FriDETAILED 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 .
Applicant cancels claims 31, 33, and 44. Claims 1-3, 5, 9, 11-14, 16-20, 23-25, 49-54 and 56 are currently pending and under examination.
Election/Restrictions
Applicant’s election with traverse of Group I: claims 1-3, 5, 9, 11-14, 16-20, 23-25, 49-54 and 56 drawn to a labeled avidin for polynucleotide sequencing, in the reply filed on March 18, 2026, is acknowledged. However the election is moot in view of cancellation of claims 31, 33, and 44. Therefore, due to the cancellation of claims 31, 33, and 44 the restriction requirement is withdrawn.
Information Disclosure Statement
The Information Disclosure Statements filed June 13, 2023; June 15, 2023; and March 18, 2026 have been considered.
Specification
The use of the term Tween®20, (see Page 40, [0124]) which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-2, 5, 9, 11-14, 16-20, 23-25, 49-54 and 56 are rejected under 35 U.S.C. 102 (a)(1) and (a)(2) as being anticipated by Kain et al. (U.S. Patent Application Publication US 2013/0079232 A1, published March 28, 2013).
Regarding claim 1, Kain teaches a labeled avidin for polynucleotide sequencing and the avidin is labeled with one or more fluorescent dye moieties (Page 1, [0005]-[0007], Pages 2-3, [0015], Page 4, [0018], Page 6, [0028], Page 10, [0044] and Figs. 3-5). Kain teaches at least one biotin-binding site of the avidin is blocked with a biotin moiety-containing molecule or an analog thereof and the labeled avidin comprises at least one open biotin-binding site (Page 16, [0064] and [0070]).
Regarding claim 2, Kain teaches one biotin-binding site of the avidin is blocked with the biotin moiety-containing molecule or the analog thereof (Page 16, [0064] and [0070]).
Regarding claim 3, Kain teaches two biotin-binding sites of the avidin are blocked with the biotin moiety-containing molecule or the analog thereof (Page 16, [0064] and [0070]).
Regarding claim 5, Kain teaches the avidin is labeled with two to eight fluorescent dye moieties (Pages 2-3, [0015] and Page 6, [0034].
Regarding claim 9, Kain teaches the fluorescent dye moieties are excitable by a light source having a wavelength between 400 nm to 650 nm (Page 20, [0094], Page 21, [0100] and Fig. 4).
Regarding claim 11, Kain teaches the avidin is streptavidin (Page 1, [0005]-[0007], Pages 2-3, [0015] and Page 4, [0018]).
Regarding claim 12, Kain teaches the biotin moiety-containing molecule or the analog thereof comprises a biotin moiety that is covalently attached to a nucleotide or nucleoside (Page 22, [0115]-[0116]).
Regarding claim 13, Kain teaches the biotin moiety-containing molecule or the analog thereof is a free biotin molecule or an analog that is not covalently attached to a nucleotide or nucleoside (Page 10, [0044]).
Regarding claim 14, Kain teaches a labeled avidin nucleotide conjugate, comprising an avidin-binding partner covalently attached to the nucleotide, via a cleavable linker (Page 1, [0005]-[0007], Pages 2-3, [0015], Page 4, [0018], Page 6, [0028], Page 22, [0115]-[0116] and Figs. 3-5). Kain teaches the avidin-binding partner is conjugated with the labeled avidin of claim 1 via non-covalent interaction (Page 1, [0005]-[0007], Pages 2-3, [0015], Page 4, [0018], Page 6, [0028], Page 10, [0044] and Figs. 3-5).
Regarding claim 16, Kain teaches the avidin-binding partner is covalently attached to the nucleobase of the nucleotide via a cleavable linker (Page 22, [0115]-[0116] and Page 23, [0121]-[0122]).
Regarding claim 17, Kain teaches the cleavable linker comprising an azido, an allyl, or a disulfide moiety (Page 22, [0115]-[0116] and Page 23, [0121]-[0122]).
Regarding claim 18, Kain teaches nucleotide conjugate comprises a 3' hydroxy blocking group (Pages 7-8, [0040] and Page 22, [0115]).
Regarding claim 19, Kain teaches an oligonucleotide or polynucleotide conjugate, comprising an avidin conjugated to a terminal nucleotide moiety of the oligonucleotide or polynucleotide as well as the avidin is labeled with one or more fluorescent dye moieties (Page 1, [0005]-[0007], Pages 2-3, [0015], Page 4, [0018], Page 6, [0028], Page 10, [0044] and Figs. 3-5). Kain teaches at least one biotin-binding site of the avidin is blocked with a biotin moiety-containing molecule or an analog thereof (Page 16, [0064] and [0070]). Kain teaches the terminal nucleotide moiety comprises an avidin binding partner covalently attached thereto, and the labeled avidin is conjugated to the avidin binding partner of the terminal nucleotide moiety by non-covalent interaction (Page 1, [0005]-[0007], Pages 2-3, [0015], Page 4, [0018], Page 6, [0028], Page 10, [0044], Page 22, [0115]-[0116] and Figs. 3-5).
Regarding claim 20, Kain teaches one, two or three biotin-binding sites of the avidin is blocked with the biotin moiety-containing molecule or the analog thereof (Page 16, [0064] and [0070]).
Regarding claim 23, Kain teaches the terminal nucleotide moiety comprises a 3' hydroxy blocking group, and the avidin binding partner comprises a biotin moiety covalently attached to the nucleobase of the terminal nucleotide moiety (Pages 7-8, [0040] and Page 22, [0115]-[0116]). Kain teaches the avidin is conjugated to the terminal nucleotide moiety through non-covalent interaction between the biotin moiety and a biotin-binding site of the avidin (Page 10, [0044]).
Regarding claim 24, Kain teaches wherein the oligonucleotide or polynucleotide conjugate is at least partially complementary and hybridized to a target polynucleotide immobilized on a surface of a solid support (Pages 24-25, [0129]-[0131], Pages 25-26, [0133]-[0135] and Page , 26, [0140]).
Regarding claim 25, Kain teaches wherein the avidin is streptavidin (Page 1, [0005]-[0007], Pages 2-3, [0015] and Page 4, [0018]).
Regarding claim 49, Kain teaches a kit for polynucleotide sequencing, comprising a labeled avidin according to claim 1 (Page 1, [0005]-[0007], Pages 2-3, [0015], Page 4, [0018], Page 6, [0028], Page 10, [0044], Page 26, [0138]-[0139] and Figs. 3-5).
Regarding claim 50, Kain teaches an incorporation composition comprising a first type of nucleotide having a first label, a second type of nucleotide having a second label, a third type of nucleotide is unlabeled and functionalized with an avidin binding partner, a fourth type of nucleotide is not labeled (Pages 1-2, [0009]-[0012], Page 5, [0027], Page 14, [0055], Page 16, [0064] and Page 34, [0159] and [0161]). Kain teaches each of the four types of nucleotides comprises a 3' hydroxy blocking group (Pages 7-8, [0040] and Page 22, [0115]-[0116]).
Regarding claim 51, Kain teaches the avidin is streptavidin and the avidin binding partner comprises a biotin moiety covalently attached to the nucleobase of the third type of nucleotide, through a cleavable linker (Page 10, [0044], Page 16, [0064] and Page 25, [0132] and [0134]).
Regarding claim 52, Kain teaches the first label is covalently attached to the nucleobase of the first type of nucleotide via a cleavable linker comprising an azido, allyl, or disulfide moiety (Pages 2-3, [0015]-[0016], Page 4, [0018], Page 10, [0049], Pages 26-27, [0140] and Page 23, [0121]-[0122]).
Regarding claim 53, Kain teaches a cleavage composition comprising a chemical reagent capable of removing the first label of the first type of nucleotide (Page 23, [0123] and Page 36, [0176]).
Regarding claim 54, Kain teaches the chemical reagent for removing the first label of the first type of nucleotide comprises tris(hydroxypropyl)phosphine (THP) (Page 23, [0123] and Page 36, [0176]).
Regarding claim 56, Kain teaches A kit for polynucleotide sequencing, comprising a labeled avidin nucleotide conjugate according to claim 14 (Page 1, [0005]-[0007], Pages 2-3, [0015], Page 4, [0018], Page 6, [0028], Page 10, [0044], Page 22, [0115]-[0116], Page 26, [0138]-[0139] and Figs. 3-5).
Kain teaches each and every limitation of claims 1-2, 5, 9, 11-14, 16-20, 23-25, 49-54 and 56, therefore Kain anticipates claims 1-2, 5, 9, 11-14, 16-20, 23-25, 49-54 and 56.
Claims 1-2, 5, 9, 11-14, 16, 19-20 and 25 are rejected under 35 U.S.C. 102 (a)(1) and (a)(2) as being anticipated by Bergbrede et al. (U.S. Patent Application Publication US 2018/0142285 A1, published May 24, 2018), cited on the IDS filed June 13, 2023.
Regarding claim 1, Bergbrede teaches a labeled avidin with one or more fluorescent dye moieties (Page 9, [0153]-[0155], Page 16, [0242] and Figs. 1A-1C). Bergbrede teaches at least one biotin-binding site of the avidin is blocked with a biotin moiety-containing molecule or an analog thereof, and the labeled avidin comprises at least one open biotin-binding site (Page 9, [0153]-[0157] and Figs. 1A-1C).
Regarding claim 2, Bergbrede teaches one biotin-binding site of the avidin is blocked with the biotin moiety-containing molecule or the analog thereof (Page 9, [0153]-[0157] and Figs. 1A-1C).
Regarding claim 5, Bergbrede teaches the avidin is labeled with two to eight fluorescent dye moieties (Page 1, [0009], Page 4, [0061], Page 8, [0146] and Page 12, [0197]).
Regarding claim 9, Bergbrede teaches the fluorescent dye moieties are excitable by a light source having a wavelength between 400 nm to 650 nm (Page 4, [0060], Page 5, [0081], Page 8, [0149], Page 10, [0168] and Page 12, [0197]).
Regarding claim 11, Bergbrede teaches the avidin is streptavidin (Page 9, [0153]-[0155] and Figs. 1A-1C).
Regarding claim 12, Bergbrede teaches the biotin moiety- containing molecule or the analog thereof comprises a biotin moiety that is covalently attached to a nucleotide or nucleoside (Page 9, [0154] and [0157]).
Regarding claim 13, Bergbrede teaches the biotin moiety-containing molecule or the analog thereof is a free biotin molecule or an analog that is not covalently attached to a nucleotide or nucleoside (Page 9, [0156]).
Regarding claim 14, Bergbrede teaches a labeled avidin nucleotide conjugate, comprising an avidin- binding partner covalently attached to the nucleotide (Page 9, [0153]-[0157] and Figs. 1A-1C). Bergbrede teaches a cleavable linker (Page 8, [0150]). Bergbrede teaches the avidin-binding partner is conjugated with the labeled avidin of claim 1 via non-covalent interaction (Page 9, [0156]).
Regarding claim 16, Bergbrede teaches the avidin-binding partner is covalently attached to the nucleobase of the nucleotide via a cleavable linker (Page 8, [0150], Page 9, [0153]-[0157] and Figs. 1A-1C).
Regarding claim 19, Bergbrede teaches an oligonucleotide or polynucleotide conjugate, comprising an avidin conjugated to a terminal nucleotide moiety of the oligonucleotide or polynucleotide (Page 4, [0070], Page 7, [0133], Page 8, [0150]—Page 9, [0157], Page 11, [0178] and Figs. 1A-1C). Bergbrede teaches the avidin is labeled with one or more fluorescent dye moieties, and at least one biotin-binding site of the avidin is blocked with a biotin moiety-containing molecule or an analog thereof (Page 9, [0153]-[0157], Page 16, [0242] and Figs. 1A-1C). Bergbrede teaches the terminal nucleotide moiety comprises an avidin binding partner covalently attached thereto, and the labeled avidin is conjugated to the avidin binding partner of the terminal nucleotide moiety by non-covalent interaction (Page 4, [0070], Page 7, [0133], Page 8, [0150]—Page 9, [0157], Page 11, [0178] and Figs. 1A-1C).
Regarding claim 20, Bergbrede teaches one biotin-binding sites of the avidin is blocked with the biotin moiety-containing molecule or the analog thereof (Page 9, [0153]-[0157] and Figs. 1A-1C).
Regarding claim 25, Bergbrede teaches the avidin is streptavidin (Page 9, [0153]-[0155] and Figs. 1A-1C).
Bergbrede teaches each and every limitation of claims 1-2, 5, 9, 11-14, 16, 19-20 and 25, therefore Bergbrede anticipates claims 1-2, 5, 9, 11-14, 16, 19-20 and 25.
Conclusion
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/JESSICA D PARISI/Examiner, Art Unit 1684
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684
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