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 .
Election/Restrictions
Applicant's election with traverse of Group I, claims 1-15 in the reply filed on 05/11/2026 is acknowledged. The traversal is on the ground(s) that they do not have a materially different design because both feature a linker and a dye. This is not found persuasive because even though they may comprise a common feature, one comprises a nucleotide and the other does not which results in the two inventions having a materially different design.
The requirement is still deemed proper and is therefore made FINAL.
Claims 16-20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected inventions, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 05/11/2026.
Claims 1-20 are pending. Claims 1-15 are being examined. Claims 16-20 are withdrawn from further consideration as being drawn to a non-elected invention.
Allowable Subject Matter
Claim 4 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 14-15 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 14 recites the limitation “wherein the bridge”. There is insufficient antecedent basis for “the bridge”. For the purpose of examination, the claim will be interpreted such that the linker of claim 1 is “the bridge”.
Claim 15 recites the limitation “the first dye and second dye”. There is insufficient antecedent basis for “second dye”.
Claim Rejections - 35 USC § 102
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 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)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1-3, 5, 9, 12, 14 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Fegan et al. (Fegan et al., “Rigid cyanine dye nucleic acid labels”, Chem Commun (Camb), 2008 May; (17)).
Considering claim 1, Fegan teaches a rigid dye system comprising a linker, a first dye, and a nucleotide (Fegan, abstract and 2nd paragraph of page 1).
Considering claims 2-3, 5 and 14, Fegan teaches the linker is a substituted acetylene by teaching that it is ethynyl (Fegan, 2nd paragraph of page 1).
Considering claim 9, Fegan teaches the first dye is a cyanine derivative by teaching Cy3 and Cy5 (Fegan, 2nd paragraph of page 1).
Considering claim 12, Fegan teaches the nucleotide is DNA (Fegan, 2nd paragraph of page 1).
Claim Rejections - 35 USC § 103
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 6-8, 15 are rejected under 35 U.S.C. 103 as being unpatentable over Fegan et al. (Fegan et al., “Rigid cyanine dye nucleic acid labels”, Chem Commun (Camb), 2008 May; (17)) in view of Hirata et al. (Hirata et al., “Development of xanthene dyes containing arylacetylenes: The role of acetylene linker and substituents on the aryl group”, Tetrahedron 74 (2018) 3608-3615).
Considering claims 6-8, all of the limitations are met by the prior art referenced in meeting claim 1 limitations except for the dye is substituted.
Although Fegan teaches a fluorescent dye attached to DNA via a rigid linker such as ethynyl (Fegan, abstract), he does not explicitly teach that the fluorescent dye is substituted.
However, Hirata teaches connecting an aryl groups such as phenyl and mesityl groups to a fluorescent dye through a triple bond to shift both absorption and emission wavelengths (Hirata, 2nd column on page 3608, 2nd column on page 3610, 1st column on page 3612, and conclusion).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to substitute the dye with an aryl such as a methyl substituted benzene or a mesityl ring. One of ordinary skill in the art, before the effective filing date of the claimed invention, would have been motivated to do so in order to shift the emission wavelengths with a reasonable expectation of success.
Considering claim 15, all of the limitations are met by the prior art referenced in meeting claim 1 limitations except for the first dye and a second dye are configured to have independent transition dipole moments.
Fegan teaches multiply labelling oligonucleotides and using rigid linkers (Fegan, abstract and end of 1st paragraph on page 2).
Therefore it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, for the system to further comprise a bridge bonded (i.e., rigid linker) to a second dye. One of ordinary skill in the art, before the effective filing date of the claimed invention would have been motivated to do so in order to enable multiply labelling the nucleotide with a reasonable expectation of success.
Fegan does not explicitly teach the first dye and a second dye are configured to have independent transition dipole moments.
Hirata teaches connecting an aryl groups such as phenyl and mesityl groups to a fluorescent dye through a triple bond to shift both absorption and emission wavelengths (Hirata, 2nd column on page 3608, 2nd column on page 3610, 1st column on page 3612, and conclusion).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to substitute the dye with an aryl such as a methyl substituted benzene or a mesityl ring. One of ordinary skill in the art, before the effective filing date of the claimed invention, would have been motivated to do so in order to shift the emission wavelengths with a reasonable expectation of success.
Paragraph [0014] of instant specification discloses that substituting the dye with a compound (i.e., mesityl) that inhibits torsional rotation of the dyes promotes J-like stacking. Paragraph [0133] of the instant specification discloses that due to the bridge (i.e., rigid linker) combining the dyes into one molecule while maintaining the positions of the dyes, and hence their transition dipole moments, the molecule may have two or more transition dipole moments. Therefore, it would be expected that the dyes of the multiply labelled nucleotide of Fegan/Hirata would also have independent transition dipole moments due to the rigid linker and substitution of the dye(s) with aryl group(s).
Claim 13 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Fegan et al. (Fegan et al., “Rigid cyanine dye nucleic acid labels”, Chem Commun (Camb), 2008 May; (17)).
Considering claim 13, Fegan teaches multiply labelling oligonucleotides (Fegan, end of 1st paragraph on page 2).
Therefore it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, for the system to further comprise a bridge bonded to a second dye. One of ordinary skill in the art, before the effective filing date of the claimed invention would have been motivated to do so in order to enable multiply labelling the nucleotide with a reasonable expectation of success.
Claims 10-11 are rejected under 35 U.S.C. 103 as being unpatentable over Fegan et al. (Fegan et al., “Rigid cyanine dye nucleic acid labels”, Chem Commun (Camb), 2008 May; (17)) in view of Hyde et al. (US 2010/0041014 A1).
Considering claims 10-11, all of the limitations are met by prior art referenced in meeting claim 9 limitations except for the first dye is a bacteriochlorin.
Fegan does not explicitly teach the first dye is a bacteriochlorin.
However, Hyde teaches labelling of DNA/RNA with a photoactivatable molecule such as bacteriochlorin and/or cyanine among others (Hyde, claims 6, 8, 13-14). Thus, Hyde establishes that both cyanine and bacteriochlorin are suitable for labelling DNA. Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, for the first dye to be a bacteriochlorin because substituting equivalents known for the same purpose is prima facie obvious (see MPEP §2144.06(II)).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ANITA NASSIRI-MOTLAGH whose telephone number is (571)270-7588. The examiner can normally be reached M-F 6:30-3:00.
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/ANITA NASSIRI-MOTLAGH/Primary Examiner, Art Unit 1734
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