Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
DETAILED ACTION
Status of the Claims
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 08/06/2024 has been entered.
Claims 2-3, 7-13, 40, 42, 45 and 48-54 are pending and the subject of this FINAL Office Action.
All claims are patentably indistinct from claims in the application prior to the entry of the submission under 37 CFR 1.114 (that is, restriction would not be proper) and all claims could have been finally rejected on the grounds and art of record in the next Office action if they had been entered in the application prior to entry under 37 CFR 1.114. Accordingly, THIS ACTION IS MADE FINAL even though it is a first action after the filing of a request for continued examination and the submission under 37 CFR 1.114. See MPEP § 706.07(b).
Claim 2 is amended to recite that the splint oligo has a “concentration of 3.1 nM to 1000 nM.” However, this, too, is very clearly taught in Kim.
Claim Interpretations
During examination, claims receive the broadest reasonable interpretation in light of the specification. MPEP § 2111. Applicants are also reminded that “[a]n essential purpose of patent examination is to fashion claims that are precise, clear, correct, and unambiguous” because “[o]nly in this way can uncertainties of claim scope be removed, as much as possible, during the administrative process.” In re Zletz, 893 F.2d 319, 322 (Fed. Cir. 1989). Finally,
the patent drafter is in the best position to resolve the ambiguity in the patent claims, and it is highly desirable that patent examiners demand that applicants do so in appropriate circumstances so that the patent can be amended during prosecution rather than attempting to resolve the ambiguity in litigation.
Halliburton Energy Servs., Inc. v. M-I LLC, 514 F.3d 1244, 1255 (Fed. Cir. 2008).
Claims 7 and 50 broadly recite “small-footprint DNA ligase (SFL)” which encompasses any ligase capable of joining polynucleotides of at least 3 nucleotides. Specifically, “small-footprint DNA ligase (SFL)” is not a standard term of art, rather this is Applicants’ own term. In other words, Applicants are their own lexicographer. See Thorner v. Sony Computer Entm’t Am. LLC, 669 F.3d 1362, 1365 (Fed. Cir. 2012) (“To act as its own lexicographer, [an applicant] must ‘clearly set forth a definition of the disputed claim term’ other than its plain and ordinary meaning.”) (citing CCS Fitness, Inc. v. Brunswick Corp., 288 F.3d 1359, 1366 (Fed. Cir. 2002)); Aventis Pharma S.A. v. Hospira, Inc., 675 F.3d 1324, 1330 (Fed. Cir. 2012) (“[T]he lexicography exception requires the patent drafter to ‘clearly set forth a definition of the disputed claim term.’) (quoting Thorner, 669 F.3d at 1365). Applicants broadly define SFL as a ligase that “has the the [sic] ability to ligate short polynucleotides (e.g., at least about 3 nucleotides)” (Specification, pg. 24, para. 0055). A “short” polynucleotide is exemplified as “an oligonucleotide that is at least 6 nucleotides, e.g., 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more nucleotides” (Specification, pg. 18, para. 0018). In other words, a short polynucleotide at least encompasses a polynucleotide 3-20 or more nucleotides in length. Furthermore, “[a] SFL can comprise a polypeptide sequence that is homologous to or a variant of a known ligase sequence or any portion thereof” (Specification, pg. 25, para. 0056) and “[e]xemplary SFLs can have amino acid sequence identity of at least 70%, optionally at least 85%, optionally at least 90 or 95%, with a known ligase, and possesses one or more functional activities of a ligase” (id.). Finally, “derivatives thereof” encompasses any fragment of SEQ ID NOS: 77-82 (ligases from Paramecium bursaria Chlorella virus I, Burkholderia pseudomallei and Haemophilus influenza); or any “derivative” of any portion of these ligases found in other ligases. This interpretation is consistent with the explanation of “[e]xemplary SFLs” that “can have amino acid sequence identity of at least 70%, optionally at least 85%, optionally at least 90 or 95%, with a known ligase, and possesses one or more functional activities of a ligase.” This interpretation is also consistent with the explanation of antibody “derivatives” found in paragraph 0081: “Suitable derivatives may include fragments (e.g., Fab, Fab2 or single chain antibodies (Fv for example)).” This broad definition employed by Applicants as their own lexicographer encompasses any ligase that has the mere ability to ligate “short” polynucleotides of 3-20 or more nucleotides, no matter how efficient and effective at ligating. Standard ligases (such as T4 ligase) meet this definition.
As to “3’ end” and “5’ end” in the phrase “a splint oligonucleotide comprising a 3' end of four to nine bases in length and a 5' end of four to nine bases in length,” these are never defined in the Specification. Thus, “3’ end” and “5’ end” encompass any portion of a larger “splint oligonucleotide”/connector that is 4-9 bases. For example, a 30-base splint oligonucleotide with 4-9 bases on a portion of each end.
Claim Rejections - 35 USC § 102 - Maintained
The following is a quotation of the appropriate paragraphs of 35 U.S.C. § 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a) the invention was known or used by others in this country, or patented or described in a printed publication in this or a foreign country, before the invention thereof by the applicant for a patent.
Claims 2-3, 7-13, 40, 42, 45 and 48-54 are rejected under 35 U.S.C. § 102(a) as being anticipated by Kim et al. (Improvement of sensitivity and dynamic range in proximity ligation assays by asymmetric connector hybridization, Anal Chem. 2010 Aug 15;82(16):6976-82).
As to claims 2-3, 7-13, 40, 42, 48-51 and 53-54, Kim teaches a method for ligating at least two oligonucleotides to produce a ligated oligonucleotide and amplifying the ligated oligonucleotide comprising: a) contacting a target protein or analyte with at least a first probe and a second probe, each probe having binding specificity for the protein or analyte, and being adjoined to at least one type of oligonucleotide (two proximity probes comprising DNA-conjugated antibodies or oligonucleotide aptamers; Fig. 1); b) ligating the oligonucleotides on the first and second probes to one another to produce a target nucleic acid using (id.): (i) a ligase selected from the group consisting of a nucleic acid ligase, oligonucleotide ligase, DNA ligase, T3 DNA ligase, T4 DNA ligase, T5 DNA ligase, T7 DNA ligase, vaccinia virus DNA ligase, E. coli DNA ligase, mammalian DNA ligase I, mammalian DNA ligase II, mammalian DNA ligase III, Tth DNA ligase, KOD DNA ligase, a thermostable DNA ligase, RNA ligase, T4 RNA ligase, bacteriophage RB69 RNA ligase, Autographa californica nuclearpolyhedrosis virus RNA ligase, a thermophilic RNA ligase, bacteriophage RM378 RNA ligase, bacteriophage TS2126 RNA ligase (T4 DNA ligase; pg. 6977, col. 2); and (ii) a splint oligonucleotide comprising a 3′ end of four to nine bases in length and a 5′ end of four to nine bases in length (connectors C15-C20; Table 1); c) amplifying the target nucleic acid (Fig. 1); and d) detecting the amplified target nucleic acid, wherein the ligation and amplification steps occur in a single reaction mixture (id.). Kim clearly teaches “5 min at 22 °C for ligation” (pg. 6978, col. 1).
As to claims 2, 50 and 52, Kim teaches the 3′ and 5′ ends of the splint oligonucleotide are symmetrical or asymmetrical to one another (id.).
Kim teaches at least one of said oligonucleotides comprises at least three nucleotides (Table 1).
Kim teaches oligonucleotides on said first and second probes, are at least partially complementary to one another (Table 1).
Kim teaches the method of claim 40, wherein a portion of at least one of said probes is an antibody (pg. 6976, col. 1).
Kim teaches a portion of each of said first and second probes are antibodies (id.).
Kim teaches the small footprint ligase is contacted with adenosine triphosphate (ATP) prior to use (pg. 6978, col. 1). Kim also teaches adenosine triphosphate is omitted from the reaction mixture in step b) and wherein the SFL is contacted with adenosine triphosphate prior to use in step b) (id.).
Kim teaches the ligated oligonucleotide is amplified using polymerase chain reaction (PCR) (id.).
Kim teaches said amplified ligated oligonucleotide is detected using quantitative PCR (qPCR) (Fig. 1).
Kim teaches said splint oligonucleotide is blocked at the 3′-end (instant Specification states that “[t]he blocking agent can be any covalently connected moiety that prevents polymerase activity” and “[i]n some embodiments, for example, the 3' blocking agent can include . . . 3'-deoxy”).
Kim teaches said ligase is inactivated after ligation using a protease or heat (heat inactivation at 95°C; pg. 6978, col. 1).
Kim teaches a) binding a first and a second probe, each of which binds specifically to the target, wherein each of the probes comprises an oligonucleotide portion or tail (probes comprise oligonucleotide portion; Fig. 1).
Previous Response to Arguments
The Examiner maintains the rejections because both Kim and LEVY clearly teach symmetrical and asymmetrical splints. Kim clearly discloses asymmetrical “connector” (AKA splint) with 15 bases total (C15; Fig. 1); and symmetric C16 (pg. 6978, col. 1). LEVY teaches the splint has “a complementarity of x bases, wherein x is 0 to 30” with the equivalent of the oligos attached to the antibodies here. In other words, “the splint oligonucleotide including 6 to 20 nucleotides in length, and the splint oligonucleotide having a 3 'end of four to nine bases in length and a 5 'end of four to nine bases in length,” or splint 10-29 bases long. The “nucleic acid splint . . . contains one or more basepair complementarity overlap with each of the first and second probes [here, oligos]” (para. 0041, for example). The oligos “may have different length of complementarity” with the splint (para. 0042). Thus, the splint can be symmetric or asymmetric with the oligos.
As was clearly expressed in the parent Applications, the claims here are not allowable.
Previous Response to Arguments
The Examiner maintains the rejections because as was previously explained “Kim teaches said ligase is inactivated after ligation using a protease or heat (heat inactivation at 95°C; pg. 6978, col. 1).”
Response to Arguments
The Examiner maintains the rejections because Kim very clearly teaches: 1) labeled qPCR detection (Fig. 1); and “400 nM C16,PLA [splint oligo] (same conditions as previously reported)” (pg. 6978, col. 1- “Proximity Ligation Assays”; citing Fredriksson et al.. Nat. Biotechnol. 2002, 20, 473–477).
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Claim Rejection - 35 USC § 103 - Maintained
The following is a quotation of 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
Claims 7-8 are rejected under 35 U.S.C. § 103(a) as being unpatentable over Kim, in view of SCHALLMEINER (WO 2007/107743 A1, published 09/27/2007), in further view of Ho et al. (Characterization of an ATP-dependent DNA ligase encoded by Chlorella virus PBCV-1, Characterization of an ATP-dependent DNA ligase encoded by Chlorella virus PBCV-1).
This rejection is presented in the interest of compact prosecution and to the extent that the “SFL” is one of SEQ ID NOS: 77-82.
It would have been prima facie obvious to one having ordinary skill in the art at the time of the invention to apply familiar “SFLs” to the proximity ligation assays (PLA) of Kim in order to more efficiently ligate short connectors/splints with a reasonable expectation of success.
Kim teach the elements of claims 40-53 as explained above. Kim demonstrate that a skilled artisan would have been motivated to shorten the length of the 3’-end and 5’-end regions of the splints/connectors that hybridize to the proximity probes in order to improve PLA sensitivity and dynamic range (Kim, Abstract). SCHALLMEINER further states that it is “desirable to design the splint so as to minimise any false amplification which may take place in such a step, for example any possibility of the splint acting as a template for the polymerase used in the amplification,” then provides the following option: “Alternatively, a similar effect [of preventing unwanted polymerization] may be achieved using a DNA splint with two short hybridisation regions; since the hybridisation is weak, such a splint will not template DNA polymerisation at the high temperatures used in PCR” (pg. 18).
Kim does not explicitly teach the “SFLs” of SEQ ID NOS: 77-82.
However, a skilled artisan would have been motivated to apply familiar “SFL” such as Chlorella virus PBCV-1 of instant SEQ ID NO: 77 in order to more specifically ligate desired oligonucleotides with a reasonable expectation of success. Specifically, Ho teaches that Chlorella virus PBCV-1 “[has] an intrinsic ability to bind preferentially to DNA sites where [its] action is required” (pg. 1936, col. 2 – pg. 1937, col. 1; see also Fig. 10). In fact, in the presence of ATP, this Chlorella virus PBCV-1 ligase has very efficient ligation activity (Figs. 6-7). And PBCV-1 ligase “is the smallest DNA ligase described to date” and “may well represent the minimum catalytic unit of an ATP-dependent ligase. This Chlorella virus PBCV-1 ligase comprises SEQ ID NO: 77:
Instant SEQ ID NO: 77/Ho (Genbank accession number U77663, Fig. 2)
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In other words, a skilled artisan would have been motivated to apply Chlorella virus PBCV-1 of instant SEQ ID NO: 77 to the PLA techniques of the prior art in order to take advantage of its “intrinsic ability to bind preferentially to DNA sites where [its] action is required,” thus increasing PLA specificity with a reasonable expectation of success.
Thus, it would have been prima facie obvious to one having ordinary skill in the art at the time of the invention to apply familiar Chlorella virus PBCV-1 of instant SEQ ID NO: 77 to the PLA techniques of Kim in order to further increase PLA specificity and efficiency with a reasonable expectation of success.
Claim 42 is rejected under 35 U.S.C. § 103(a) as being unpatentable over Kim, in view of Univ. of Calgary (3'End Modifications, University Core DNA Services, 06/14/2010).
This rejection is presented in the interest of compact prosecution and to the extent that the “blocked” “splint oligonucleotide” actually prevent polymerase extension.
It would have been prima facie obvious to one having ordinary skill in the art at the time of the invention to add a blocking moiety at the 3’-end of the connector of Kim in order to prevent unwanted extension of the connector with a reasonable expectation of success.
Kim teach the elements of claim 40 as explained above. Kim does not explicitly teach wherein said splint oligonucleotide is blocked at the 3′-end with a moiety that actually blocks polymerase extension (e.g. phosphothioate).
However, Univ. of Calgary demonstrates that a skilled artisan would have been familiar with any number of “common” 3’-end modifications to prevent unwanted polymerase extension with a reasonable expectation of success (“Some common 3'end modifications are listed below. . . . 3'- Amino . . . . 3'-Black Hole Quenchers . . . 3’-Biotin . . . . 3’-Dyes . . . . 3’-Phosphate . . . This is the simplest way to block the 3'end of an oligonucleotide from polymerase extension.”).
Thus, it would have been prima facie obvious to one having ordinary skill in the art at the time of the invention to apply familiar 3’-end blockages to the splint oligonucleotides of Kim in order to prevent unwanted polymerase extension with a reasonable expectation of success.
Response to Arguments
The Examiner maintains the rejections for the reasons stated above.
Prior Art
The following prior art is pertinent: 2009/0162840; Gustafsdottir et al. (Proximity ligation assays for sensitive and specific protein analyses, Anal Biochem. 2005 Oct 1;345(1):2-9. Epub 2005 Feb 7); US 2011/0008788; US 6,949,370.
Conclusion
No claims are allowed.
All claims are either identical to or patentably indistinct from claims in the application prior to the entry of the submission under 37 CFR 1.114 (that is, restriction would not be proper) and all claims could have been finally rejected on the grounds and art of record in the next Office action if they had been entered in the application prior to entry under 37 CFR 1.114. Accordingly, THIS ACTION IS MADE FINAL even though it is a first action after the filing of a request for continued examination and the submission under 37 CFR 1.114. See MPEP § 706.07(b). 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 extension fee 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 Aaron Priest whose telephone number is (571)270-1095. The examiner can normally be reached 8am-6pm.
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/AARON A PRIEST/Primary Examiner, Art Unit 1681