Polynucleotides for use as tags and tag complements, manufacture and use thereof
First Claim
Patent Images
1. A composition comprising molecules for use as tags or tag complements wherein each molecule comprises an oligonucleotide selected from a set of oligonucleotides based on a following group of sequences:
3 Assignments
0 Petitions
Accused Products
Abstract
A family of minimally cross-hybridizing nucleotide sequences, methods of use, etc. A specific family of 210 24mers is described.
-
Citations
113 Claims
-
1. A composition comprising molecules for use as tags or tag complements wherein each molecule comprises an oligonucleotide selected from a set of oligonucleotides based on a following group of sequences:
- View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106)
-
2. The composition of claim 1, wherein the composition includes at least ten said molecules, or at least eleven said molecules, or at least twelve said molecules, or at least thirteen said molecules, or at least fourteen said molecules, or at least fifteen said molecules, or at least sixteen said molecules, or at least seventeen said molecules, or at least eighteen said molecules, or at least nineteen said molecules, or at least twenty said molecules, or at least twenty-one said molecules, or at least twenty-two said molecules, or at least twenty-three said molecules, or at least twenty-four said molecules, or at least twenty-five said molecules, or at least twenty-six said molecules, or at least twenty-seven said molecules, or at least twenty-eight said molecules, or at least twenty-nine said molecules, or at least thirty said molecules, or at least thirty-one said molecules, or at least thirty-two said molecules, or at least thirty-three said molecules, or at least thirty-four said molecules, or at least thirty-five said molecules, or at least thirty-six said molecules, or at least thirty-seven said molecules, or at least thirty-eight said molecules, or at least thirty-nine said molecules, or at least forty said molecules, or at least forty-one said molecules, or at least forty-two said molecules, or at least forty-three said molecules, or at least forty-four said molecules, or at least forty-five said molecules, or at least forty-six said molecules, or at least forty-seven said molecules, or at least forty-eight said molecules, or at least forty-nine said molecules, or at least fifty said molecules, or at least sixty said molecules, or at least seventy said molecules, or at least eighty said molecules, or at least ninety said molecules, or at least one hundred said molecules, or at least one hundred and ten said molecules, or at least one hundred and twenty said molecules, or at least one hundred and thirty said molecules, or at least one hundred and forty said molecules, or at least one hundred and fifty said molecules, or at least one hundred and sixty said molecules, or at least one hundred and seventy said molecules, or at least one hundred and eighty said molecules, or at least one hundred and ninety said molecules, or at least two hundred said molecules.
-
3. The composition of claim 1, wherein said set of oligonucleotides is based on the sequences tested in Example 2, as set out in Table I.
-
4. The composition of claim 3, wherein the composition includes at least ten said molecules, or at least eleven said molecules, or at least twelve said molecules, or at least thirteen said molecules, or at least fourteen said molecules, or at least fifteen said molecules, or at least sixteen said molecules, or at least seventeen said molecules, or at least eighteen said molecules, or at least nineteen said molecules, or at least twenty said molecules, or at least twenty-one said molecules, or at least twenty-two said molecules, or at least twenty-three said molecules, or at least twenty-four said molecules, or at least twenty-five said molecules, or at least twenty-six said molecules, or at least twenty-seven said molecules, or at least twenty-eight said molecules, or at least twenty-nine said molecules, or at least thirty said molecules, or at least thirty-one said molecules, or at least thirty-two said molecules, or at least thirty-three said molecules, or at least thirty-four said molecules, or at least thirty-five said molecules, or at least thirty-six said molecules, or at least thirty-seven said molecules, or at least thirty-eight said molecules, or at least thirty-nine said molecules, or at least forty said molecules, or at least forty-one said molecules, or at least forty-two said molecules, or at least forty-three said molecules, or at least forty-four said molecules, or at least forty-five said molecules, or at least forty-six said molecules, or at least forty-seven said molecules, or at least forty-eight said molecules, or at least forty-nine said molecules, or at least fifty said molecules, or at least sixty said molecules, or at least seventy said molecules, or at least eighty said molecules, or at least ninety said molecules, or at least one hundred said molecules.
-
5. The composition of claim 1, wherein:
(G) for the group of 24mer sequences in which each 1=GATT, each 2=TGAT, each 3=AAAG, each 4=TGTA, each 5=GTAT, each 6=TTGA, each 7=TGAA, each 8=GTAA, each 9=ATTG, each 10=ATGA, each 11=TTAG, each 12=GTTA, each 13=ATAG, each 14=GTTT, each 15=GATG, each 16=GTAG, each 17=GAAG, each 18=GTTG, each 19=ATTA, each 20=TATA, each 21=TAAT and each 22=ATAT, under a defined set of conditions in which the maximum degree of hybridization between a sequence and any complement of a different sequence of the group of 24mer sequences does not exceed 30% of the degree of hybridization between said sequence and its complement, for all oligonucleotides of the set, the maximum degree of hybridization between an oligonucleotide and a complement of any other oligonucleotide of the set does not exceed 50% of the degree of hybridization of the oligonucleotide and its complement.
-
6. The composition of claim 3, wherein:
(G) for the group of 24mer sequences in which each 1=GATT, each 2=TGAT, each 3=AAAG, each 4=TGTA, each 5=GTAT, each 6=TTGA, each 7=TGAA, each 8=GTAA, each 9=ATTG, each 10=ATGA, each 11=TTAG, each 12=GTTA, each 13=ATAG, each 14=GTTT, each 15=GATG, each 16=GTAG, each 17=GAAG, each 18=GTTG, each 19=ATTA, each 20=TATA, each 21=TAAT and each 22=ATAT, under a defined set of conditions in which the maximum degree of hybridization between a sequence and any complement of a different sequence of the group of 24mer sequences does not exceed 30% of the degree of hybridization between said sequence and its complement, for all oligonucleotides of the set, the maximum degree of hybridization between an oligonucleotide and a complement of any other oligonucleotide of the set does not exceed 50% of the degree of hybridization of the oligonucleotide and its complement.
-
7. The composition of claim 5 wherein, in (G) under said defined set of conditions in which the maximum degree of hybridization between a sequence and any complement of a different sequence does not exceed 30% of the degree of hybridization between said sequence and its complement, the degree of hybridization between each sequence and its complement varies by a factor of between 1 and 10, more preferably between 1 and 9, and more preferably between 1 and 8.
-
8. The composition of claim 6 wherein, in (G) under said defined set of conditions in which the maximum degree of hybridization between a sequence and any complement of a different sequence does not exceed 30% of the degree of hybridization between said sequence and its complement, the degree of hybridization between each sequence and its complement varies by a factor of between 1 and 10, more preferably between 1 and 9, and more preferably between 1 and 8.
-
9. The composition of claim 7 wherein the maximum degree of hybridization in (G) between a sequence and any complement of a different sequence does not exceed 25%, more preferably wherein the maximum degree of hybridization in (G) between a sequence and any complement of a different sequence does not exceed 20%, more preferably wherein the maximum degree of hybridization in (G) between a sequence and any complement of a different sequence does not exceed 15%, more preferably wherein the maximum degree of hybridization in (G) between a sequence and any complement of a different sequence does not exceed 11%.
-
10. The composition of claim 8 wherein the maximum degree of hybridization in (G) between a sequence and any complement of a different sequence does not exceed 25%, more preferably wherein the maximum degree of hybridization in (G) between a sequence and any complement of a different sequence does not exceed 20%, more preferably wherein the maximum degree of hybridization in (G) between a sequence and any complement of a different sequence does not exceed 15%, more preferably wherein the maximum degree of hybridization in (G) between a sequence and any complement of a different sequence does not exceed 11%.
-
11. The composition of claim 7 wherein under said defined set of conditions of (G), the maximum degree of hybridization between a sequence and a complement of any other sequence of the set is no more than 15% greater than the maximum degree of hybridization between a sequence and any complement of a different sequence of the said group of 24mer sequences, more preferably no more than 10% greater, more preferably no more than 5% greater.
-
12. The composition of claim 8 wherein under said defined set of conditions of (G), the maximum degree of hybridization between a sequence and a complement of any other sequence of the set is no more than 15% greater than the maximum degree of hybridization between a sequence and any complement of a different sequence of the said group of 24mer sequences, more preferably no more than 10% greater, more preferably no more than 5% greater.
-
13. The composition of claim 9 wherein under said defined set of conditions of (G), the maximum degree of hybridization between a sequence and a complement of any other sequence of the set is no more than 15% greater than the maximum degree of hybridization between a sequence and any complement of a different sequence of the said group of 24mer sequences, more preferably no more than 10% greater, more preferably no more than 5% greater.
-
14. The composition of claim 10 wherein under said defined set of conditions of (G), the maximum degree of hybridization between a sequence and a complement of any other sequence of the set is no more than 15% greater than the maximum degree of hybridization between a sequence and any complement of a different sequence of the said group of 24mer sequences, more preferably no more than 10% greater, more preferably no more than 5% greater.
-
15. The composition of claim 5, wherein said defined set of conditions results in a level of hybridization that is the same as the level of hybridization obtained when hybridization conditions include 0.2 M NaCl, 0.1 M Tris, 0.08% Triton X-100, pH 8.0 at 37°
- C.
-
16. The composition of claim 6, wherein said defined set of conditions results in a level of hybridization that is the same as the level of hybridization obtained when hybridization conditions include 0.2 M NaCl, 0.1 M Tris, 0.08% Triton X-100, pH 8.0 at 37°
- C.
-
17. The composition of claim 15 wherein, in (G) said defined set of conditions includes the group of 24mer sequences of (G) being covalently linked to beads.
-
18. The composition of claim 16 wherein, in (G) said defined set of conditions includes the group of 24mer sequences of (G) being covalently linked to beads.
-
19. The composition of claim 17 or 18 wherein, in (G) for the group of 24mers the maximum degree of hybridization between a sequence and any complement of a different sequence does not exceed 15% of the degree of hybridization between said sequence and its complement and the degree of hybridization between each sequence and its complement varies by a factor of between 1 and 9, and for all oligonucleotides of the set, the maximum degree of hybridization between an oligonucleotide and a complement of any other oligonucleotide of the set does not exceed 20% of the degree of hybridization of the oligonucleotide and its complement.
-
20. The composition of claim 1 or claim 3, wherein each of the 4mers represented by numerals 1 to 22 is selected from the group of 4mers consisting of WXXX, WXXY, WXYX, WXYY, WYXX, WYXY, WYYX, WYYY, XWXX, XWXY, XWYX, XWYY, XXWX, XXWY, XXXW, XXYW, XYWX, XYWY, XYXW, XYYW, YWXX, YWXY, YWYX, YWYY, YXWX, YXWY, YXXW, YXYW, YYWX, YYWY, YYXW, and YYYW.
-
21. The composition of claim 20, wherein each of the 4mers represented by numeral 1 are identical to each other, each of the 4mers represented by numeral 2 are identical to each other, each of the 4mers represented by numeral 3 are identical to each other, each of the 4mers represented by numeral 4 are identical to each other, each of the 4mers represented by numeral 5 are identical to each other, each of the 4mers represented by numeral 6 are identical to each other, each of the 4mers represented by numeral 7 are identical to each other, each of the 4mers represented by numeral 8 are identical to each other, each of the 4mers represented by numeral 9 are identical to each other, each of the 4mers represented by numeral 10 are identical to each other, each of the 4mers represented by numeral 11 are identical to each other, each of the 4mers represented by numeral 12 are identical to each other, each of the 4mers represented by numeral 13 are identical to each other, each of the 4mers represented by numeral 14 are identical to each other, each of the 4mers represented by numeral 15 are identical to each other, each of the 4mers represented by numeral 16 are identical to each other, each of the 4mers represented by numeral 17 are identical to each other, each of the 4mers represented by numeral 18 are identical to each other, each of the 4mers represented by numeral 19 are identical to each other, each of the 4mers represented by numeral 20 are identical to each other, each of the 4mers represented by numeral 21 are identical to each other, and each of the 4mers represented by numeral 22 are identical to each other.
-
22. The composition of claim 20, wherein at least one of the 4mers represented by the numeral 1 has the sequence WXYY, at least one of the 4mers represented by the numeral 2 has the sequence YWXY, at least one of the 4mers represented by the numeral 3 has the sequence XXXW, at least one of the 4mers represented by the numeral 4 has the sequence YWYX, at least one of the 4mers represented by the numeral 5 has the sequence WYXY, at least one of the 4mers represented by the numeral 6 has the sequence YYWX, at least one of the 4mers represented by the numeral 7 has the sequence YWXX, at least one of the 4mers represented by the numeral 8 has the sequence WYXX, at least one of the 4mers represented by the numeral 9 has the sequence XYYW, at least one of the 4mers represented by the numeral 10 has the sequence XYWX, at least one of the 4mers represented by the numeral 11 has the sequence YYXW, at least one of the 4mers represented by the numeral 12 has the sequence WYYX, at least one of the 4mers represented by the numeral 13 has the sequence XYXW, at least one of the 4mers represented by the numeral 14 has the sequence WYYY, at least one of the 4mers represented by the numeral 15 has the sequence WXYW, at least one of the 4mers represented by the numeral 16 has the sequence WYXW, at least one of the 4mers represented by the numeral 17 has the sequence WXXW, at least one of the 4mers represented by the numeral 18 has the sequence WYYW, at least one of the 4mers represented by the numeral 19 has the sequence XYYX, at least one of the 4mers represented by the numeral 20 has the sequence YXYX, at least one of the 4mers represented by the numeral 21 has the sequence YXXY, and at least one of the 4mers represented by the numeral 22 has the sequence XYXY.
-
23. The composition of claim 22, wherein in each 1=WXYY, each 2=YWXY, each 3=XXXW, each 4=YWYX, each 5=WYXY, each 6=YYWX, each 7=YWXX, each 8=WYXX, each 9=XYYW, each 10=XYWX, each 11=YYXW, each 12=WYYX, each 13=XYXW, each 14=WYYY, each 15=WXYW, each 16=WYXW, each 17=WXXW, each 18=WYYW, each 19=XYYX, each 20=YXYX, each 21=YXXY and each 22=XYXY.
-
24. The composition of claim 1, wherein a said group of sequences is based on the sequences having sequence identifiers 1 to 173 as set out in Table IA, and wherein each of the 4mers represented by numerals 1 to 14 in (A) is selected from the group of 4mers consisting of WXYY, YWXY, XXXW, YWYX, WYXY, YYWX, YWXX, WYXX, XYYW, XYWX, YYXW, WYYX, XYXW, and WYYY.
-
25. The composition of claim 24, wherein the composition includes at least ten said molecules, or at least eleven said molecules, or at least twelve said molecules, or at least thirteen said molecules, or at least fourteen said molecules, or at least fifteen said molecules, or at least sixteen said molecules, or at least seventeen said molecules, or at least eighteen said molecules, or at least nineteen said molecules, or at least twenty said molecules, or at least twenty-one said molecules, or at least twenty-two said molecules, or at least twenty-three said molecules, or at least twenty-four said molecules, or at least twenty-five said molecules, or at least twenty-six said molecules, or at least twenty-seven said molecules, or at least twenty-eight said molecules, or at least twenty-nine said molecules, or at least thirty said molecules, or at least thirty-one said molecules, or at least thirty-two said molecules, or at least thirty-three said molecules, or at least thirty-four said molecules, or at least thirty-five said molecules, or at least thirty-six said molecules, or at least thirty-seven said molecules, or at least thirty-eight said molecules, or at least thirty-nine said molecules, or at least forty said molecules, or at least forty-one said molecules, or at least forty-two said molecules, or at least forty-three said molecules, or at least forty-four said molecules, or at least forty-five said molecules, or at least forty-six said molecules, or at least forty-seven said molecules, or at least forty-eight said molecules, or at least forty-nine said molecules, or at least fifty said molecules, or at least sixty said molecules, or at least seventy said molecules, or at least eighty said molecules, or at least ninety said molecules, or at least one hundred said molecules, or at least one hundred and ten said molecules, or at least one hundred and twenty said molecules, or at least one hundred and thirty said molecules, or at least one hundred and forty said molecules, or at least one hundred and fifty said molecules, or at least one hundred and sixty said molecules, or at least one hundred and seventy said molecules, or at least one hundred and eighty said molecules, or at least one hundred and ninety said molecules, or at least two hundred said molecules.
-
26. The composition of claim 24, wherein:
(G) for the group of 24mer sequences in which each 1=GATT, each 2=TGAT, each 3=AAAG, each 4=TGTA, each 5=GTAT, each 6=TTGA, each 7=TGAA, each 8=GTAA, each 9=ATTG, each 10=ATGA, each 11=TTAG, each 12=GTTA, each 13=ATAG, each 14=GTTT, under a defined set of conditions in which the maximum degree of hybridization between a sequence and any complement of a different sequence of the group of 24mer sequences does not exceed 30% of the degree of hybridization between said sequence and its complement, for all oligonucleotides of the set, the maximum degree of hybridization between an oligonucleotide and a complement of any other oligonucleotide of the set does not exceed 50% of the degree of hybridization of the oligonucleotide and its complement.
-
27. The composition of claim 26 wherein, in (G) under said defined set of conditions in which the maximum degree of hybridization between a sequence and any complement of a different sequence does not exceed 30% of the degree of hybridization between said sequence and its complement, the degree of hybridization between each sequence and its complement varies by a factor of between 1 and 10, more preferably between 1 and 9, and more preferably between 1 and 8.
-
28. The composition of claim 27 wherein the maximum degree of hybridization in (G) between a sequence and any complement of a different sequence does not exceed 25%, more preferably wherein the maximum degree of hybridization in (G) between a sequence and any complement of a different sequence does not exceed 20%, more preferably wherein the maximum degree of hybridization in (G) between a sequence and any complement of a different sequence does not exceed 15%, more preferably wherein the maximum degree of hybridization in (G) between a sequence and any complement of a different sequence does not exceed 11%.
-
29. The composition of claim 27 wherein under said defined set of conditions of (G), the maximum degree of hybridization between a sequence and a complement of any other sequence of the set is no more than 15% greater than the maximum degree of hybridization between a sequence and any complement of a different sequence of the said group of 24mer sequences, more preferably no more than 10% greater, more preferably no more than 5% greater.
-
30. The composition of claim 26, wherein said defined set of conditions results in a level of hybridization that is the same as the level of hybridization obtained when hybridization conditions include 0.2 M NaCl, 0.1 M Tris, 0.08% Triton X-100, pH 8.0 at 37°
- C.
-
31. The composition of claim 30 wherein, in (G) said defined set of conditions includes the group of 24mer sequences of (G) being covalently linked to beads.
-
32. The composition of claim 24, wherein each of the 4mers represented by numeral 1 are identical to each other, each of the 4mers represented by numeral 2 are identical to each other, each of the 4mers represented by numeral 3 are identical to each other, each of the 4mers represented by numeral 4 are identical to each other, each of the 4mers represented by numeral 5 are identical to each other, each of the 4mers represented by numeral 6 are identical to each other, each of the 4mers represented by numeral 7 are identical to each other, each of the 4mers represented by numeral 8 are identical to each other, each of the 4mers represented by numeral 9 are identical to each other, each of the 4mers represented by numeral 10 are identical to each other, each of the 4mers represented by numeral 11 are identical to each other, each of the 4mers represented by numeral 12 are identical to each other, each of the 4mers represented by numeral 13 are identical to each other, and each of the 4mers represented by numeral 14 are identical to each other.
-
33. The composition of claim 24, wherein at least one of the 4mers represented by the numeral 1 has the sequence WXYY, at least one of the 4mers represented by the numeral 2 has the sequence YWXY, at least one of the 4mers represented by the numeral 3 has the sequence XXXW, at least one of the 4mers represented by the numeral 4 has the sequence YWYX, at least one of the 4mers represented by the numeral 5 has the sequence WYXY, at least one of the 4mers represented by the numeral 6 has the sequence YYWX, at least one of the 4mers represented by the numeral 7 has the sequence YWXX, at least one of the 4mers represented by the numeral 8 has the sequence WYXX, at least one of the 4mers represented by the numeral 9 has the sequence XYYW, at least one of the 4mers represented by the numeral 10 has the sequence XYWX, at least one of the 4mers represented by the numeral 11 has the sequence YYXW, at least one of the 4mers represented by the numeral 12 has the sequence WYYX, at least one of the 4mers represented by the numeral 13 has the sequence XYXW, and at least one of the 4mers represented by the numeral 14 has the sequence WYYY.
-
34. The composition of claim 33, wherein each 1=WXYY, each 2=YWXY, each 3=XXXW, each 4=YWYX, each 5=WYXY, each 6=YYWX, each 7=YWXX, each 8=WYXX, each 9=XYYW, each 10=XYWX, each 11=YYXW, each 12=WYYX, each 13=XYXW, and each 14=WYYY.
-
35. The composition of claim 1, wherein a said group of sequences is based on those sequences having sequence identifiers 1 to 100 as set out in Table IA and wherein each of the 4mers represented by numerals 1 to 10 in (A) is selected from the group of 4mers consisting of WXYY, YWXY, XXXW, YWYX, WYXY, YYWX, YWXX, WYXX, XYYW, and XYWX.
-
36. The composition of claim 35, wherein the composition includes at least ten said molecules, or at least eleven said molecules, or at least twelve said molecules, or at least thirteen said molecules, or at least fourteen said molecules, or at least fifteen said molecules, or at least sixteen said molecules, or at least seventeen said molecules, or at least eighteen said molecules, or at least nineteen said molecules, or at least twenty said molecules, or at least twenty-one said molecules, or at least twenty-two said molecules, or at least twenty-three said molecules, or at least twenty-four said molecules, or at least twenty-five said molecules, or at least twenty-six said molecules, or at least twenty-seven said molecules, or at least twenty-eight said molecules, or at least twenty-nine said molecules, or at least thirty said molecules, or at least thirty-one said molecules, or at least thirty-two said molecules, or at least thirty-three said molecules, or at least thirty-four said molecules, or at least thirty-five said molecules, or at least thirty-six said molecules, or at least thirty-seven said molecules, or at least thirty-eight said molecules, or at least thirty-nine said molecules, or at least forty said molecules, or at least forty-one said molecules, or at least forty-two said molecules, or at least forty-three said molecules, or at least forty-four said molecules, or at least forty-five said molecules, or at least forty-six said molecules, or at least forty-seven said molecules, or at least forty-eight said molecules, or at least forty-nine said molecules, or at least fifty said molecules, or at least sixty said molecules, or at least seventy said molecules, or at least eighty said molecules, or at least ninety said molecules, or at least one hundred said molecules.
-
37. The composition of claim 35, wherein:
(G) for the group of 24mer sequences in which each 1=GATT, each 2=TGAT, each 3=AAAG, each 4=TGTA, each 5=GTAT, each 6=TTGA, each 7=TGAA, each 8=GTAA, each 9=ATTG, each 10=ATGA, under a defined set of conditions in which the maximum degree of hybridization between a sequence and any complement of a different sequence of the group of 24mer sequences does not exceed 30% of the degree of hybridization between said sequence and its complement, for all oligonucleotides of the set, the maximum degree of hybridization between an oligonucleotide and a complement of any other oligonucleotide of the set does not exceed 50% of the degree of hybridization of the oligonucleotide and its complement.
-
38. The composition of claim 37 wherein, in (G) under said defined set of conditions in which the maximum degree of hybridization between a sequence and any complement of a different sequence does not exceed 30% of the degree of hybridization between said sequence and its complement, the degree of hybridization between each sequence and its complement varies by a factor of between 1 and 10, more preferably between 1 and 9, and more preferably between 1 and 8.
-
39. The composition of claim 38 wherein the maximum degree of hybridization in (G) between a sequence and any complement of a different sequence does not exceed 25%, more preferably wherein the maximum degree of hybridization in (G) between a sequence and any complement of a different sequence does not exceed 20%, more preferably wherein the maximum degree of hybridization in (G) between a sequence and any complement of a different sequence does not exceed 15%, more preferably wherein the maximum degree of hybridization in (G) between a sequence and any complement of a different sequence does not exceed 11%.
-
40. The composition of claim 38 or claim 39 wherein under said defined set of conditions of (G), the maximum degree of hybridization between a sequence and a complement of any other sequence of the set is no more than 15% greater than the maximum degree of hybridization between a sequence and any complement of a different sequence of the said group of 24mer sequences, more preferably no more than 10% greater, more preferably no more than 5% greater.
-
41. The composition of claim 37, wherein said defined set of conditions results in a level of hybridization that is the same as the level of hybridization obtained when hybridization conditions include 0.2 M NaCl, 0.1 M Tris, 0.08% Triton X-100, pH 8.0 at 37°
- C.
-
42. The composition of claim 41 wherein, in (G) said defined set of conditions includes the group of 24mer sequences of (G) being covalently linked to beads.
-
43. The composition of claim 35, wherein each of the 4mers represented by numeral 1 are identical to each other, each of the 4mers represented by numeral 2 are identical to each other, each of the 4mers represented by numeral 3 are identical to each other, each of the 4mers represented by numeral 4 are identical to each other, each of the 4mers represented by numeral 5 are identical to each other, each of the 4mers represented by numeral 6 are identical to each other, each of the 4mers represented by numeral 7 are identical to each other, each of the 4mers represented by numeral 8 are identical to each other, each of the 4mers represented by numeral 9 are identical to each other, and each of the 4mers represented by numeral 10 are identical to each other.
-
44. The composition of claim 43, wherein at least one of the 4mers represented by the numeral 1 has the sequence WXYY, at least one of the 4mers represented by the numeral 2 has the sequence YWXY, at least one of the 4mers represented by the numeral 3 has the sequence XXXW, at least one of the 4mers represented by the numeral 4 has the sequence YWYX, at least one of the 4mers represented by the numeral 5 has the sequence WYXY, at least one of the 4mers represented by the numeral 6 has the sequence YYWX, at least one of the 4mers represented by the numeral 7 has the sequence YWXX, at least one of the 4mers represented by the numeral 8 has the sequence WYXX, at least one of the 4mers represented by the numeral 9 has the sequence XYYW, and at least one of the 4mers represented by the numeral 10 has the sequence XYWX.
-
45. The composition of claim 44, wherein each 1=WXYY, each 2=YWXY, each 3=XXXW, each 4=YWYX, each 5=WYXY, each 6=YYWX, each 7=YWXX, each 8 WYXX, each 9=XYYW, and each 10=XYWX.
-
46. The composition of any of claims 1 or 3 wherein in (C)(i)(a):
- W=one of G and C;
X=one of A and T/U; and
Y=one of A and T/U.
- W=one of G and C;
-
47. The composition of claim 46, wherein in (C)(i)(a):
- W=G;
X=one of A, and T/U; and
Y=one of A and T/U.
- W=G;
-
48. The composition of claim 47, wherein W=G;
- X=A; and
Y=T/U.
- X=A; and
-
49. The composition of claims 1 or 3, wherein in (F)(I), said quotient for each sequence of the set does not vary from the quotient for the combined sequences by more than 0.1.
-
50. The composition of claim 49, wherein in (F)(I), said quotient for each sequence of the set does not vary from the quotient for the combined sequences by more than 0.05.
-
51. The composition of claim 50, wherein in (F)(I), said quotient for each sequence of the set does not vary from the quotient for the combined sequences by more than 0.01.
-
52. The composition of claims 1 or 3, wherein in (F)(I) the quotient of the sum of G and C divided by the sum of A, T/U, G and C for all combined sequences of the set is between about 0.15 and 0.35.
-
53. The composition of claim 52, wherein in (F)(I) the quotient of the sum of G and C divided by the sum of A, T/U, G and C for all combined sequences of the set is between about 0.2 and 0.3.
-
54. The composition of claim 53, wherein in (F)(I) the quotient of the sum of G and C divided by the sum of A, T/U, G and C for all combined sequences of the set is between about 0.21 and 0.29.
-
55. The composition of claim 54, wherein in (F)(I) the quotient of the sum of G and C divided by the sum of A, T/U, G and C for all combined sequences of the set is between about 0.22 and 0.28.
-
56. The composition of claim 55, wherein in (F)(I) the quotient of the sum of G and C divided by the sum of A, T/U, G and C for all combined sequences of the set is between about 0.23 and 0.27.
-
57. The composition of claim 56, wherein in (F)(I) the quotient of the sum of G and C divided by the sum of A, T/U, G and C for all combined sequences of the set is between about 0.24 and 0.26.
-
58. The composition of claim 57, wherein in (F)(I) the quotient of the sum of G and C divided by the sum of A, T/U, G and C for all combined sequences of the set is 0.25.
-
59. The composition of claims 1 or 3, wherein in (D) up to two bases can be inserted at any location of any of the sequences or up to two bases can be deleted from any of the sequences.
-
60. The composition of claim 59, wherein in (D) one base can be inserted at any location of any of the sequences or one base can be deleted from any of the sequences.
-
61. The composition of claim 60, wherein in (D) no base can be inserted at any location of any of the sequences.
-
62. The composition of claim 60, wherein in (D) no base can be deleted from any of the sequences.
-
63. The composition of claim 60, wherein in (D) no base can be inserted at or deleted from any location of any of the sequences.
-
64. The composition of claims 1 or 3, wherein each of the oligonucleotides of a said set has a sequence at least eleven contiguous bases of the sequence on which it is based;
- or wherein each of the oligonucleotides of a said set has a sequence at least twelve contiguous bases of the sequence on which it is based;
or wherein each of the oligonucleotides of a said set has a sequence at least thirteen contiguous bases of the sequence on which it is based;
or wherein each of the oligonucleotides of a said set has a sequence at least fourteen contiguous bases of the sequence on which it is based;
or wherein each of the oligonucleotides of a said set has a sequence at least fifteen contiguous bases of the sequence on which it is based;
or wherein each of the oligonucleotides of a said set has a sequence at least sixteen contiguous bases of the sequence on which it is based;
or wherein each of the oligonucleotides of a said set has a sequence at least seventeen contiguous bases of the sequence on which it is based;
or wherein each of the oligonucleotides of a said set has a sequence at least eighteen contiguous bases of the sequence on which it is based;
or wherein each of the oligonucleotides of a said set has a sequence at least nineteen contiguous bases of the sequence on which it is based;
or wherein each of the oligonucleotides of a said set has a sequence at least twenty contiguous bases of the sequence on which it is based;
or wherein each of the oligonucleotides of a said set has a sequence at least twenty-one contiguous bases of the sequence on which it is based;
or wherein each of the oligonucleotides of a said set has a sequence at least twenty-two contiguous bases of the sequence on which it is based;
or wherein each of the oligonucleotides of a said set has a sequence at least twenty-three contiguous bases of the sequence on which it is based;
or wherein each of the oligonucleotides of a said set has a sequence at least twenty-four contiguous bases of the sequence on which it is based.
- or wherein each of the oligonucleotides of a said set has a sequence at least twelve contiguous bases of the sequence on which it is based;
-
65. The composition of claims 1 or 3, wherein in each oligonucleotide of the set, there is a maximum of six bases other than G between every neighboring pair of G'"'"'s.
-
66. The composition according to claim 65, wherein each initial G of an oligonucleotide of the set sequence occupies a position in the terminal selected from a first, second, third, fourth, fifth, sixth or seventh position thereof.
-
67. The composition of claims 1 or 3, wherein the contiguous bases of each oligonucleotide of a said set are selected such that the position of the first base of each said oligonucleotide within the sequence on which it is based is the same for all nucleotides of the set.
-
68. The composition of claims 1 or 3, wherein each of the oligonucleotides of a said set is up to thirty bases in length;
- or each of the oligonucleotides of a said set is up to twenty-nine bases in length;
or each of the oligonucleotides of a said set is up to twenty-eight bases in length;
or each of the oligonucleotides of a said set is up to twenty-seven bases in length;
or each of the oligonucleotides of a said set is up to twenty-six bases in length;
or each of the oligonucleotides of a said set is up to twenty-five bases in length;
or each of the oligonucleotides of a said set is up to twenty-four bases in length.
- or each of the oligonucleotides of a said set is up to twenty-nine bases in length;
-
69. The composition of claims 1 or 3, wherein each of the oligonucleotides of a said set has a length of within five bases of the average length of all of the oligonucleotides in the set;
- or each of the oligonucleotides of a said set has a length of within four bases of the average length of all of the oligonucleotides in the set;
or each of the oligonucleotides of a said set has a length of within three bases of the average length of all of the oligonucleotides in the set;
or each of the oligonucleotides of a said set has a length of within two bases of the average length of all of the oligonucleotides in the set;
or each of the oligonucleotides of a said set has a length of within one base of the average length of all of the oligonucleotides in the set.
- or each of the oligonucleotides of a said set has a length of within four bases of the average length of all of the oligonucleotides in the set;
-
70. The composition of claims 1 or 3, wherein in (II)(i), any consecutive sequence of bases in the phantom sequence which is identical to a consecutive sequence of bases in each of the first and second sequences from which it is generated is no more ((⅔
- ×
L)−
1) bases in length.
- ×
-
71. The composition of claims 1 or 3, wherein in (II)(ii), the phantom sequence, if greater than or equal to (¾
- ×
L) in length, contains at least 3 insertions/deletions or mismatches when compared to the first and second sequences from which it is generated.
- ×
-
72. The composition of claim 71, wherein in (II)(ii), the phantom sequence, if greater than or equal to (⅔
- ×
L) in length, contains at least 3 insertions/deletions or mismatches when compared to the first and second sequences from which it is generated.
- ×
-
73. The composition of claims 1 or 3, wherein in (II)(iii), the phantom sequence is not greater than or equal to (⅚
- ×
L) in length.
- ×
-
74. The composition of claim 73, wherein in (II)(iii), the phantom sequence is not greater than or equal to (¾
- ×
L) in length.
- ×
-
82. A composition of claims 1, 3, or 75, wherein each molecule is linked to a solid phase support so as to be distinguishable from a mixture of said molecules by hybridization to its complement.
-
83. The composition of claim 82, wherein each molecule is linked to a defined location on a said solid phase support, the defined location for each said molecule being different than the defined location for different other said molecules.
-
84. The composition of claim 82, wherein each said solid phase support is a microparticle and each said molecule is covalently to a different microparticle than each other different said molecule.
-
85. A composition according to any of claims 1, 3, or 75, wherein each said molecule comprises a tag complement.
-
86. A kit for sorting and identifying polynucleotides, the kit comprising one or more solid phase supports each having one or more spatially discrete regions, each such region having a uniform population of substantially identical tag complements covalently attached, and the tag complements each being selected from the set of oligonucleotides as defined in any of claims 1 to 85.
-
87. A kit according to claim 86, wherein there is a tag complement for each said oligonucleotide of a said composition.
-
88. A kit according to claim 86 wherein said one or more solid phase supports is a planar substrate and wherein said one or more spatially discrete regions is a plurality of spatially addressable regions.
-
89. A kit according to claim 86 wherein said one or more solid phase supports is a plurality of microparticles.
-
90. A kit according to claim 89 wherein said microparticles each have a diameter in the range of from 5 to 40 μ
- m.
-
91. A kit according to claim 89 or 90, wherein each microparticle is spectrophotometrically unique from each other microparticle having a different oligonucleotide attached thereto.
-
92. A method of analyzing a biological sample comprising a biological sequence for the presence of a mutation or polymorphism at a locus of the nucleic acid, the method comprising:
-
(A) amplifying the nucleic acid molecule in the presence of a first primer having a 5′
-sequence having the sequence of a tag complementary to the sequence of a tag complement belonging to a family of tag complements as defined in claim 85 to form an amplified molecule with a 5′
-end with a sequence complementary to the sequence of the tag;
(B) extending the amplified molecule in the presence of a polymerase and a second primer having 5′
-end complementary the 3′
-end of the amplified sequence, with the 3′
-end of the second primer extending to immediately adjacent said locus, in the presence of a plurality of nucleoside triphosphate derivatives each of which is;
(i) capable of incorporation during transciption by the polymerase onto the 3′
-end of a growing nucleotide strand;
(ii) causes termination of polymerization; and
(iii) capable of differential detection, one from the other, wherein there is a said derivative complementary to each possible nucleotide present at said locus of the amplified sequence;
(C) specifically hybridizing the second primer to a tag complement having the tag complement sequence of (A); and
(D) detecting the nucleotide derivative incorporated into the second primer in (B) so as to identify the base located at the locus of the nucleic acid.
-
-
93. A method of analyzing a biological sample comprising a plurality of nucleic acid molecules for the presence of a mutation or polymorphism at a locus of each nucleic acid molecule, for each nucleic acid molecule, the method comprising:
-
(A) amplifying the nucleic acid molecule in the presence of a first primer having a 5′
-sequence having the sequence of a tag complementary to the sequence of a tag complement belonging to a family of tag complements as defined in claim 85 to form an amplified molecule with a 5′
-end with a sequence complementary to the sequence of the tag;
(B) extending the amplified molecule in the presence of a polymerase and a second primer having 5′
-end complementary the 3′
-end of the amplified sequence, the 3′
-end of the second primer extending to immediately adjacent said locus, in the presence of a plurality of nucleoside triphosphate derivatives each of which is;
(i) capable of incorporation during transciption by the polymerase onto the 3′
-end of a growing nucleotide strand;
(ii) causes termination of polymerization; and
(iii) capable of differential detection, one from the other, wherein there is a said derivative complementary to each possible nucleotide present at said locus of the amplified molecule;
(C) specifically hybridizing the second primer to a tag complement having the tag complement sequence of (A); and
(D) detecting the nucleotide derivative incorporated into the second primer in (B) so as to identify the base located at the locus of the nucleic acid;
wherein each tag of (A) is unique for each nucleic acid molecule and steps (A) and (B) are carried out with said nucleic molecules in the presence of each other.
-
-
94. A method of analyzing a biological sample comprising a plurality of double stranded complementary nucleic acid molecules for the presence of a mutation or polymorphism at a locus of each nucleic acid molecule, for each nucleic acid molecule, the method comprising:
-
(A) Amplifying the double stranded molecule in the presence of a pair of first primers, each primer having an identical 5′
-sequence having the sequence of a tag complementary to the sequence of a tag complement belonging to a family of tag complements as defined in claim 85 to form amplified molecules with 5′
-ends with a sequence complementary to the sequence of the tag;
(B) Extending the amplified molecules in the presence of a polymerase and a pair of second primers each second primer having a 5′
-end complementary a 3′
-end of the amplified sequence, the 3′
-end of each said second primer extending to immediately adjacent said locus, in the presence of a plurality of nucleoside triphosphate derivatives each of which is;
(i) capable of incorporation during transciption by the polymerase onto the 3′
-end of a growing nucleotide strand;
(ii) causes termination of polymerization; and
(iii) capable of differential detection, one from the other;
(C) Specifically hybridizing each of the second primers to a tag complement having the tag complement sequence of (A); and
(D) Detecting the nucleotide derivative incorporated into the second primers in (B) so as to identify the base located at said locus;
wherein the sequence of each tag of (A) is unique for each nucleic acid molecule and steps (A) and (B) are carried out with said nucleic molecules in the presence of each other.
-
-
95. A method of analyzing a biological sample comprising a plurality of nucleic acid molecules for the presence of a mutation or polymorphism at a locus of each nucleic acid molecule, for each nucleic acid molecule, the method comprising:
-
(a) hybridizing the molecule and a primer, the primer having a 5′
-sequence having the sequence of a tag complementary to the sequence of a tag complement belonging to a family of tag complements as defined in claim 85 and a 3′
-end extending to immediately adjacent the locus;
(b) enzymatically extending the 3′
-end of the primer in the presence of a plurality of nucleoside triphosphate derivatives each of which is;
(i) capable of enzymatic incorporation onto the 3′
-end of a growing nucleotide strand;
(ii) causes termination of said extension; and
(iii) capable of differential detection, one from the other, wherein there is a said derivative complementary to each possible nucleotide present at said locus;
(c) specifically hybridizing the extended primer formed in step (b) to a tag complement having the tag complement sequence of (a); and
(d) detecting the nucleotide derivative incorporated into the primer in step (b) so as to identify the base located at the locus of the nucleic acid molecule;
wherein each tag of (a) is unique for each nucleic acid molecule and steps (a) and (b) are carried out with said nucleic molecules in the presence of each other.
-
-
96. The method of claim 93 wherein each said derivative is a dideoxy nucleoside triphosphate.
-
97. The method of claim 95, wherein each respective complement is attached as a uniform population of substantially identical complements in a spacially discrete region on one or more said solid phase supports.
-
98. The method of claim 97, each said tag complement comprises a label, each such label being different for respective complements, and step (d) includes detecting the presence of the different labels for respective hybridization complexes of bound tags and tag complements.
-
99. The hybridized molecule and primer of step (A) of claim 95.
-
100. A method of determining the presence of a target suspected of being contained in a mixture, the method comprising the steps of:
-
(i) labelling the target with a first label;
(ii) providing a first detection moiety capable of specific binding to the target and including a first tag;
(iii) exposing a sample of the mixture to the detection moiety under conditions suitable to permit (or cause) said specific binding of the molecule and target;
(iv) providing a family of tag complements as defined in claim 85 wherein the family contains a first tag complement having a sequence complementary to that of the first tag;
(v) exposing the sample to the family of tag complements under conditions suitable to permit (or cause) specific hybridization of the first tag and its tag complement;
(vi) determining whether a said first detection moiety hybridized to a first said tag complement is bound to a said labelled target in order to determine the presence or absence said target in the mixture.
-
-
101. The method of claim 100 wherein said first tag complement is linked to a solid support at a specific location of the support and step (vi) includes detecting the presence the first label at said specified location.
-
102. The method of claim 100 wherein said first tag complement comprises a second label and step (vi) includes detecting the presence of the first and second labels in a hybridized complex of the moiety and the first tag complement.
-
103. The method of claim 100 wherein said target is selected from the group consisting of organic molecules, antigens, proteins, polypeptides, antibodies and nucleic acids.
-
104. The method of claim 103, wherein said target is an antigen and said first molecule is an antibody specific for said antigen.
-
105. The method of claim 104, wherein the antigen is a polypeptide or protein and the labelling step includes conjugation of fluorescent molecules, digoxigenin, biotinylation and the like.
-
106. The method of claim 105, wherein said target is a nucleic acid and the labelling step includes incorporation of fluorescent molecules, radiolabelled nucleotide, digoxigenin, biotinylation and the like.
-
2. The composition of claim 1, wherein the composition includes at least ten said molecules, or at least eleven said molecules, or at least twelve said molecules, or at least thirteen said molecules, or at least fourteen said molecules, or at least fifteen said molecules, or at least sixteen said molecules, or at least seventeen said molecules, or at least eighteen said molecules, or at least nineteen said molecules, or at least twenty said molecules, or at least twenty-one said molecules, or at least twenty-two said molecules, or at least twenty-three said molecules, or at least twenty-four said molecules, or at least twenty-five said molecules, or at least twenty-six said molecules, or at least twenty-seven said molecules, or at least twenty-eight said molecules, or at least twenty-nine said molecules, or at least thirty said molecules, or at least thirty-one said molecules, or at least thirty-two said molecules, or at least thirty-three said molecules, or at least thirty-four said molecules, or at least thirty-five said molecules, or at least thirty-six said molecules, or at least thirty-seven said molecules, or at least thirty-eight said molecules, or at least thirty-nine said molecules, or at least forty said molecules, or at least forty-one said molecules, or at least forty-two said molecules, or at least forty-three said molecules, or at least forty-four said molecules, or at least forty-five said molecules, or at least forty-six said molecules, or at least forty-seven said molecules, or at least forty-eight said molecules, or at least forty-nine said molecules, or at least fifty said molecules, or at least sixty said molecules, or at least seventy said molecules, or at least eighty said molecules, or at least ninety said molecules, or at least one hundred said molecules, or at least one hundred and ten said molecules, or at least one hundred and twenty said molecules, or at least one hundred and thirty said molecules, or at least one hundred and forty said molecules, or at least one hundred and fifty said molecules, or at least one hundred and sixty said molecules, or at least one hundred and seventy said molecules, or at least one hundred and eighty said molecules, or at least one hundred and ninety said molecules, or at least two hundred said molecules.
-
75. A composition comprising molecules for use as tags or tag complements wherein each molecule comprises an oligonucleotide selected from a set of oligonucleotides based on a following group of sequences having the one hundred sequence identifiers of the sequences tested in Example 2 as set out in Table I, wherein:
-
(A) wherein 1=WXYY, each 2=YWXY, each 3=XXXW, each 4=YWYX, each 5=WYXY, each 6=YYWX, each 7=YWXX, each 8=WYXX, each 9=XYYW, each 10=XYWX, each 11=YYXW, each 12=WYYX, each 13=XYXW, each 14=WYYY, each 15=WXYW, each 16=WYXW, each 17=WXXW, each 18=WYYW, each 19=XYYX, each 20=YXYX, each 21=YXXY and each 22=XYXY;
(B) each of W, X and Y is a base in which either;
(i) (a) W=one of A, T/U, G, and C, X=one of A, T/U, G, and C, Y=one of A, T/U, G, and C, and each of W, X and Y is selected so as to be different from all of the others of W, X and Y, (b) an unselected said base of (i)(a) can be substituted any number of times for any one of W, X and Y, or (ii) (a) W=G or C, X=A or T/U, Y=A or T/U, and X # Y, and (b) a base not selected in (ii)(a) can be inserted into each sequence at one or more locations, the location of each insertion being the same in all the sequences;
(C) up to three bases can be inserted at any location of any of the sequences or up to three bases can be deleted from any of the sequences;
(D) all of the sequences of a said group of oligonucleotides are read 5′
to 3′
or are read 3′
to 5′
; and
wherein each oligonucleotide of a said set has a sequence of at least ten contiguous bases of the sequence on which it is based, provided that;
(E) the quotient of the sum of G and C divided by the sum of A, T/U, G and C for all combined sequences of the set is between about 0.1 and 0.40 and said quotient for each sequence of the set does not vary from the quotient for the combined sequences by more than 0.2; and
(F) for the group of 24mer sequences in which each 1=GATT, each 2=TGAT, each 3=AAAG, each 4=TGTA, each 5=GTAT, each 6=TTGA, each 7=TGAA, each 8=GTAA, each 9=ATTG, each 10=ATGA, each 11=TTAG, each 12=GTTA, each 13=ATAG, each 14=GTTT, each 15=GATG, each 16=GTAG, each 17=GAAG, each 18=GTTG, each 19=ATTA, each 20=TATA, each 21=TAAT and each 22=ATAT, under a defined set of conditions in which the maximum degree of hybridization between a sequence and any complement of a different sequence of the group of 24mer sequences does not exceed 30% of the degree of hybridization between said sequence and its complement, for all oligonucleotides of the set, the maximum degree of hybridization between an oligonucleotide and a complement of any other oligonucleotide of the set does not exceed 50% of the degree of hybridization of the oligonucleotide and its complement;
wherein any base present may be substituted by an analogue thereof. - View Dependent Claims (76, 77, 78, 79, 80, 81)
-
76. The composition of claim 75 wherein the contiguous bases of each oligonucleotide of a said set are selected such that the position of the first base of each said oligonucleotide within the sequence on which it is based is the same for all nucleotides of the set.
-
77. The composition of claim 75 wherein, subject to the provisos of (E) and (F), each oligonucleotide of a said set comprises a said sequence of twenty-four contiguous bases of the sequence on which it is based.
-
78. The composition of claim 75 wherein, subject to the proviso of (F) each oligonucleotide of a said set comprises a said sequence of twenty-four contiguous bases of the sequence on which it is based.
-
79. The composition of claim 75, wherein in (B):
- W=one of G and C;
X=one of A and T/U; and
Y=one of A and T/U.
- W=one of G and C;
-
80. The composition of claim 79, wherein in (B):
- W=G;
X=one of A, and T/U; and
Y=one of A and T/U.
- W=G;
-
81. The composition of claim 75, wherein the composition includes at least ten said molecules, or at least eleven said molecules, or at least twelve said molecules, or at least thirteen said molecules, or at least fourteen said molecules, or at least fifteen said molecules, or at least sixteen said molecules, or at least seventeen said molecules, or at least eighteen said molecules, or at least nineteen said molecules, or at least twenty said molecules, or at least twenty-one said molecules, or at least twenty-two said molecules, or at least twenty-three said molecules, or at least twenty-four said molecules, or at least twenty-five said molecules, or at least twenty-six said molecules, or at least twenty-seven said molecules, or at least twenty-eight said molecules, or at least twenty-nine said molecules, or at least thirty said molecules, or at least thirty-one said molecules, or at least thirty-two said molecules, or at least thirty-three said molecules, or at least thirty-four said molecules, or at least thirty-five said molecules, or at least thirty-six said molecules, or at least thirty-seven said molecules, or at least thirty-eight said molecules, or at least thirty-nine said molecules, or at least forty said molecules, or at least forty-one said molecules, or at least forty-two said molecules, or at least forty-three said molecules, or at least forty-four said molecules, or at least forty-five said molecules, or at least forty-six said molecules, or at least forty-seven said molecules, or at least forty-eight said molecules, or at least forty-nine said molecules, or at least fifty said molecules, or at least sixty said molecules, or at least seventy said molecules, or at least eighty said molecules, or at least ninety said molecules, or at least one hundred said molecules.
-
76. The composition of claim 75 wherein the contiguous bases of each oligonucleotide of a said set are selected such that the position of the first base of each said oligonucleotide within the sequence on which it is based is the same for all nucleotides of the set.
-
-
107. A set of molecules consisting essentially of two or more of the following-listed sequences for use as tags or tag complements:
- View Dependent Claims (108, 109, 110, 111, 112, 113)
-
108. The set of molecules of claim 107, wherein the set includes at least ten said sequences, or at least eleven said sequences, or at least twelve said sequences, or at least thirteen said sequences, or at least fourteen said sequences, or at least fifteen said sequences, or at least sixteen said sequences, or at least seventeen said sequences, or at least eighteen said sequences, or at least nineteen said sequences, or at least twenty said sequences, or at least twenty-one said sequences, or at least twenty-two said sequences, or at least twenty-three said sequences, or at least twenty-four said sequences, or at least twenty-five said sequences, or at least twenty-six said sequences, or at least twenty-seven said sequences, or at least twenty-eight said sequences, or at least twenty-nine said sequences, or at least thirty said sequences, or at least thirty-one said sequences, or at least thirty-two said sequences, or at least thirty-three said sequences, or at least thirty-four said sequences, or at least thirty-five said sequences, or at least thirty-six said sequences, or at least thirty-seven said sequences, or at least thirty-eight said sequences, or at least thirty-nine said sequences, or at least forty said sequences, or at least forty-one said sequences, or at least forty-two said sequences, or at least forty-three said sequences, or at least forty-four said sequences, or at least forty-five said sequences, or at least forty-six said sequences, or at least forty-seven said sequences, or at least forty-eight said sequences, or at least forty-nine said sequences, or at least fifty said sequences, or at least sixty said sequences, or at least seventy said sequences, or at least eighty said sequences, or at least ninety said sequences, or the one hundred said sequences.
-
109. The set of claim 107 wherein, under a defined set of conditions in which the maximum degree of hybridization between a molecule having a first said sequence and a molecule having any complement of a different second said sequence does not exceed 30% of the degree of hybridization between a molecule having the first sequence and a molecule having its complement, for all molecules of the set, the maximum degree of hybridization between a molecule and a complement of any other molecule of the set does not exceed 50% of the degree of hybridization of the molecule and its complement.
-
110. The set of claim 109 wherein, under said defined set of conditions, the degree of hybridization between each sequence and its complement varies by a factor of between 1 and 10, more preferably between 1 and 9, and more preferably between 1 and 8.
-
111. The set of claim 110 wherein said maximum degree of hybridization between a said molecule having a first said sequence and a said molecule having any complement of a different second said sequence does not exceed 25%, more preferably 20%, more preferably 15%, more preferably 11%.
-
112. The composition of claim 110 wherein under said defined set of conditions, the maximum degree of hybridization between a molecule and a complement of any other molecule of the set is no more than 15% greater than the maximum degree of hybridization between a molecule and any complement of a molecule of the set, more preferably no more than 10% greater, more preferably no more than 5% greater.
-
113. The composition of claim 109, wherein said defined set of conditions results in a degree of hybridization that is the same as the degree of hybridization obtained when hybridization conditions include 0.2 M NaCl, 0.1 M Tris, 0.08% Triton X-100, pH 8.0 at 37°
- C.
-
108. The set of molecules of claim 107, wherein the set includes at least ten said sequences, or at least eleven said sequences, or at least twelve said sequences, or at least thirteen said sequences, or at least fourteen said sequences, or at least fifteen said sequences, or at least sixteen said sequences, or at least seventeen said sequences, or at least eighteen said sequences, or at least nineteen said sequences, or at least twenty said sequences, or at least twenty-one said sequences, or at least twenty-two said sequences, or at least twenty-three said sequences, or at least twenty-four said sequences, or at least twenty-five said sequences, or at least twenty-six said sequences, or at least twenty-seven said sequences, or at least twenty-eight said sequences, or at least twenty-nine said sequences, or at least thirty said sequences, or at least thirty-one said sequences, or at least thirty-two said sequences, or at least thirty-three said sequences, or at least thirty-four said sequences, or at least thirty-five said sequences, or at least thirty-six said sequences, or at least thirty-seven said sequences, or at least thirty-eight said sequences, or at least thirty-nine said sequences, or at least forty said sequences, or at least forty-one said sequences, or at least forty-two said sequences, or at least forty-three said sequences, or at least forty-four said sequences, or at least forty-five said sequences, or at least forty-six said sequences, or at least forty-seven said sequences, or at least forty-eight said sequences, or at least forty-nine said sequences, or at least fifty said sequences, or at least sixty said sequences, or at least seventy said sequences, or at least eighty said sequences, or at least ninety said sequences, or the one hundred said sequences.
Specification
- Resources
Thank you for your request. You will receive a custom alert email when the Litigation Campaign Assessment is available.
×
-
Current AssigneeLuminex Molecular Diagnostics Incorporated (DiaSorin S.p.A.)
-
Original AssigneeLuminex Molecular Diagnostics Incorporated (DiaSorin S.p.A.)
-
InventorsBullock, Richard S, Riccelli, Peter V, Benight, Albert S, Janota, Vit, Kobler, Daniel, Pancoska, Petr, Fieldhouse, Daniel
-
Granted Patent
-
Time in Patent OfficeDays
-
Field of Search
-
US Class Current435/6
-
CPC Class CodesC12Q 1/6855 Ligating adaptorsC12Q 1/6876 Nucleic acid products used ...Y10T 436/13 Tracers or tagsY10T 436/143333 Saccharide [e.g., DNA, etc.]