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 .
DETAILED ACTION
This action is FINAL.
Status of Claims
Claims 1-6, and 12-14 are pending.
Claims 1, 13, and 14 are examined.
Claims 2-6, and 12 are withdrawn (see restriction in the previous action).
Priority
This application is filed 02/22/2023 and claims the benefit of domestic priority as below:
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Information Disclosure Statement
Two IDS(s) received on 09/28/2023 have been considered unless marked with a strikethrough. Two additional IDS(s) is/are provided on 07/21/2026, and 08/28/2026.
Response to Arguments
Applicant's arguments/amendments filed on 7/20/2026, and in the amendments, claims 1 and 13 have been amended, claim 11 has been cancelled, and no claims have been added.
With respect to the IDS, the Applicant's arguments based on the compliance with 37 C.F.R. § 1.98(d), and as indicated in the IDS letter accompanying the IDS in question, have been fully considered and are persuasive. Therefore, all IDS references are reviewed and the considerations updated.
With respect to the objections of abstract, drawings, specification, and claims have been fully considered and are persuasive. Therefore, the previous objections of abstract, drawings, specification, and claims have been withdrawn.
The Applicant's arguments of the rejections of 35 U.S.C 103 and double patenting have been considered but are moot in view of the new ground of rejections for the amended claims 1, 13 and 14. The previous rejections of record are withdrawn in view of the amendment.
New Ground of Rejections
Claim Interpretation
Claims are interpreted in accordance with the broadest reasonable interpretation (BRI) standard
consistent with the specification (See MPEP 2111). Claims 1, 11, 13, and 14 are interpreted as follows:
The claims and specification did not provide an explicit definition as to the term “kit”. To apply BRI, the term “kit” is interpreted to encompass a collection, set of components or containers.
The term “plurality of oligonucleotides” did not provide an explicit definition in the claims and specification. To apply BRI, the term “plurality of oligonucleotides” is interpreted to encompass plurality of probes, plurality of nucleic acid molecules, or plurality of nucleotides.
Chemical formulas that are recited in claims have wavy bond/floating bond. As a consistent with the specification (paragraph [00120]-[00121]), the recited formulas are not limited to a single phosphor designated by a specific name/compound but are construed to encompass phosphor species having the illustrated core structure, acid form, and permissible bonding configurations.
Claim Objections
Claim 1 is objected to because of the following informalities:
Claim 1 is objected to because the phrase “wherein… nucleic acid molecule,” should be ““wherein… nucleic acid molecule;”, and the phrase “nucleic acid sequence, and” should be “nucleic acid sequence; and”.
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 text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 1, 13, and 14 is/are rejected under 35 U.S.C. 103 as being unpatentable over Su et al. (US 2005/0064435 A1, pub'd 03/24/2005, made of record in the IDS) in view of Stupi et al. (US 2013/0122489 A1, pub’d 05/16/2013).
With respect to independent claim 1, the claim recites a kit comprising a first plurality of oligonucleotides, wherein the oligonucleotides in the first plurality comprise at least one of the following chemical formulas:
wherein the kit further comprises at least a second plurality of oligonucleotides, wherein the oligonucleotides in the second plurality comprise a target binding domain and a barcode domain;
wherein said target binding domain comprises at least 12 nucleotides and is capable of binding a target nucleic acid;
wherein said barcode domain comprises a synthetic backbone, said barcode domain comprising at least four attachment positions, each attachment position comprising at least one attachment region, said attachment region comprising at least one nucleic acid sequence capable of being bound by a complementary nucleic acid molecule,
wherein the at least four attachment positions correspond to the sequence of the target binding domain and wherein each of the at least four attachment positions have a different nucleic acid sequence, and
wherein said nucleic acid sequences of each position of the at least four attachment positions determine the identity of the target nucleic acid that is bound by said target binding domain.
Su discloses the claimed target binding/barcode architecture as follows.
Su states that “The barcode 530 is formed by hybridization of a series of tagged oligonucleotides 520 to a single stranded DNA template 500. The template 500 comprises a container section 540 and a probe section 550. The probe section 550 is designed to hybridize to a complementary target nucleic acid sequence … The probe region 540 may between 2 to 30, 4 to 20 or 14 to 15 nucleotides long.” (paragraph [0037], and Fig. 5]. Thus, Su teaches a target binding probe section and a barcode forming container section on the same template with nucleotides length.
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Su states that “the container section 540 will be designed to hybridize to a series of unique 5-mers, out of the 974 types available. Tagged oligonucleotides 520 comprising the appropriate code sequences may be introduced and hybridized to the container section 540. Each tagged oligonucleotide 520 will contain tags providing a unique signal, so that it may be identified from other code components.” (paragraph [0041]). Thus, Su teaches the container section includes sequence defined regions capable of binding complementary tagged oligonucleotides.
Su exemplifies at least four distinct attachment positions, as stating “With the specific container sequence 540 disclosed in SEQ ID NO:1, only 4 tagged 3-mers are required-TCA, TGT, ATG and CAG. Each tagged 3-mer can bind at one and only one site on the template 500 (paragraph [0043]). Su further explains that the tagged oligonucleotides are complementary to the container section (paragraph [0043]). Thus, Su teaches at least four nucleic four acid attachment positions capable of being bound by complementary nucleic acid molecules, wherein the attachment positions are defined by different nucleic acid sequences.
Su teaches correspondence between the target binding sequence and the barcode forming position as Su states “any changes in the sequence of the probe section 550 will require corresponding changes to be made in the container section 540 sequence. For example, if the probe sequence 550 is changed from AGAA to AGTA, the container sequence 540 must be changed also, since the AGT in the probe 550 overlaps with the AGT in the container 540” (paragraph [0043]). Su identifies the corresponding tagged oligonucleotide sequences resulting from that change (paragraph [0044])
Su teaches to identify the target nucleic acid. Su explains that “When barcode 530 molecules are designed for specific target molecules, the structure and signal component of the barcode 530 is fixed”, and that a new barcode is prepared for a different target (paragraph [0043]). Thus, since the container sequence and the corresponding combination of tagged oligonucleotides depend on the target-specific probe sequence, the resulting sequence defined barcode is associated with, and identifies, the target recognized by the corresponding probe section (paragraph [0037], [0041], [0043]-[0045], and Fig.5).
Su teaches synthetic nucleic acid barcode backbones, as stating “standard phosphoramidite chemistry may be used to make backbones 110 comprising DNA chains” (paragraph [0034]). Su also teaches tagged oligonucleotides produced by “known chemical synthesis techniques” (paragraph [0037]), and Su further states that “The tags linked to the oligonucleotide are not limited to Raman tags. For example, fluorescent, nanoparticle, nanotube, fullerenes and quantum dot tags may also be attached to the oligonucleotide” (paragraph [0048]).
Accordingly, Su teaches the claimed target binding/barcode architecture, including a target binding nucleic acid domain, a synthetic nucleic acid barcode structure, at least four different sequence defined attachment positions capable of binding complementary nucleic acid molecules, and correspondence between the target binding probe sequence and the barcode forming sequence.
Su fails to teach the recited fluorophore structured compounds that have the core structures of fluorescent dyes.
In view of the claim interpretation, Stupi teaches that a “reporter” is a chemical moiety capable of producing a detectable signal and identifies fluorescent dye groups including ALEXA Fluor 350, ALEXA Fluor 405, ALEXA Fluor 546, ALEXA Fluor 555, ALEXA Fluor 594, ALEXA Fluor 488, and ALEXA Fluor 647 (paragraph [0320]) that have the core structures of compounds and permitted attachment configuration in claim 1. Stupi further teaches that “a linker connects a reporter to a biological and non-biological component, for example, a nucleobase, a nucleoside or a nucleotide” (paragraph [0316]).
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one of fluorescents in claim 1 commercial Fluor 488 commercial Fluor 488 acid form
It would have been obvious to a PHOSITA at the time of the invention to select the known fluorescent reporters disclosed by Stupi for use as the florescent tags contemplated by Su. Su proves the reason to employ a fluorescent reporter on the barcode forming oligonucleotides by disclosing that fluorescent tags may be attached to those oligonucleotides. The proposed modification involves using a known fluorescent reporter to perform a known function as obtaining a detectable and distinguishable signal from a labeled oligonucleotide. Therefore, a PHOSITA would have been motivated to use the known fluorescent reporter disclosed by Stupi as a fluorescent label on Su’s labeled oligonucleotide in order to provide a known fluorescent signal for detecting and distinguishing Su’s target-specific molecular barcodes. A PHOSITA would have had a reasonable expectation of successfully making the combination because Su already teaches tagged nucleic acid components and permits fluorescent dyes as tags, while Stupi teaches Alexa Fluor dyes as established fluorescent reporters.
With respect to claims 13 and 14, the claims recite the oligonucleotides in the first plurality comprise: Alexa Fluor 647 fluorescent dye group in claim 13, and Alexa Fluor 488 fluorescent dye group in claim 14, as discussed in claim interpretation.
Stupi teaches that a “reporter” is a chemical moiety capable of producing a detectable signal and identifies fluorescent dye groups including ALEXA Fluor 647 and ALEXA Fluor 488 (paragraph [0320]). Thus, claims 13 and 14 would have been obvious for the same reasons set forth above with respect to claim 1.
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, 13, and 14 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 3 of U.S. Patent No. 12,281,356 B2 in view of Su et al. (US 2005/0064435 A1, pub'd 03/24/2005, made of record in the IDS) and Stupi et al. (US 2013/0122489 A1, pub’d 05/16/2013).
Claim 1 of ‘356 patent recites that “a probe comprising: a target binding domain and a barcode domain; wherein the target binding domain is at least 12 nucleotides in length; wherein the barcode domain comprises a synthetic backbone, the barcode domain comprising at least two attachment positions, each attachment position comprising at least one attachment region comprising at least one nucleic acid sequence that hybridizes to a complementary nucleic acid molecule, and wherein the synthetic backbone comprises L-DNA; wherein each of the at least two attachment positions has a different nucleic acid sequence; wherein the at least two attachment positions correspond to the sequence of the target binding domain; wherein said nucleic acid sequence of each position of the at least two attachment positions determines the identity of the target nucleic acid that is bound by said target binding domain; and wherein each nucleotide of the at least one nucleic acid sequence of each attachment region is L-DNA”. Claim 3 further limits that the barcode domain comprises: a) at least three attachment positions; or b) at least four attachment positions.
Thus, ‘356 patent teaches that the target binding/barcode architecture recited in instant claim 1, including a target binding domain of at least 12 nucleotides, a synthetic backbone, an embodiment having at least four sequence defined attachment positions, complementary nucleic acid binding at the attachment regions, correspondence between the attachment positions and the target binding domain sequence, and use of the attachment position sequences to determine the identity of the bound target nucleic acid. ‘356 patent further teaches the synthetic backbone to L-DNA and requires each nucleotide of the nucleic acid sequence of each attachment region to be L-DNA. Instant claim 1 recites a synthetic backbone but does not exclude L-DNA. Accordingly, the L-DNA embodiment falls within the broader synthetic backbone of instant claim 1.
The relevant differences are that instinct claim 1 requires combination of a kit comprising 1) a first plurality of oligonucleotides having the recited fluorophore chemistry; and 2) at least a second plurality of oligonucleotides comprising the target binding/barcode architecture.
The teachings of Su and Stupi are as discussed supra in the 35 U.S.C. 103 are herein incorporated by reference in their entirety.
Su teaches the use of multiple target specific probes associated with distinguishable molecular barcodes. Su states that “different probes 210, 220, 230 that recognize specific targets may be attached to distinguishable barcodes 201, 202, 203”, and that the known barcode signal corresponding to a given probe specificity permits detection of individual target species (paragraph [0033], and Fig.2). Su further teaches a nucleic acid barcode in which “The barcode 530 is formed by hybridization of a series of tagged oligonucleotides 520 to a single stranded DNA template 500. The template 500 comprises a container section 540 and a probe section 550. The probe section 550 is designed to hybridize to a complementary target nucleic acid sequence”, and Su contemplates probe sections of 12 nucleotides and longer (paragraph [0037], and Fig. 5).
Su also teaches an embodiment in which “4 tagged 3-mers are required-TCA, TGT, ATG and CAG. Each tagged 3-mer can bind at one and only one site on the template 500” (paragraph [0043]), and “any changes in the sequence of the probe section 550 will require corresponding changes to be made in the container section 540 sequence” (paragraph [0043]). For example, when the probe sequence is changed from AGAA to AGTA, “the container sequence 540 must be changed also” (paragraph [0043]). Thus, Su identifies that the corresponding tagged oligonucleotide sequences resulting from a change in probe sequence as stating, “the corresponding oligonucleotide 520 sequences would be TCT TGT ATA and CAG.” (paragraph [0044]). Su also discloses that “The tags linked to the oligonucleotide are not limited to Raman tags. For example, fluorescent, nanoparticle, nanotube, fullerenes and quantum dot tags may also be attached to the oligonucleotide” (paragraph [0048]). Accordingly, Su provides a known target detection system in which a plurality of target-specific probes is associated with identifiable barcodes formed using complementary, sequence-defined tagged oligonucleotides.
Stupi teaches that a “reporter” is a chemical moiety capable of producing a detectable signal and identifies fluorescent dye groups including ALEXA Fluor 350, ALEXA Fluor 405, ALEXA Fluor 546, ALEXA Fluor 555, ALEXA Fluor 594, ALEXA Fluor 488 and ALEXA Fluor 647 (paragraph [0320]). Stupi further teaches that “a linker connects a reporter to a biological and non-biological component, for example, a nucleobase, a nucleoside or a nucleotide” (paragraph [0316]).
It would have been obvious to one of ordinary skills in the art to provide a plurality of the probe claims of the ‘356 patent together with complementary tagged oligonucleotides for use in a multiplexed target detection system as disclosed by Su, and use the known fluorescent reporters disclosed by Stupi as the fluorescent tags on the associated oligonucleotides. Accordingly, the differences between instant claims and ‘356 patent would have been an obvious variation in view of the combined teachings of Su and Stupi for the same reasons discussed supra in the 35 U.S.C. 103 rejection, which reasons are herein incorporated by reference in their entirety.
Claims 1, 13, and 14 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 77 and 78 of copending Application No. 18/985,839 in view of Su et al. (US 2005/0064435 A1, pub'd 03/24/2005, made of record in the IDS) and Stupi et al. (US 2013/0122489 A1, pub’d 05/16/2013).
This is a provisional nonstatutory double patenting rejection.
The claim 77 of ‘839 application recites that “A set of probes, comprising: a primary nucleic acid molecule including a target binding domain and a barcode domain attached thereto, wherein the target binding domain includes at least six nucleotides and is capable of binding a target nucleic acid, wherein the barcode domain includes at least three attachment positions, each attachment position including at least one attachment region including at least one nucleic acid sequence capable of being bound by a reporter probe, wherein the nucleic acid sequence of the at least three attachment positions is associated with the at least six nucleotides in the target nucleic acid that is bound by the target binding domain; at least one reporter probe including at least a first domain and a second domain with a linker modification positioned between the first and second domains, wherein the first domain includes a nucleotide sequence complementary to the nucleic acid sequence of at least one attachment position of the primary nucleic acid molecule, and the second domain includes at least three attachment positions, wherein each attachment position in the second domain of the reporter probe includes the same nucleotide sequence capable of hybridizing to at least one complementary secondary nucleic acid molecule; and at least one secondary nucleic acid molecule capable of hybridizing to one of the attachment positions of the second domain of the reporter probe, the secondary nucleic acid molecule attached to at least one detectable label.”, and claim 78 further limits that the barcode domain of the primary nucleic acid molecule includes a synthetic backbone, and wherein said synthetic backbone comprises a polysaccharide, a polynucleotide, a peptide, a peptide nucleic acid, or a polypeptide.
Thus, 839 application teaches that a set of probes having the same general target binding/barcode relationship as instant claim 1, including a target binding domain, a barcode domain, sequence defined attachment positions capable of complementary nucleic acid binding, a synthetic backbone, and reporter nucleic acids used to detect the barcode.
The relevant differences are that instinct claim 1 requires 1) a target binding domain comprising at least 12 nucleotides rather than the minimum of 6 nucleotides; 2) at least 4 attachment positions rather than the minimum of 3; 3) different nucleic acid sequences at the attachment positions; 4) correspondence between the attachment positions and the target binding domain sequence, with the attachment position sequences determining the identity of the bound target nucleic acid; and (5) a first plurality of oligonucleotides having the recited fluorophore chemistry.
Su teaches that 1) “The probe 550 length is not limiting and probe sections 550” and identifies probe sections of “12, 13, 14, 15” nucleotides and longer (paragraph [0037]); 2) the 4-position example in which “only 4 tagged 3-mers are required-TCA, TGT, ATG and CAG. Each tagged 3-mer can bind at one and only one site on the template 500” (paragraph [0043]); 3) the tagged oligonucleotides are complementary to sequence defined sites in the container section and that ““any changes in the sequence of the probe section 550 will require corresponding changes to be made in the container section 540 sequence” (paragraph [0043]). Su further identifies the corresponding replacement tagged oligonucleotide sequences resulting from such a probe sequence change (paragraph [0044]).
Accordingly, Su provides a known target detection system having at least four distinct sequence defined binding sites, the sequences of which vary according to the target-specific probe sequence, thereby providing a detectable barcode associated with the target recognized by the probe.
Stupi teaches that a “reporter” is a chemical moiety capable of producing a detectable signal and identifies fluorescent dye groups including ALEXA Fluor 350, ALEXA Fluor 405, ALEXA Fluor 546, ALEXA Fluor 555, ALEXA Fluor 594, ALEXA Fluor 488 and ALEXA Fluor 647 (paragraph [0320]). Stupi further teaches that “a linker connects a reporter to a biological and non-biological component, for example, a nucleobase, a nucleoside or a nucleotide” (paragraph [0316]).
It would have been obvious to one of ordinary skills in the art to use a target binding domain of at least 12 nucleotides and at least 4 different sequence defined barcode positions having the correspondence described by Su, and use the known fluorescent reporters disclosed by Stupi as the fluorescent tags on the associated oligonucleotides. Accordingly, the differences between instant claims and ‘839 application would have been an obvious variation in view of the combined teachings of Su and Stupi for the same reasons discussed supra in the 35 U.S.C. 103 rejection, which reasons are herein incorporated by reference in their entirety.
Conclusion
Claims 1, 13, and 14 are rejected.
Claim 1 is objected to.
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 SEONG JONG KIM whose telephone number is (571)272-6918. The examiner can normally be reached 7:00am-3:30pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Clinton A. Brooks can be reached at 571-270-7682. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/SEONG JONG KIM/Examiner, Art Unit 1621
/CLINTON A BROOKS/Supervisory Patent Examiner, Art Unit 1621
