JPWO2020227016A5

JPWO2020227016A5 -

Info

Publication number: JPWO2020227016A5
Application number: JP2021565115A
Authority: JP
Publication date: 2023-05-11

Claims

A set of two or more non-cross-reactive capture oligonucleotides (“capture set”) , said capture set being a subset of the set of parent capture oligonucleotides (“parent capture set”) , said Each capture oligonucleotide in a capture set has: a) a nucleotide sequence comprising at least 20 contiguous nucleotides of a nucleotide sequence from said parental capture set , or b) at least 95% of a nucleotide sequence from said parental capture set. wherein said parental capture set comprises a nucleotide sequence having the identity of
(a) a parent capture set 1 comprising capture oligonucleotides having nucleotide sequences selected from SEQ ID NOs: 1-64;
(b) parental capture set 2, comprising capture oligonucleotides having nucleotide sequences selected from SEQ ID NOS: 65-122;
(c) parental capture set 3, comprising capture oligonucleotides having nucleotide sequences selected from SEQ ID NOs: 123-186;
(d) parental capture set 4, comprising capture oligonucleotides having nucleotide sequences selected from SEQ ID NOS: 187-250;
(e) parental capture set 5, comprising capture oligonucleotides having nucleotide sequences selected from SEQ ID NOS: 251-308;
(f) parental capture set 6, comprising capture oligonucleotides having nucleotide sequences selected from SEQ ID NOS: 309-372;
(g) parental capture set 7, comprising capture oligonucleotides having nucleotide sequences selected from SEQ ID NOS: 373-436;
(h) a parent capture set 8 comprising capture oligonucleotides having nucleotide sequences selected from SEQ ID NOS: 437-494;
(i) a parent capture set 9 comprising capture oligonucleotides having nucleotide sequences selected from SEQ ID NOS: 495-558;
(j) a parent capture set 10 comprising capture oligonucleotides having nucleotide sequences selected from SEQ ID NOs:559-662;
(k) a parent capture set 11 comprising capture oligonucleotides having nucleotide sequences selected from SEQ ID NOS: 623-680;
(l) a set of two or more non-cross-reactive capture oligonucleotides selected from a parent capture set 12 comprising capture oligonucleotides having nucleotide sequences selected from SEQ ID NOs:681-744;

each capture oligonucleotide in the capture set comprising:
(a) a capture oligonucleotide having at least 20 contiguous nucleotides of a sequence selected from SEQ ID NOs: 1-64;
(b) a capture oligonucleotide comprising a sequence having at least 95 % identity to a sequence selected from SEQ ID NOs: 1-64;
(c) a capture oligonucleotide having at least 20 contiguous nucleotides of a sequence having at least 95 % identity to a sequence selected from SEQ ID NOs: 1-64;
(d) a capture oligonucleotide comprising a sequence selected from SEQ ID NOs: 1-64;
(e) a capture oligonucleotide selected from any of (a ) -(d).

each capture oligonucleotide in the set comprising:
(a) a capture oligonucleotide comprising a sequence having at least 20 contiguous nucleotides of a sequence selected from SEQ ID NOs: 1-10;
(b) a capture oligonucleotide comprising a sequence having at least 95 % identity to a sequence selected from SEQ ID NOs: 1-10;
(c) a capture oligonucleotide having at least 20 contiguous nucleotides of a sequence having at least 95 % identity to a sequence selected from SEQ ID NOS: 1-10;
(d) a capture oligonucleotide comprising a sequence selected from SEQ ID NOs: 1-10;
(e) a capture oligonucleotide selected from any of (a)-( d ).

The capture set of any one of claims 1-3 , wherein one or more capture oligonucleotides in the capture set comprises a reactive functional group.

said reactive functional group is attached to said capture oligonucleotide via a linker;
5. The capture set of claim 4 .

6. A capture set according to claim 4 or 5 , wherein said reactive functional group comprises a thiol group.

A capture set according to any one of claims 4 to 6 , wherein said capture oligonucleotides are immobilized on a surface via said reactive functional groups.

8. The capture set of Claim 7 , wherein the surface comprises an electrode surface.

9. The capture set of claim 8 , wherein said electrodes comprise carbon-based electrodes.

10. The capture set of claim 9 , wherein said electrodes comprise carbon ink electrodes.

A capture set according to any one of claims 1 to 10 , wherein the one or more non-reactive capture oligonucleotides is at least 24 nucleotides in length.

The capture set of any one of claims 1-11 , wherein the one or more capture oligonucleotides is at least 36 nucleotides in length.

A kit comprising a capture set according to any one of claims 1-12 .

A kit comprising a set of at least 2 to 64 non-cross-reactive capture oligonucleotides according to any one of claims 1-12 .

A kit comprising a capture set of at least 10 capture oligonucleotides according to any one of claims 1-12 .

A set of two or more non-cross-reactive oligonucleotide tags ("tag set") , said set of oligonucleotide tags being a subset of the set of parent oligonucleotide tags ("parent tag set") , said each oligonucleotide in the tag set has: a) a nucleotide sequence comprising at least 20 contiguous nucleotides of a nucleotide sequence from said parent tag set ; or b) at least 95 nucleotide sequences from said parent tag set. % identity , the parent tag set comprising:
(a) parent tag set 1, comprising oligonucleotide tags having nucleotide sequences selected from SEQ ID NOS: 745-808;
(b) parent tag set 2, comprising oligonucleotide tags having nucleotide sequences selected from SEQ ID NOs:809-866;
(c) parent tag set 3, comprising oligonucleotide tags having nucleotide sequences selected from SEQ ID NOS:867-930;
(d) parent tag set 4, comprising oligonucleotide tags having nucleotide sequences selected from SEQ ID NOS: 931-994;
(e) parent tag set 5, comprising oligonucleotide tags having nucleotide sequences selected from SEQ ID NOs:995-1052;
(f) parent tag set 6, comprising oligonucleotide tags having nucleotide sequences selected from SEQ ID NOS: 1053-1116;
(g) parent tag set 7, comprising oligonucleotide tags having nucleotide sequences selected from SEQ ID NOS: 1117-1180;
(h) parent tag set 8, comprising oligonucleotide tags having nucleotide sequences selected from SEQ ID NOs: 1181-1238;
(i) parent tag set 9, comprising oligonucleotide tags having nucleotide sequences selected from SEQ ID NOs: 1239-1302;
(j) a parent tag set 10 comprising oligonucleotide tags having nucleotide sequences selected from SEQ ID NOs: 1303-1366;
(k) parent tag set 11, comprising oligonucleotide tags having nucleotide sequences selected from SEQ ID NOS: 1367-1424;
(l) a set of two or more non-cross-reactive oligonucleotide tags selected from a parent tag set 12 comprising oligonucleotide tags having nucleotide sequences selected from SEQ ID NOs: 1425-1488.

A method of immobilizing oligonucleotides containing thiol groups to a carbon-based support surface, said method comprising:
(a) printing one or more droplets comprising said oligonucleotide onto said carbon-based support surface;
(b) allowing the droplet to spread over the surface;
(c) drying the droplets to form dried droplets;
(d) immobilizing the oligonucleotide to the carbon-based support surface via the thiol group;
(e) washing the dried droplets with a wash solution comprising a thiol-containing compound to remove non-immobilized oligonucleotides.

18. The method of claim 17 , comprising printing an array of droplets containing said capture oligonucleotides onto a plurality of binding domains on said support surface.

A method of immobilizing an array of capture oligonucleotides on the surface of one or more carbon-based electrodes, said method comprising:
(a) printing an array of droplets comprising one or more capture oligonucleotides on a plurality of binding domains on the surface of said one or more carbon-based electrodes, said one or more capture oligonucleotides comprises a thiol group; and
(b) allowing the droplet to spread over the surface;
(c) drying the droplets to form dried droplets;
(d) incubating the dried droplets for a time sufficient to immobilize one or more oligonucleotides to the surface of the carbon-based electrode via the thiol groups;
(e) washing the dried droplets with a wash solution comprising a thiol-containing compound to remove excess non-immobilized oligonucleotides.

(a) one or more substrate surfaces;
(b) a capture set according to any one of claims 1-12 , wherein said capture set is immobilized on one or more support surfaces;
kit, including

(a) one or more carbon-based electrodes having one or more surfaces;
(b) The capture set of any one of claims 1-12 , wherein said capture set is immobilized on one or more surfaces of said carbon-based electrode . and
kit, including

A method of identifying, detecting, or quantifying a target analyte in a sample, said method comprising :
(a )
(i) one or more carbon-based electrodes having one or more surfaces;
(ii) a capture set according to any one of claims 1-12, wherein said capture set is immobilized on one or more surfaces of said carbon-based electrode;
contacting the array with a composition comprising one or more target analytes comprising
associating and contacting said one or more target analytes with labels and oligonucleotide tags that are complementary to at least a portion of capture oligonucleotides immobilized on said support surface and labels;
( b ) incubating said composition of one or more target analytes under conditions in which said oligonucleotide tags hybridize to their corresponding complementary capture oligonucleotides to form hybridization complexes;
( c ) identifying, detecting, or quantifying said target analyte based on the presence or absence of said label at array locations;
A method, including