Optimally labeled oligonucleotides
First Claim
Patent Images
1. A method of synthesizing an oligonucleotide containing a single fluorescent dye moiety, comprising:
- (a) preparing a primer;
(b) preparing a template oligonucleotide containing a nucleotide sequence complementary to said primer and a nucleotide repeat region downstream from said complementary nucleotide sequence, said nucleotide repeat region having the formula;
space="preserve" listing-type="equation">(N.sub.m N.sup.t) wherein m is an integer from 1 to 11, N is a nucleotide that does not form a base pair with a fluorescent dye-conjugated nucleotide triphosphate, and Nt is a nucleotide that forms a base pair with the fluorescent dye-conjugated nucleotide triphosphate, wherein for each repeat, Nt is the same;
(c) annealing the template and the primer in a reaction medium comprising a first polymerase, unlabeled nucleotide triphosphates and a predetermined concentration of fluorescent dye-conjugated nucleotide triphosphate;
(d) initiating synthesis of a complementary strand on the template which defines said optimally fluorescent oligonucleotide; and
(e) isolating said oligonucleotide from the reaction medium, wherein m, said fluorescent dye moiety, and said polymerase are selected such that said oligonucleotide exhibits maximum specific fluorescence.
4 Assignments
0 Petitions
Accused Products
Abstract
A method for the preparation of optimally labeled oligonucleotides wherein label-conjugated nucleotide triphosphates are incorporated into a nucleic acid sequence in a defined repetitive manner which allows for the optimal specific detectability of the oligonucleotide. The oligonucleotides of the present invention are useful in the assay of a wide variety of nucleic acid sequences, specifically wherever labeled nucleic acid probes are desired.
44 Citations
16 Claims
-
1. A method of synthesizing an oligonucleotide containing a single fluorescent dye moiety, comprising:
-
(a) preparing a primer; (b) preparing a template oligonucleotide containing a nucleotide sequence complementary to said primer and a nucleotide repeat region downstream from said complementary nucleotide sequence, said nucleotide repeat region having the formula;
space="preserve" listing-type="equation">(N.sub.m N.sup.t)wherein m is an integer from 1 to 11, N is a nucleotide that does not form a base pair with a fluorescent dye-conjugated nucleotide triphosphate, and Nt is a nucleotide that forms a base pair with the fluorescent dye-conjugated nucleotide triphosphate, wherein for each repeat, Nt is the same; (c) annealing the template and the primer in a reaction medium comprising a first polymerase, unlabeled nucleotide triphosphates and a predetermined concentration of fluorescent dye-conjugated nucleotide triphosphate; (d) initiating synthesis of a complementary strand on the template which defines said optimally fluorescent oligonucleotide; and (e) isolating said oligonucleotide from the reaction medium, wherein m, said fluorescent dye moiety, and said polymerase are selected such that said oligonucleotide exhibits maximum specific fluorescence. - View Dependent Claims (2, 3, 4, 5, 6)
-
-
7. A method for preparing an optimally fluorescent probe that hybridizes with a target sequence of interest, comprising:
-
(a) preparing a primer; (b) preparing a template oligonucleotide containing, from 5'"'"' to 3'"'"', a nucleotide sequence complementary to said primer, a nucleotide repeat region having the formula;
space="preserve" listing-type="equation">(N.sub.m N.sup.t)wherein m is an integer from 1 to 11, N is a nucleotide that does not form a base pair with a fluorescent dye-conjugated nucleotide triphosphate, and Nt is a nucleotide that forms a base pair with the fluorescent dye-conjugated nucleotide triphosphate, wherein for each repeat, Nt is the same, and an overhang region comprising 6-200 nucleotides; (c) annealing the template and the primer in a reaction medium comprising a first polymerase, unlabeled nucleotide triphosphates and a predetermined concentration of fluorescent dye-conjugated nucleotide triphosphate; (d) initiating synthesis of a complementary strand on the template which defines said optimally fluorescent oligonucleotide having a 3'"'"'end complementary to said overhang region; (e) isolating said oligonucleotide from the reaction medium, wherein m, said fluorescent dye moiety, and said polymerase are selected such that said oligonucleotide exhibits maximum specific fluorescence (f) denaturing a target sequence, thus producing a denatured target sequence; and (g) adding an excess of said optimally fluorescent nucleotide, nucleotide triphosphates and a second polymerase in a reaction medium, whereby said 3'"'"' region of said optimally labeled oligonucleotide anneals to said target and is extended so as to produce an optimally fluorescent probe. - View Dependent Claims (8)
-
-
9. A method of preparing an optimally fluorescent probe that hybridizes with a target nucleic acid sequence of interest, comprising:
-
(a) preparing a recombinant nucleic acid molecule comprising from 5'"'"' to 3'"'"' and in operable association, a promoter, a template oligonucleotide containing, from 5'"'"' to 3'"'"', a nucleotide repeat region having the formula;
space="preserve" listing-type="equation">(N.sub.m N.sup.t)wherein m is an integer from 1 to 11, N is a nucleotide that does not form a base pair with a fluorescent dye-conjugated nucleotide triphosphate, and Nt is a nucleotide that forms a base pair with the fluorescent dye-conjugated nucleotide triphosphate, wherein for each repeat, Nt is the same, and a target sequence of interest; and (b) providing a reaction medium comprising said recombinant DNA molecule, a polymerase, nucleotide triphosphates conjugated to a fluorescent dye and non-labeled nucleotide triphosphates, to allow synthesis of said probe that is complementary to said template and said target sequence, wherein said polymerase, said fluorescent dye and m are chosen to cause said probe to exhibit maximum specific fluorescence. - View Dependent Claims (10, 11, 12, 13, 14, 15, 16)
-
Specification