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 .
This action is in response to papers filed 5/26/2026.
Claims 3-5,10-12, 14-18, 20-22,25-26,29-30,47, 52-53 are pending. Claims 1-2,6-9,13, 19, 23-24,27-28,31-46, 48-51 have been cancelled.
The following rejections are newly applied as necessitated by amendment.
The following action is final.
Withdrawn Rejections
The 35 USC 112b and 35 USC 102 made in the previous office action is withdrawn based upon amendments to the claims.
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.
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) 3-5,10-12, 14-18, 20-22,25-26,29-30,47, 52-53 is/are rejected under 35 U.S.C. 103 as being unpatentable over Bernitz et al. (US Patent No. 8551710 October 8, 2012).
With regard to claim 3, Bernitz et al. teaches a method of using a padlock probe to a sample with one or more targets such that the padlock probes comprise binding sites (para 13 and Figure 1). Bernitz et al. teaches contacting one or more secondary probes, one or more tertiary probes (figure 1, figure 8 and para 13-18, and 43). Although Bernitz et al. does not teach that the probes are orthogonal, figure 1 and 8 suggest these probes can be orthogonal. Bernitz et al. teaches using ligation during these steps and imaging (para 13-18, and 43 and 112).
With regard to claim 4-5, 13-18, and 43teaches that the steps can be repeated and that ligation will stabilize the probes (para 13-18, and 43 and 112).
With regard to claims 10-12, as the padlock probes hybridize to different targets the padlock probes would comprise amplifier fragments that would be complementary to each of the padlock probes (see figure 1 and 8).
With regard to claim 14, Bernitz et al. teaches a method of using a ligase (para 100).
With regard to claim 15, Bernitz et al. teaches a sequence that interacts with padlock probes directing our indirectly (para 26 claims 15-18 and figure 8) and as such suggests a splint sequencing interacting.
With regard to claim 16, Bernitz et al. teaches that these fragments are ligated with a ligase (para 100).
With regard to claims 17-18, Bernitz et al teaches a method of hybridizing the padlock probes with detection probes to detect the presence of sequences (para 15-17). These detection probes would be considered readout probes.
With regard to claim 20, Bernitz et al. teaches that the targets can be DNA or RNA (para 20).
With regard to claim 21, Bernitz et al. teaches that the targets are conjugated to oligonucleotide sequences (para 55).
With regard to claims 22 and 25 and 47, although Bernitz et al does not recite cis-ligation, Bernitz et al. teaches hybridizing a contacting RNA probes for rolling circle amplification (para 20-60). This ligation performed by Bernitz et al. would be considered a type of cis-ligation.
With regard to claim 26, Bernitz et al. teaches a method of using a padlock probe to a sample with one or more targets such that the padlock probes comprise binding sites (para 13 and Figure 1).
With regard to claim 29, Bernitz et al. teaches the use of reactive groups of phosphate and amines (para 31).
With regard to claims 30, Bernitz et al teaches a method of hybridizing the padlock probes with detection probes to detect the presence of sequences (para 15-17). These detection probes would be considered readout probes.
With regard to claims 52-53, as the padlock probes hybridize to different targets the padlock probes would comprise amplifier fragments that would be complementary to each of the padlock probes (see figure 1 and 8). Bernitz et al. teaches that there are tertiary and quaternary probes that bind to target regions and bind to detection probes (see figure 1).
Conclusion
No claims are allowed.
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 KATHERINE D SALMON whose telephone number is (571)272-3316. The examiner can normally be reached 9-530.
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, Wu Cheng (Winston) Shen can be reached at 5712723157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KATHERINE D SALMON/Primary Examiner, Art Unit 1682
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