches the cleavage of this DNA linker to remove the streptavidin from the bead, rather than cleaving the streptavidin and biotin apart (Figure 1). Such cleavage can be done with a nuclease. By removing targets from beads in this manner, Santala teaches that high total recovery was achieved with low nonspecific background noise (page 162, column 2, para. 1).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the teachings of Santala in the method of Halbert, in view of Feagin, and further in view of Domenyuk to cleave the streptavidin from the primer described above in the rejection of claims 4 and 45 before aptamer sequencing, and additionally before bridge amplification. As the biotin/streptavidin linkage connects the primer and the target, this binding would make it difficult for the primer sequence to participate in bridge amplification. By cleaving the streptavidin from the primer, the biotin/streptavidin/target complex could be moved, leaving the primers and aptamers and resulting in more efficient bridge amplification with less background noise. This efficiency would then extend to the sequencing of the clustered amplification products, and would be motivating to the ordinary artisan. There would be a reasonable expectation of success as the cleavage method of Santala specifically works on a bond between DNA and streptavidin, where the streptavidin is bound to biotin.
Thus, claims 5 and 46 are prima facie obvious over Halbert, in view of Feagin, in view of Domenyuk, and further in view of Santala.
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Halbert et al. (US 2016/0003835 A1), in view of Feagin et al. (WO 2019/236548 A1), and further in view of Wanekaya et al. (US 2012/0088232 A1).
Regarding claim 8, Halbert teaches that their aptamers may be generated via the SELEX process (para. 144). This process “is based on the unique insight that nucleic acids have sufficient capacity for forming a variety of two- and three-dimensional structures and sufficient chemical versatility available within their monomers to act as ligands (i.e., form specific binding pairs) with virtually any chemical compound, whether monomeric or polymeric.” Feagin also teaches that their aptamers can be developed with SELEX (para. 62). Halbert also defines aptamers as nucleic acids that have specific binding affinity through interactions other than Watson-Crick base pairing (para. 7). Thus, tertiary structure is important to aptamers generally. Halbert also teaches scenarios in which aptamer folding and rearrangement can occur (paras. 289 and 613-614). Halbert also teaches that aptamers may contain reporter elements, such as a fluorescent label (e.g. paras. 22, 24, and 113).
However, neither Halbert nor Feagin specifically teach that aptamers may change tertiary structure when coupled to a target.
Wanekaya teaches the use of aptamers for detecting components or molecules in a sample (Abstract). Specifically, the reference teaches that when an aptamer binds to a target molecule, the tertiary structure of said aptamer may be altered. This could in turn result in changes to reporter signals present on the aptamer (paras. 17-20).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the teachings of Wanekaya to design aptamers that would undergo confirmational tertiary structure changes when bound to a target in the method of Halbert in view of Feagin. Wanekaya teaches that this type of confirmational change can involve changes to aptamer reporter signals, and thus could provide a clear indication to a user when target binding has occurred. By utilizing such a method in the methods of Halbert in view of Feagin, it could be noted when no aptamer binding has occurred, and would thus prevent a waste of resources and time from performing washing steps that are not necessary. This addition would also note when a large amount of aptamer binding has occurred, which would provide an early indicator of a promising aptamer candidate. As aptamers that undergo confirmational changes generally and the addition of reporters to aptamers are both well-known in the art, as evidenced by Halbert and Wanekaya, there would be a reasonable expectation of success.
Thus, claim 8 is prima facie obvious over Halbert, in view of Feagin, and further in view of Wanekaya.
Conclusion
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 FRANCESCA F GIAMMONA whose telephone number is (571)270-0595. The examiner can normally be reached M-Th, 7-5pm.
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/F.F.G./Examiner, Art Unit 1681
/SAMUEL C WOOLWINE/Primary Examiner, Art Unit 1681
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