Molecular torches
First Claim
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1. A method for determining the presence of a target nucleic acid sequence in a sample, said method comprising the steps of:
- a) contacting said sample with a molecular torch comprising;
a target binding domain comprising nucleotide base recognition groups;
a target closing domain comprising nucleotide base recognition groups, wherein said target binding domain is biased toward said target sequence, such that said target binding domain forms a more stable hybrid with said target sequence than with said target closing domain under strand displacement conditions; and
a joining region which joins said target binding domain and said target closing domain, wherein said joining region is selected from the group consisting of;
one or more non-nucleotide linkers;
first and second polynucleotides, or derivatives thereof, said first and second polynucleotides, or derivatives thereof, being substantially complementary to each other; and
a combination of said one or more non-nucleotide linkers and said first and second polynucleotides or derivatives thereof, wherein said joining region facilitates the formation of a target binding domain;
target closing domain hybrid in the absence of said target sequence;
b) exposing said sample to strand displacement conditions; and
c) determining whether a target binding domain;
target sequence hybrid is present in said sample as an indication of the presence or absence of said target sequence in said sample.
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Abstract
The present invention features “molecular torches” and the use of molecular torches for detecting the presence of a target nucleic acid sequence. Molecular torches contain a target binding domain, a target closing domain, and a joining region. The target binding domain is biased towards the target sequence such that the target binding domain forms a more stable hybrid with the target sequence than with the target closing domain under the same hybridization conditions. The joining region facilitates the formation or maintenance of a closed torch.
147 Citations
65 Claims
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1. A method for determining the presence of a target nucleic acid sequence in a sample, said method comprising the steps of:
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a) contacting said sample with a molecular torch comprising;
a target binding domain comprising nucleotide base recognition groups;
a target closing domain comprising nucleotide base recognition groups, wherein said target binding domain is biased toward said target sequence, such that said target binding domain forms a more stable hybrid with said target sequence than with said target closing domain under strand displacement conditions; and
a joining region which joins said target binding domain and said target closing domain, wherein said joining region is selected from the group consisting of;
one or more non-nucleotide linkers;
first and second polynucleotides, or derivatives thereof, said first and second polynucleotides, or derivatives thereof, being substantially complementary to each other; and
a combination of said one or more non-nucleotide linkers and said first and second polynucleotides or derivatives thereof, wherein said joining region facilitates the formation of a target binding domain;
target closing domain hybrid in the absence of said target sequence;
b) exposing said sample to strand displacement conditions; and
c) determining whether a target binding domain;
target sequence hybrid is present in said sample as an indication of the presence or absence of said target sequence in said sample.- 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)
said target sequence is RNA;
said target binding domain is substantially comprised of nucleotide base recognition groups which more stably bind to ribonucleotides than to deoxyribonucleotides; and
said target closing domain is substantially comprised of deoxyribonucleotides.
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15. The method of claim 14, wherein said target binding domain substantially comprises 2′
- -methoxy or 2′
-fluoro substituted ribonucleotides.
- -methoxy or 2′
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16. The method of claim 1, wherein each of said first and second polynucleotides substantially comprises nucleotide base recognition groups which more stably bind to ribonucleotides than to deoxyribonucleotides.
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17. The method of claim 16, wherein said first and second polynucleotides comprise 2′
- -methoxy or 2′
-fluoro substituted ribonucleotides.
- -methoxy or 2′
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18. The method of claim 1, wherein said joining region consists of said one or more non-nucleotide linkers.
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19. The method of claim 18, wherein at least one of said non-nucleotide linkers is a polysaccharide or a polypeptide.
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20. The method of claim 1, wherein said joining region consists of said first and second polynucleotides or derivatives thereof.
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21. The method of claim 1, wherein said joining region consists of two of said non-nucleotide linkers and said first and second polynucleotides or derivatives thereof.
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22. The method of claim 1, wherein:
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said target binding domain or said target closing domain comprises a label; and
said label produces a first signal when said target binding domain;
target closing domain hybrid is formed and a second signal when said target binding domain;
target closing domain hybrid is not formed, said first and second signals being distinguishable.
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23. The method of claim 1, wherein:
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said target binding domain comprises a first label and said target closing domain comprises a second label;
said first and second labels interact to produce a first signal when said target binding domain and said target closing domain form a target binding domain;
target closing domain hybrid and a second signal when said target binding domain and said target closing domain do not form said target binding domain;
target closing domain hybrid, said first and second signals being distinguishable; and
an interaction change between said first and second labels is detected in step c) as an indication of the presence of a target binding domain;
target sequence hybrid.
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24. The method of claim 23, wherein said first label is attached to the end of said target binding domain which is not joined to said joining region and said second label is attached to the end of said target closing domain which is not joined to said joining region.
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25. The method of claim 23, wherein said first and second labels comprise a luminescent/quencher pair.
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26. The method of claim 23, wherein said first and second labels comprise a fluorophore/quencher pair.
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27. The method of claim 23, wherein said first and second labels comprise a luminescent/adduct pair.
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28. The method of claim 23, wherein said first and second labels comprise a Fö
- rrester energy transfer pair.
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29. The method of claim 23, wherein said first and second labels comprise a dye dimer pair.
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30. The method of claim 1, wherein said molecular torch further comprises a blocking group which can inhibit primer extension by a nucleic acid polymerase.
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31. The method of claim 30, wherein said blocking group is located at or near a 3′
- end of said molecular torch.
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32. The method of claim 31, wherein said blocking group is selected from the group consisting of an alkyl group, a non-nucleotide linker, an alkane-diol dideoxynucleotide residue and cordycepin.
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33. The method of claim 1, wherein said strand displacement conditions constitute essentially constant environmental conditions.
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34. The method of claim 1 further comprising separating said molecular torch which has formed said target binding domain:
- target sequence hybrid from molecular torches present in said sample which have not formed a target binding domain;
target sequence hybrid.
- target sequence hybrid from molecular torches present in said sample which have not formed a target binding domain;
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35. The method of claim 1, wherein said target sequence is the product of a transcription-associated amplification and said molecular torch is added to said sample prior to said amplification.
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36. A molecular torch comprising:
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a target binding domain comprising nucleotide base recognition groups;
a target closing domain comprising nucleotide base recognition groups, wherein said target binding domain is biased toward a target nucleic acid sequence, such that said target binding domain forms a more stable hybrid with said target sequence than with said target closing domain under strand displacement conditions; and
a joining region which joins said target binding domain and said target closing domain, wherein said joining region is selected from the group consisting of;
one or more non-nucleotide linkers;
first and second polynucleotides, or derivatives thereof, said first and second polynucleotides, or derivatives thereof, being substantially complementary to each other; and
a combination of said one or more non-nucleotide linkers and said first and second polynucleotides or derivatives thereof, wherein said joining region facilitates the hybridization of said target binding domain to said target closing domain. - View Dependent Claims (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)
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Specification