SCAFFOLD-BASED POLYMERASE ENZYME SUBSTRATES
First Claim
Patent Images
1. A composition comprising a compound of the structure:
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(DLD)n-X-(LNPN)m wherein each D is a fluorescent dye moiety, X is a multifunctional core with multiple linking sites, P is a polyphosphate moiety having 2 to 10 phosphates, N is a nucleoside moiety, m+n=3 or greater, and LD and LN are either direct bonds or linkers.
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Abstract
The invention provides a novel class of scaffold-based labeled polymerase enzyme substrates. The polymerase enzyme substrates have a multivalent core or scaffold to which is attached fluorescent dye moieties and nucleoside phosphate moities. The polymerase enzyme substrates have multiple fluorescent dye moities and/or multiple nucleoside phosphate moieties. Preferred multivalent cores comprise trifunctional six membered aromatic moities. The invention also provides for sequencing methods and kits with scaffold-based labeled polymerase enzyme substrates.
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Citations
49 Claims
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1. A composition comprising a compound of the structure:
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(DLD)n-X-(LNPN)mwherein each D is a fluorescent dye moiety, X is a multifunctional core with multiple linking sites, P is a polyphosphate moiety having 2 to 10 phosphates, N is a nucleoside moiety, m+n=3 or greater, and LD and LN are either direct bonds or linkers. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 28, 29)
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3. The composition of claim 1 comprising a compound of the structure:
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4. The composition of claim 2 wherein D1 is a FRET donor and D2 is a FRET acceptor.
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5. The composition of claim 1 comprising a compound of the structure:
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6. The composition of claim 5 wherein D1 and D2 are FRET donors and D3 is a FRET acceptor.
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7. The composition of claim 1 comprising a compound of the structure
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8. The composition of claim 1 wherein D1, D2, and D3 are FRET donors and D4 is a FRET acceptor.
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9. The composition of claim 2 wherein X comprises a trifunctional six-membered aromatic moiety.
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10. The composition of claim 9 wherein the trifunctional six-membered aromatic moiety comprise either a tri-substituted benzene or a tri-substituted triazine.
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22. The composition of claim 1 wherein X comprises the structure:
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23. The composition of claim 1 wherein X comprises the structure:
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24. The composition of claim 1 wherein X comprises the structure:
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28. A sequencing mixture comprising a set of 4 nucleotide analog substrates, each having one of the bases A, G, C, T, or A, G, C, U, at least two of the substrates having the structure of claim 1, and each substrate having at least one fluorescent dye moiety different from the fluorescent dye moieties on the other three substrates.
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29. A method for nucleic acid sequencing comprising:
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immobilizing a polymerase enzyme complex comprising a polymerase enzyme and a template nucleic acid; exposing the immobilized polymerase enzyme complex to a plurality of labeled nucleotide analog substrates, at least one of the substrates comprising a compound having the structure of claim 1; detecting the incorporation of substrates by observing fluorescence from the nucleotide analog substrates; and using the detected incorporation over time to obtain sequence information about the template nucleic acid.
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11-21. -21. (canceled)
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25-27. -27. (canceled)
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31. A composition comprising a compound having the structure:
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Y-(L-D-P—
N)mwherein Y is a multifunctional core having m linking sites, L is either a direct bond or a linker, D is a fluorescent dye moiety, P is a polyphosphate having from 2 to 10 phosphates, and N is a nucleoside moiety, and m is greater than 2.
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33-37. -37. (canceled)
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38. A composition comprising a compound having the structure:
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D-(L-P—
N)mwherein D is a fluorescent dye moiety having m linking sites, L is either a direct bond or a linker, P is a polyphosphate moiety having 2 to 10 phosphates, N is a nucleoside moiety, and m is from 2 to 8. - View Dependent Claims (39)
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40-43. -43. (canceled)
- 44. A composition comprising a compound having the structure:
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49-57. -57. (canceled)
Specification