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 .
Please note: The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim Status
Claims 1-17 are pending.
Claims 9-12 and 15-17 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 10/8/2025.
Claims 1-8 and 13-14 are being examined on the merits.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement (for example, see paragraphs [0030 and 0036]). 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
No IDSs were filed in the applicant’s reply on 3/2/2026, therefore, any references in the specification (and not present on an IDS) not cited by the examiner on form PTO-892 remain unconsidered.
Title
The objection to the title is withdrawn in light of Applicant’s submission of a corrected title in the replay of 3/2/2026. The title has been corrected on the Bib Data Sheet included with this Office Action to reflect this change.
Specification
Applicant’s amendment to the specification to properly denote trade names or marks used in commerce is acknowledged. Notification of the presence of trade names or marks used in commerce is not a formal objection to the specification (as evidenced by form PTO-326 of 10/31/2025), and therefore there is no objection to be withdrawn.
Claim Objections
Withdrawn:
The objection to claim 5 is withdrawn in light of Applicant’s amendment to the claim.
New (Necessitated by Amendments):
Claims 4-5, 8, and 13 are objected to because of the following informalities:
Claim 4 reads “wherein the double hairpin contains” and should read “wherein the double hairpin nucleic acid contains” to maintain consistent claim language.
Claim 5 reads “two regions of complementarity to the oligonucleotide to be removed” and should read “two regions of complementarity to the undesired oligonucleotide to be [[removed]]sequestered” to maintain consistent claim language.
Claim 8 read “wherein the oligonucleotide to be removed” and should read “wherein the undesired oligonucleotide to be [[removed]]sequestered” to maintain consistent claim language.
Claim 13 reads “binding to the targets in a plurality of cells a plurality of unique binding agents that are each specific for one of the targets” and should read “binding to the plurality of targets in [[a]]the plurality of cells a plurality of unique binding agents that are each specific for one of the plurality of targets” to maintain consistent claim language.
Appropriate correction is required.
Claim Interpretation
Claim 5 is directed to the method of claim 1 “wherein the single-stranded region comprises two regions of complementarity to the oligonucleotide to be removed flanking a single middle region”. However, the middle region is given no structural limitations or sequence identification. Therefore, included in the scope of the claim is any sequence for the middle region, including a sequence which is also complementary to the oligonucleotide to be removed.
Claim Rejections - 35 USC § 103
Modified as Necessitated by Claim Amendments
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.
Claims 1-5, 8, and 13 are rejected under 35 U.S.C. 103 as being unpatentable over Chavez (Chavez et al., US 20220049285 A1, EFD of 2/8/2019; cited on PTO-892 of 10/31/2025) in view of Dahl (Dahl et al., US 10,240,198 B2; cited on PTO-892 of 10/31/2025) and Shuman (Journal of Biological Chemistry, 2009; cited on PTO-892 of 10/31/2025).
Regarding claim 1: Chavez teaches a reaction mixture in which splint oligonucleotides are used to facilitate sequential additions of barcoded sequences to an antibody in a split-pool methodology of barcoding surfaces of cells or exosomes (paragraph [0009, 0040-0041, and 0109-0110]). Chavez teaches after each round of barcode addition via splint oligonucleotide mediated annealing and ligation, removing the splint oligonucleotide by hybridizing with a blocking strand that is complementary to the splint oligonucleotide in order to prevent “inappropriate subsequent ligations” (paragraph [0114, 0118, and 0235]).
Chavez does not teach sequestering the undesired splint oligonucleotide via a double hairpin nucleic acid. However, targeting of specific sequences for sequestration from a reaction mixture with a double hairpin nucleic acid is known in the art, as taught by Dahl.
Dahl teaches a method in which a double hairpin single nucleic acid strand having a first hairpin at the 5’ end, a second hairpin at the 3’ end, and a single-stranded region in between the 5’ and 3’ ends that comprises a sequence capable of hybridizing to a target oligonucleotide is contacted with a reaction mixture (col 4 ln 16-47, col 5 ln 47-50 and ln 56-59, and Figure 4). Dahl teaches annealing the complementary oligonucleotide to the double hairpin and then ligating the oligonucleotide to either end of the double hairpin oligonucleotide (col 4, ln 16-47). The ligation of the target nucleic acid into the double hairpin molecule inherently renders this nucleic acid “inert” and sequestered (see paragraph [0023] of the instant specification).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Chavez with that of Dahl. One would be motivated to do so given the assertion by Dahl that the combination of using a double hairpin oligonucleotide with the sequence-specificity of ligase, increases the specificity of targeting of a particular DNA sequence (col 5, ln 19-29). One would have a reasonable expectation of success given that Dahl successfully uses a double hairpin oligonucleotide to target specific oligonucleotide sequences.
Regarding claim 2: Dahl teaches contacting the reaction mixture with a ligase (col 5, ln 19-29)
Regarding claim 3: Dahl does not explicitly teach that the ligase is already present in the reaction mixture prior to the addition of the double hairpin nucleic acid. However, with respect to the order of steps, it is noted that the courts have held that any order of performing process steps is prima facie obvious in the absence of new or unexpected results (In re Gibson, 39 F.2d 975, 5 USPQ 230 (CCPA 1930); Ex parte Rubin, 128 USPQ 440 (Bd. App. 1959)). See MPEP §2144.04 IV C. Therefore, the claimed order of steps is an obvious variant of the steps of the cited prior art.
Regarding claim 4: Dahl does not explicitly teach that the double hairpin oligonucleotide has a 5’ phosphate group. However, Dahl teaches using ligase to ligate the complementary target nucleotide at either end of the single oligonucleotide double hairpin structure. Given that ligase requires a 5’ phosphate group to act as a “donor” for bond formation (as taught by Shuman, 2009; Abstract, DNA Ligase, and Fig 1), it is inherent that the double hairpin oligonucleotide as taught by Dahl has a 5’ phosphate group.
Regarding claim 5: Dahl teaches that the double hairpin oligonucleotide is complementary and able to hybridize to the target oligonucleotide sequence (col 4, ln 16-47). This reads on two flanking regions of complementarity to the oligonucleotide to be removed (the target oligonucleotide) and a single middle region, given that the single middle region is not given any structural definition (see Claim Interpretation above).
Regarding claims 8 and 13: Chavez teaches a method of detecting a plurality of targets in a plurality of cells in a reaction mixture which comprises binding to the targets in a plurality of cells a plurality of unique binding agents that are each specific for one of the targets (antibodies; Abstract, paragraph [0009], and Figure 9). Chavez teaches adding multiple subcode oligonucleotides to each of the bound agents in successive rounds of split pool synthesis wherein the subcode oligonucleotides in each round anneal adjacently to the subcode oligonucleotide from a previous round via an annealing region, and teaches covalently linking the subcode oligonucleotides together to create a unique cell-originating nucleotide code (paragraphs [0040-0047] and Figure 9). Chavez teaches that this is achieved through the use of a splint oligonucleotide, which mediates the adjacent annealing of successive rounds of subcode oligonucleotides (paragraph [0040]). Chavez teaches that the subcode oligonucleotides are oligonucleotides composed of two constant regions flanking a barcode region that varies among the plurality of subcode oligonucleotides (relevant to claim 8; paragraph [0112 and 0116], Fig 1 and 9). Chavez teaches after each round of barcode addition via splint oligonucleotide mediated annealing and ligation, removing the splint oligonucleotide by hybridizing with a blocking strand that is complementary to the splint oligonucleotide in order to prevent “inappropriate subsequent ligations” (paragraph [0114, 0118, and 0235]).
While Chavez does not teach removal of the subcode oligonucleotides via hybridization with a blocking probe before the next round of ligation with new subcode oligonucleotides, Chavez does exemplify removal of a splint oligonucleotide via hybridization with a blocking probe. Chavez teaches removal of one (splint oligonucleotide) of two reagents necessary for the annealing and adjacent linkage of subcode oligonucleotides (splint oligonucleotides and subcode oligonucleotides). It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified Chavez to remove the subcode oligonucleotide rather than the splint oligonucleotide. It would be a simple substitution of subcode oligonucleotides for splint oligonucleotides and would yield the predictable result of preventing inappropriate subsequent ligations, thus achieving the same goal.
Chavez also teaches a method in which the oligonucleotide to be removed is a plurality of oligonucleotides having two constant regions, flanking a single barcode region that varies among the plurality of oligonucleotides (the subcode oligonucleotides, see above; claim 8).
Chavez does not teach removing the undesired oligonucleotides via a double hairpin nucleic acid. However, targeting of specific sequences for removal from a reaction mixture with a double hairpin nucleic acid is known in the art, as taught by Dahl.
Dahl teaches a method in which a double hairpin single nucleic acid strand having a first hairpin at the 5’ end, a second hairpin at the 3’ end, and a single-stranded region in between the 5’ and 3’ ends that comprises a sequence capable of hybridizing to a target oligonucleotide is contacted with a reaction mixture (col 4 ln 16-47, col 5 ln 47-50 and ln 56-59, and Figure 4). Dahl teaches annealing the complementary oligonucleotide to the double hairpin and then ligating the oligonucleotide to either end of the double hairpin oligonucleotide (col 4, ln 16-47). The ligation of the target nucleic acid into the double hairpin molecule inherently renders this nucleic acid “inert” (see paragraph [0023] of the instant specification).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Chavez with that of Dahl. One would be motivated to do so given the assertion by Dahl that the combination of using a double hairpin oligonucleotide with the sequence-specificity of ligase, increases the specificity of targeting of a particular DNA sequence (col 5, ln 19-29). One would have a reasonable expectation of success given that Dahl successfully uses a double hairpin oligonucleotide to target specific oligonucleotide sequences.
Claims 6-7 and 14 are rejected under 35 U.S.C. 103 as being unpatentable over Chavez (Chavez et al., US 20220049285 A1, EFD of 2/8/2019; cited on PTO-892 of 10/31/2025) in view of Dahl (Dahl et al., US 10,240,198 B2; cited on PTO-892 of 10/31/2025) and Shuman (Journal of Biological Chemistry, 2009; cited on PTO-892 of 10/31/2025) as applied to claims 1-5, 8, and 13 above, and further in view of Slatter (Slatter et al., US 20200224246 A1, EFD of 1/11/2019; cited on PTO-892 of 10/31/2025).
The teachings of Chavez in view of Dahl and Shuman as they apply to claims 1-5 and 13 are detailed above. Relevant to the instantly rejected claims, Chavez in view of Dahl and Shuman teach removing excess oligonucleotides from reactions with a double hairpin oligonucleotide structure. Chavez in view of Dahl and Shuman teach that the hairpin oligonucleotide contains sequences complementary to the oligonucleotide to be removed.
Chavez teaches adding multiple subcode oligonucleotides to each of the bound agents in successive rounds of split pool synthesis wherein the subcode oligonucleotides in each round anneal adjacently to the subcode oligonucleotide from a previous round via an annealing region, and teaches covalently linking the subcode oligonucleotides together to create a unique cell-originating nucleotide code (paragraphs [0040-0047] and Figure 9). Chavez teaches that this is achieved through the use of a splint oligonucleotide, which mediates the adjacent annealing of successive rounds of subcode oligonucleotides (paragraph [0040]). Chavez teaches after each round of barcode addition via splint oligonucleotide mediated annealing and ligation, removing the splint oligonucleotide by hybridizing with a blocking strand that is complementary to the splint oligonucleotide in order to prevent “inappropriate subsequent ligations” (paragraph [0114, 0118, and 0235]). As mentioned above, while Chavez does not teach removal of the subcode oligonucleotides in this way before the next round of ligation with new subcode oligonucleotides, it would be a simple substitution of one element for another (subcode oligonucleotide for splint oligonucleotide) and would yield the predictable result of preventing inappropriate subsequent ligations, thus achieving the same goal. Therefore, Chavez teaches a method in which the oligonucleotide to be removed is a plurality of oligonucleotides having two constant regions, flanking a single barcode region that varies among the plurality of oligonucleotides (claim 8 and 14; Fig 9 of Chavez).
However, Chavez in view of Dahl and Shuman do not teach that the double hairpin nucleic acid single-stranded region is comprised of two regions of complementarity to the oligonucleotide to be removed flanking a single middle region comprised of a spacer (claim 14) that is either a non-nucleotide spacer (claim 6) or an inosine spacer (claim 7). However, use of spacers flanked by regions of complementarity for binding to barcode sequences is known in the art, as taught by Slatter.
Slatter teaches a method of binding indexing adapters using a sequence comprised of two regions of complementarity to a target sequence which flank a spacer region (Fig 3 and paragraph [0076]). Slatter teaches that the spacer region can be a non-nucleotide spacer (claim 6; “sp18 linker”, paragraph [0076]) or can be composed of inosine nucleotides (claim 7; paragraph [0076]). Slatter also teaches that the spacer region can be the same length as the index (reads on barcode region, claim 14; paragraph [0076] and Fig 3).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Chavez in view of Dahl and Shuman with that of Slatter. One would be motivated to include this middle region spacer between two complementary regions given the assertion by Slatter that this region is “capable of aligning with indexing oligonucleotides with varied sequences” (paragraph [0076]). One would have a reasonable expectation of success given that Slatter successfully designs a sequence with complementary annealing regions flanking a spacer that is able to hybridize to varying indexing sequences (Fig 3).
Response to Remarks
Applicant's arguments filed 3/2/2026 have been fully considered but they are not deemed persuasive for the following reasons.
Applicant argues on pages 11-12 of the Remarks of 3/2/2026 (hereinafter “Remarks”) that Chavez “does not disclose removing the splint oligonucleotides from the reaction mixture” but instead binds them to a blocking strand which renders them “inactivated” which is “reversible and non-destructive”. In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Furthermore, in response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., being irreversible or destructive) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
Applicant argues on page 12 of Remarks that “modifying Chavez to incorporate the method of Dahl as suggested by the Patent Office contradicts Chavez’s stated objective”. Applicant argues that incorporating the method of Dahl would generate new ligation products with the same mixture, whereas Chavez is “concerned with prevented ‘inappropriate subsequent ligations’”. The examiner respectfully disagrees. The inappropriate subsequest ligations that Chavez is aiming to prevent is the ligation between subcode oligonucleotides mediated by splint oligonucleotides. Therefore, by targeting the splint oligonucleotide (or the subcode oligonucleotide as in claim 13) for ligation to a double hairpin and generation of an inert circular product would therefore accomplish the stated goal of Chavez which is to prevent inappropriate subsequent ligation reactions between the subcode oligonucleotides and would allow for the split-pool synthesis methodology to work. Chavez was seeking to avoid addition of subcode oligonucleotides with one well-specific barcode (from a previous well) from being added to the growing oligonucleotide chain in a subsequent well with new well-specific barcode oligonucleotides. Adding the “new ligation products” would serve an equivalent function as that provided by the blocking oligonucleotide in preventing this from occurring. Chavez was not concerned with competing side reactions, rather inappropriate addition of well-specific barcodes within the wrong well.
Applicant argues on page 13 of Remarks that “there would be no reason for the skilled artisan to modify Chavez to incorporate the methods of Dahl, especially when Chavez already provides a solution to its stated problem of preventing “inappropriate subsequent ligation” and that “substituting Dahl’s method would add complexity without any clear benefit in Chavez’s context”. However, as stated above, the methodology of Dahl ensures more accurate targeting of target sequences given the sequence specificity requirement of ligase. A skilled artisan would recognize this as beneficial when targeting nucleic acid molecules in solution. This is a reason why a skilled artisan would be motivated to choose a more “complex ligation-based capture method” of Dahl to substitute in place of the blocking oligonucleotide method of removal as taught in Chavez. This is a reason why an artisan would do it and employing this methodology additionally achieves the stated purpose of Chavez, which is to prevent the unwanted ligation reactions (mediated by splint oligonucleotides between adjacent subcode oligonucleotides) from occurring. Additionally, Dahl does in fact teach capturing the target nucleic acid molecule upon ligation into the double hairpin nucleic acid, but Dahl is not being relied upon for this particular teaching and thus this argument about the capturing making the methodology of Chavez overly complex is moot.
Applicant argues on page 13 of Remarks that there is not an established reasonable expectation of success given that this proposed modification would “add complexity, by introducing competing ligation pathways and creating additional ligation products that could potentially be present in subsequent rounds of splint-ligation”. However, the “additional ligation products” would inherently be inactive given the ligation into the double hairpin as taught by Dahl and thus would not present a problem if present in subsequent rounds of splint-ligation. Additionally, as demonstrated by Chavez with the usage of the blocking oligonucleotide, the first round of ligation (desired ligation between adjacent subcode oligonucleotides) is allowed to occur before addition of the agent used to remove undesired oligonucleotides, therefore not posing a problem in terms of “competing ligation pathways” (paragraph [0114] of Chavez).
Applicant notes on page 14 of Remarks that Shuman “provides only general disclosures pertaining to enzymology and does not teach” features of the claims. The Examiner notes that Shuman was merely relied upon as evidence of an inherent feature of ligase that was not noted by Dahl.
For these reasons, the rejections of the claims under 35 USC 103, as presented above, are maintained.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1, 5, 8, and 13 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 16 and 18 of copending Application No. 18/012,607 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are drawn to the same limitations. Any additional limitations of '607 claims are encompassed by the open claim language “comprising” found in the instant claims.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 2-4, 6-7, and 14 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 16 and 18 of copending Application No. 18/012,607 as applied to claims 1, 5, 8, and 13 above, and in view of Shuman (Journal of Biological Chemistry, 2009; cited on PTO-892 of 10/31/2025), and Slatter (Slatter et al., US 20200224246 A1, EFD of 1/11/2019; cited on PTO-892 of 10/31/2025) according to citations and rationales provided above.
This is a provisional nonstatutory double patenting rejection.
Response to Remarks
In light of Applicant’s argument that a prima facie case has not been established in the double patenting rejections above, below the Examiner has outlined more clearly for Applicant how the claims of the instant application are taught by the co-pending claims.
Claims 1, 5, 8, and 13 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 16 and 18 of copending Application No. 18/012,607 (reference application).
Regarding claim 1: Claim 18 of ‘607 teaches removing excess oligonucleotides from a reaction mixture (thus inherently making said oligonucleotides unavailable for subsequent ligation reactions). Claim 18 recites:
a. after attaching the subcode oligonucleotides to the subcode oligonucleotide of the
previous round, contacting the reaction mixture with a double hairpin nucleic acid comprising a single nucleic acid strand having:
i. a first hairpin at the 5'-end;
ii. a second hairpin at the 3'-end; and
iii. a single-stranded region between the 5'-end and the 3'-end, wherein the single-stranded region comprises a sequence capable of hybridizing to the subcode oligonucleotide;
b. annealing the excess subcode oligonucleotide to the double hairpin nucleic acid;
c. ligating the excess subcode oligonucleotide to the ends of the double hairpin nucleic acid thereby removing the excess subcode oligonucleotide from the reaction mixture.
The italicized regions above represent word-for-word teachings corresponding to claim 1 of the instant application. The underlined portions are slightly different wordings that teach essentially the same patentably indistinct thing. The excess subcode oligonucleotides are the “undesired oligonucleotides” of the instant claim. The ligation of the excess subcode oligonucleotide to the ends of the double hairpin nucleic acid inherently forms an inert circular product and thus also reads on claim 1.
Regarding claim 5: As mentioned in the claim interpretation section above, given that the instant claim 5 does not provide a structural limitation to the “middle region”, said middle region can also be comprised of a sequence that is complementary to the oligonucleotide to be removed. Thus, claim 18 of the ‘607 claims also reads on this claim given that the single-stranded region comprises a sequence capable of hybridizing to the subcode oligonucleotide.
Regarding claim 8: The claims of ‘607 teach that the oligonucleotides to be removed comprise a plurality of subcode oligonucleotides (claim 16 – “adding to the nucleic acids multiple subcode oligonucleotides”). Claim 16 of ‘607 does not define the claim term “subcode oligonucleotide”, but subcode oligonucleotides are defined paragraph [0064] of the specification as oligonucleotides containing flanking annealing regions around a middle region comprising the diverse code in the plurality of the subcode oligonucleotides. As stated in MPEP 804(II)(B)(1), “The specification can be used as a dictionary to learn the meaning of a term in the claim. Toro Co. v. White Consol. Indus., Inc., 199 F.3d 1295, 1299, 53 USPQ2d 1065, 1067 (Fed. Cir. 1999) ("[W]ords in patent claims are given their ordinary meaning in the usage of the field of the invention, unless the text of the patent makes clear that a word was used with a special meaning."); Renishaw PLC v. Marposs Societa' per Azioni, 158 F.3d 1243, 1250, 48 USPQ2d 1117, 1122 (Fed. Cir. 1998) ("Where there are several common meanings for a claim term, the patent disclosure serves to point away from the improper meanings and toward the proper meanings.").”
Regarding claim 13: Claims 16 and 18 of ‘607 teach the following.
Claim 16 (‘607): A method of simultaneously detecting the presence and location of multiple targets in a tissue sample, the method comprising: (multiple targets reads on a plurality of targets and tissue sample reads on a plurality of cells)
a. contacting a tissue sample with one or more unique binding agents, wherein the agents include a target-identifying nucleic acid conjugated to a capture moiety; (one or more unique binding agents reads on a plurality of unique binding agents and target-identifying nucleic acid reads on specific for one of the targets)
b. forming on the tissue sample a layer of particles conjugated to a capture molecule capable of selectively binding the capture moiety;
c. contacting the layer of particles with a plurality of location-identifying nucleic acids conjugated to the capture moiety;
d. capturing the target-identifying nucleic acids and the location-identifying nucleic acids on the particles via the capture moiety and separating the particles from the tissue sample into a liquid sample;
e. assembling unique particle-specific codes on each particle-bound target-identifying nucleic acid and each location-identifying nucleic acid by adding to the nucleic acids multiple subcode oligonucleotides in an ordered manner during successive rounds of split-pool synthesis wherein each round comprises: (unique particle-specific code reads on unique cell-originating nucleotide code).
i. splitting the liquid sample into reaction volumes, each volume comprising a species of subcode oligonucleotide;
ii. annealing the subcode oligonucleotide adjacently to the subcode oligonucleotide from a previous round via an annealing region;
iii. covalently linking the adjacently annealed subcode oligonucleotides to each other; and
iv. pooling the reaction volumes into a liquid sample;
f. detecting the sequence of the target-identifying nucleic acids and the location-identifying nucleic acids and associated unique particle-specific codes;
g. for each target, correlating the target-identifying nucleic acids and the location-identifying nucleic acids having the same unique particle-specific code thereby detecting the presence and location of multiple targets in the tissue sample.
(The additional limitations of claim 16 of ‘607 are encompassed by the open claim language “comprising” found in the instant claims.)
Claim 18 (‘607): The method of claim 16, further comprising a step of removing excess subcode oligonucleotides from a reaction mixture, the method comprising: (this inherently renders them unavailable for subsequent covalent linking reacitons)
a. after attaching the subcode oligonucleotides to the subcode oligonucleotide of the previous round, contacting the reaction mixture with a double hairpin nucleic acid comprising a single nucleic acid strand having:
i. a first hairpin at the 5'-end;
ii. a second hairpin at the 3'-end; and
iii. a single-stranded region between the 5'-end and the 3'-end, wherein the single- stranded region comprises a sequence capable of hybridizing to the subcode oligonucleotide;
b. annealing the excess subcode oligonucleotide to the double hairpin nucleic acid;
c. ligating the excess subcode oligonucleotide to the ends of the double hairpin nucleic acid thereby removing the excess subcode oligonucleotide from the reaction mixture.
Therefore, claims 16 and 18 of ‘607 directly anticipate claim 13 of the instant application.
Claims 2-4, 6-7, and 14 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 16 and 18 of copending Application No. 18/012,607 as applied to claims 1, 5, 8, and 13 above, and in view of Shuman (Journal of Biological Chemistry, 2009; cited on PTO-892 of 10/31/2025), and Slatter (Slatter et al., US 20200224246 A1, EFD of 1/11/2019; cited on PTO-892 of 10/31/2025) according to citations and rationales provided above.
Regarding claims 2 and 3: Given that claims 16 and 18 of ‘607 teach ligating the excess subcode oligonucleotides to the double hairpin nucleic acid, it would be obvious to those skilled in the art that the reaction mixture was contact with a ligase enzyme. With respect to the order of steps, it is noted that the courts have held that any order of performing process steps is prima facie obvious in the absence of new or unexpected results (In re Gibson, 39 F.2d 975, 5 USPQ 230 (CCPA 1930); Ex parte Rubin, 128 USPQ 440 (Bd. App. 1959)). See MPEP §2144.04 IV C. Therefore, the claimed order of steps is an obvious variant of the steps of the cited prior art.
Regarding claim 4: Claims 16 and 18 of ‘607 do not explicitly teach that the double hairpin oligonucleotide has a 5’ phosphate group. However, the claims of ‘607 teach ligating the excess subcode oligonucleotides at either end of the single oligonucleotide double hairpin structure (with ligase, as defined as obvious above). Given that ligase requires a 5’ phosphate group to act as a “donor” for bond formation (as taught by Shuman, 2009; Abstract, DNA Ligase, and Fig 1), it is inherent that the double hairpin oligonucleotide as taught by ‘607 has a 5’ phosphate group.
Regarding claims 6-7 and 14: The claims of ‘607 do not teach that the double hairpin nucleic acid single-stranded region is comprised of two regions of complementarity to the oligonucleotide to be removed flanking a single middle region comprised of a spacer (claim 14) that is either a non-nucleotide spacer (claim 6) or an inosine spacer (claim 7). However, use of spacers flanked by regions of complementarity for binding to barcode sequences is known in the art, as taught by Slatter.
Slatter teaches a method of binding indexing adapters using a sequence comprised of two regions of complementarity to a target sequence which flank a spacer region (Fig 3 and paragraph [0076]). Slatter teaches that the spacer region can be a non-nucleotide spacer (claim 6; “sp18 linker”, paragraph [0076]) or can be composed of inosine nucleotides (claim 7; paragraph [0076]). Slatter also teaches that the spacer region can be the same length as the index (reads on barcode region, claim 14; paragraph [0076] and Fig 3).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of ‘607 with that of Slatter. One would be motivated to include this middle region spacer between two complementary regions given the assertion by Slatter that this region is “capable of aligning with indexing oligonucleotides with varied sequences” (paragraph [0076]). One would have a reasonable expectation of success given that Slatter successfully designs a sequence with complementary annealing regions flanking a spacer that is able to hybridize to varying indexing sequences (Fig 3).
Given the above reasonings the double patenting rejections are deemed proper and are maintained.
Conclusion
THIS ACTION IS MADE FINAL. 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 KAILEY E CASH whose telephone number is (571)272-0971. The examiner can normally be reached Monday-Friday 8:30am-6pm ET.
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, Anne Gussow can be reached at (571)272-6047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/KAILEY ELIZABETH CASH/Examiner, Art Unit 1683
/STEPHEN T KAPUSHOC/Primary Examiner, Art Unit 1683
Prosecution Insights