Oligonucleotides labeled with a plurality of fluorophores
First Claim
1. A probe comprising a nucleic acid sequence, said sequence having a 5′
- end and a 3′
end, wherein the 3′
end is blocked to prevent extension via polymerization, and wherein the nucleic acid sequence is labeled with only two spectrally similar or identical fluorophores, wherein a first fluorophore is attached to a first site of said probe and a second fluorophore is attached to a second site of said probe, the first site and the second site being separated from one another by about 3 to about 60 nucleotides, and wherein said probe exhibits a random coil conformation when unhybridized with a target polynucleotide and yields an increase in detectable emission from the first fluorophore and the second fluorophore upon separation of the first or the second fluorophore from said probe.
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Abstract
An embodiment of the invention discloses new methods for designing labeled nucleic acid probes and primers by labeling oligonucleotides with a plurality of spectrally identical or similar dyes and optionally with one or more quencher dyes. Oligonucleotides labeled in accordance with some embodiments of the invention exhibit a detectable increase in signal, for example, fluorescent signal when the labeling dyes are separated from one another. Methods for separating the dye include cleaving the labeled oligonucleotides include using enzymes that have 5′-exonuclease activity. In one embodiment nucleic acid primers of the present invention may fluoresce upon hybridization to a target sequence and incorporation into the amplification product. Nucleic acid probes and primers of the present invention have wide applications ranging from general detection of a target nucleic acid sequence to clinical diagnostics. Major advantages of the oligonucleotides including nucleic acid probes and primers of many embodiments of the present invention are their synthetic simplicity, spectral versatility and superior fluorescent signal.
57 Citations
42 Claims
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1. A probe comprising a nucleic acid sequence, said sequence having a 5′
- end and a 3′
end, wherein the 3′
end is blocked to prevent extension via polymerization, and wherein the nucleic acid sequence is labeled with only two spectrally similar or identical fluorophores, wherein a first fluorophore is attached to a first site of said probe and a second fluorophore is attached to a second site of said probe, the first site and the second site being separated from one another by about 3 to about 60 nucleotides, and wherein said probe exhibits a random coil conformation when unhybridized with a target polynucleotide and yields an increase in detectable emission from the first fluorophore and the second fluorophore upon separation of the first or the second fluorophore from said probe. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 38, 39, 40, 41, 42)
- end and a 3′
-
11. A method of labeling a probe having a 5′
- end and a 3′
end, wherein the 3′
end is blocked to prevent extension via polymerization, wherein said probe is labeled with two spectrally similar or identical fluorophores, said method comprising;attaching a first fluorophore to a first site of said probe sequence and a second fluorophore to a second site of said probe sequence, the first site and the second site being separated from one another by about 3 to about 60 nucleotides, thereby labeling said probe, such that said probe sequence exhibits a random coil conformation when unhybridized with a target polynucleotide and yields an increase in detectable emission from the first fluorophore and the second fluorophore upon separation of the first or the second fluorophore from said probe. - View Dependent Claims (12, 13, 14, 15, 16, 35)
- end and a 3′
-
17. A kit for labeling a probe, the kit comprising:
-
a probe, said probe having a random coil conformation when unhybridized with a target polynucleotide, a length of at least 7 nucleotides and including at least a first site and a second site, said probe having a 5′
end and a 3′
end, wherein the 3′
end is blocked to prevent extension via polymerization;two spectrally similar or identical fluorophores each having a reactive group, wherein a first fluorophore is reactive for attaching to the first site of said probe, and a second fluorophore is reactive for attaching to the second site of said probe such that the first fluorophore and the second fluorophores attached to said probe are separated from one another by about 3 to about 60 nucleotides, and wherein said probe when labeled yields an increase in detectable emission from the first fluorophore and the second fluorophore upon separation of the first or the second fluorophore from said probe. - View Dependent Claims (18, 33, 34, 37)
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Specification