Methods for detecting and measuring spliced nucleic acids
First Claim
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1. A method for detecting a fusion nucleic acid comprising the steps of:
- a) providing a sample containing a first single-stranded fusion nucleic acid comprising a bcr-abl splice junction site;
b) contacting under nucleic acid amplification conditions;
the first single-stranded fusion nucleic acid, a first primer which hybridizes to the fusion nucleic acid at a first primer binding site of SEQ ID NO;
22 located 3′
to the splice junction site, and at least one enzyme having nucleic acid polymerase activity;
c) amplifying the fusion nucleic acid in a single isothermal nucleic acid amplification reaction using the first primer to produce a plurality of second nucleic acid strands complementary to at least a portion of the first single-stranded fusion nucleic acid that contains the bcr-abl splice junction site, wherein each second nucleic acid strand comprises;
a complementary splice junction site, a first probe binding site located 3′
to and not overlapping the complementary splice junction site, and a second probe binding site located 5′
to and not overlapping the complementary splice junction site;
d) hybridizing the second nucleic acid strands with an oligonucleotide probe under hybridization conditions in which the probe hybridizes to the first or second probe binding site, thereby forming a probe;
target hybrid; and
e) detecting the probe;
target hybrid as an indication of the presence of the fusion nucleic add in the sample.
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Abstract
The invention includes methods of detecting and measuring the amount of one or more species of bcr-abl spliced mRNA present in the sample, following nucleic acid amplification.
66 Citations
23 Claims
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1. A method for detecting a fusion nucleic acid comprising the steps of:
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a) providing a sample containing a first single-stranded fusion nucleic acid comprising a bcr-abl splice junction site;
b) contacting under nucleic acid amplification conditions;
the first single-stranded fusion nucleic acid, a first primer which hybridizes to the fusion nucleic acid at a first primer binding site of SEQ ID NO;
22 located 3′
to the splice junction site, andat least one enzyme having nucleic acid polymerase activity;
c) amplifying the fusion nucleic acid in a single isothermal nucleic acid amplification reaction using the first primer to produce a plurality of second nucleic acid strands complementary to at least a portion of the first single-stranded fusion nucleic acid that contains the bcr-abl splice junction site, wherein each second nucleic acid strand comprises;
a complementary splice junction site, a first probe binding site located 3′
to and not overlapping the complementary splice junction site, anda second probe binding site located 5′
to and not overlapping the complementary splice junction site;
d) hybridizing the second nucleic acid strands with an oligonucleotide probe under hybridization conditions in which the probe hybridizes to the first or second probe binding site, thereby forming a probe;
target hybrid; and
e) detecting the probe;
target hybrid as an indication of the presence of the fusion nucleic add in the sample. - View Dependent Claims (2, 3, 4, 5, 6, 7, 16)
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8. A method of detecting a fusion mRNA transcript produced as a result of a chromosomal translocation comprising the steps of
a) providing a sample containing a fusion mRNA transcription comprising a bcr-abl splice junction site; -
b) contacting under isothermal nucleic acid amplification conditions;
the fusion mRNA transcript, a first primer which hybridizes to a sequence of SEQ ID NO;
22, andat least one enzyme having nucleic acid polymerase activity, c) amplifying the fusion mRNA transcript in a single nucleic acid amplification reaction that uses the first primer to produce a plurality of second nucleic acid strands complementary to at least a portion of the fusion mRNA transcript containing the splice junction site, wherein each second nucleic acid strand comprises;
a complementary splice junction site, a first probe binding site located 3′
to and not overlapping the complementary splice junction site, anda second probe binding site located 5′
to and not overlapping the complementary splice junction site;
wherein the second probe binding site overlaps or is located 3′
to sequence complementary to SEQ ID NO;
22;
d) hybridizing the second nucleic acid stands with an oligonucleotide probe which hybridizes to the second nucleic acid strands at either the first probe binding site or the second probe binding site but does not hybridize to the fusion mRNA transcript, thereby forming a hybridization complex of the first probe or the second probe and the second nucleic acid strand; and
e) detecting the hybridization complex as an indication of the presence of the fusion transcript in the sample. - View Dependent Claims (9, 10, 11, 12, 13, 14, 15, 23)
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17. A method of detecting a fusion mRNA transcript produced as a result of a human bcr-abl translocation comprising the steps of:
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a) providing a sample containing a human fusion mRNA transcript comprising a bcr-abl splice junction site;
b) contacting under isothermal nucleic acid amplification conditions;
the fusion mRNA transcript, a first primer that binds to a primer binding site of SEQ ID NO;
22 which is located in an abl sequence flanking the bcr-abl splice junction site,a second primer having a sequence of SEQ ID NO;
5, which hybridizes to a bcr sequence flanking the bcr-abl splice junction site,at least one enzyme having an RNA-directed DNA polymerase activity, and at least one enzyme having an DNA-directed RNA polymerase activity, c) amplifying the fusion mRNA transcript in a single nucleic acid amplification reaction that uses the first primer, the second primer, and the DNA-dependent RNA polymerase activity to produce amplified RNA that is complementary to the fusion mRNA transcript comprising the bcr-abl splice junction;
d) hybridizing the amplified RNA with an oligonucleotide probe which hybridizes to a probe binding site located in an amplified bcr sequence flanking the bcr-abl splice junction, thereby forming a hybridization complex; and
e) detecting the hybridization complex as an indication of the presence of the fusion mRNA transcript in the sample. - View Dependent Claims (18, 19, 20, 21, 22)
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Specification