Detection of a nucleic acid sequence or a change therein
First Claim
1. A method for detecting whether a specific nucleotide or base is at a particular position in a specific polynucleotide sequence comprising:
- a) exposing, under hybridizing conditions, said specific polynucleotide sequence to an oligonucleotide primer wherein said primer has a sequence complementary to part of the specific polynucleotide sequence wherein said primer has incorporated at its 5'"'"' end an element selected from the group consisting of a separation element and a detectable element, and wherein said primer hybridizes at a location selected from the group consisting of (i) immediately adjacent to the particular position and (ii) not immediately adjacent to the particular position whereby there is an intervening sequence between the particular position and primer bound to the specific polynucleotide sequence;
b) extending said hybridized primer up to and including said specific nucleotide or base wherein the 3'"'"' terminal nucleotide is a ddNTP and further includes an element selected from the group consisting of a separation element and a detectable element with the proviso that said extended primer has at least one separation element and at least one detectable element;
c) separating the product of step b) into fractions wherein one said fraction contains the primer extension product that contains the chain terminating nucleotide at said particular position; and
d) determining whether said primer extension product having said chain terminating nucleotide at said particular position is present in said fraction by assaying said fraction wherein the assay does not include a digestion step.
8 Assignments
0 Petitions
Accused Products
Abstract
A method for detecting a specific polynucleotide sequence in a material is disclosed. The method includes exposing said material to an oligonucleotide primer having a sequence complementary to part of said specific polynucleotide sequence wherein said primer binds to part of said polynucleotide sequence when present in said material. Primer bound to the polynucleotide sequence is extended wherein any extended primer includes a detectable element and/or a separation element. Any extended primer is then separated into a fraction wherein said fraction does not have detectable element not included in said extended primer. One then determines whether any extended primer is present in said fraction by assaying said fraction for said extended primer wherein the presence of said extended primer is indicative of the presence of the specific polynucleotide sequence in said material and the absence of said extended primer is indicative of the presence of the specific polynucleotide sequences in said material and the absence of said extended primer in said fraction is indicative of the absence of the specific polynucleotide sequence in said material.
-
Citations
29 Claims
-
1. A method for detecting whether a specific nucleotide or base is at a particular position in a specific polynucleotide sequence comprising:
-
a) exposing, under hybridizing conditions, said specific polynucleotide sequence to an oligonucleotide primer wherein said primer has a sequence complementary to part of the specific polynucleotide sequence wherein said primer has incorporated at its 5'"'"' end an element selected from the group consisting of a separation element and a detectable element, and wherein said primer hybridizes at a location selected from the group consisting of (i) immediately adjacent to the particular position and (ii) not immediately adjacent to the particular position whereby there is an intervening sequence between the particular position and primer bound to the specific polynucleotide sequence; b) extending said hybridized primer up to and including said specific nucleotide or base wherein the 3'"'"' terminal nucleotide is a ddNTP and further includes an element selected from the group consisting of a separation element and a detectable element with the proviso that said extended primer has at least one separation element and at least one detectable element; c) separating the product of step b) into fractions wherein one said fraction contains the primer extension product that contains the chain terminating nucleotide at said particular position; and d) determining whether said primer extension product having said chain terminating nucleotide at said particular position is present in said fraction by assaying said fraction wherein the assay does not include a digestion step. - View Dependent Claims (2, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24)
-
-
5. A method for detecting whether the same or different specific nucleotides or bases are at particular positions in at least two different specific polynucleotide sequences comprising:
-
a) exposing, under hybridizing conditions, said specific polynucleotide sequences to at least two different oligonucleotide primers, wherein each of said different oligonucleotide primers has a sequence complementary to part of one of said different specific polynucleotide, sequences wherein; each of said primers hybridizes to its complementary polynucleotide sequence when present in said material, each of said oligonucleotide primers hybridizing to part of a different specific polynucleotide sequence to that of the other primer(s), each of said primers hybridizes to its complementary specific polynucleotide sequence in said material a location selected from the group consisting of (i) immediately adjacent to the particular position and (ii) not immediately adjacent to the particular position whereby there is an intervening sequence between the particular position and primer hybridized to the specific polynucleotide sequence, and each of said primers has incorporated at their 5'"'"' end an element selected from the group consisting of a separation element and a detectable element; b) extending said hybridized different oligonucleotide primers up to and including said specific nucleotide or base wherein the 3'"'"' terminal nucleotide is a ddNTP and further includes an element selected from the group consisting of a detectable element and a separation element, with the proviso that each of said extended primers has at least one separation element and at least on detectable element; c) separating the product(s) of step b) into fractions wherein one said fraction contains the primer extension product(s) that contain the chain terminating nucleotide at said particular position; and d) determining whether any of said primer extension product having said chain terminating nucleotide at said particular position is present in said fraction by assaying said fraction wherein the assay does not include a digestion step. - View Dependent Claims (25, 26, 27, 28, 29)
-
-
6. A screening method for detecting whether the same or different specific nucleotides or bases are at particular positions in at least two different specific polynucleotide sequences comprising:
-
a) exposing, under hybridizing conditions, said specific nucleotide sequences to at least two different oligonucleotide primers, each of said different oligonucleotide primers having a sequence complementary to part of one of said different specific polynucleotide sequences wherein; each of said primers hybridize to its complementary polynucleotide sequence when present in said material, each of said oligonucleotide primers hybridizing to part of a different specific polynucleotide sequence to that of the other primer(s), each of said primers hybridizes to its complementary specific polynucleotide sequence in said material at a location selected from the group consisting of (i) immediately adjacent to the particular position and (ii) not immediately adjacent to the particular position whereby there is an intervening sequence between the particular position and primer hybridized to the specific polynucleotide sequence when presenting said material; and each of said primers has incorporated at their 5'"'"' end an element selected from the group consisting of a separation element and a detectable element; b) extending said hybridized different oligonucleotide primers up to and including said specific nucleotide or bas e wherein the 3'"'"' terminal nucleotide is a ddNTP and further includes an element selected from the group consisting of a detectable element and a separation element with the proviso that each of said extended primers as at least one separation element and at least one detectable element; c) separating the product(s) of step b) into fractions wherein one said fraction contains the primer extension product(s) that contain the chain terminating nucleotide at said particular position; and d) determining whether at least one of said primers extension products having said chain terminating nucleotide at said particular position is present in said fraction by assaying said fraction wherein the assay does not include a digestion step.
-
Specification