Methods, systems, and reagents for direct RNA sequencing
First Claim
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1. A reaction mixture comprising a polymerase enzyme complex comprising a polymerase enzyme and a template nucleic acid that is bound to the polymerase,wherein the polymerase is a recombinant Φ
- 29-type polymerase, which recombinant polymerase comprises an amino acid sequence that is at least 80% identical to SEQ ID NO;
1 or at least 80% identical to SEQ ID NO;
2, and which recombinant polymerase comprises a) a first cysteine residue at position V19 and a second cysteine residue at position N409, b) a first cysteine residue at position D84 and a second cysteine residue at position E418, c) a first cysteine residue at position N409 and a second cysteine residue at position V568, or d) a first cysteine residue at position A83 and a second cysteine residue at position E420, wherein identification of positions is relative to SEQ ID NO;
1,wherein the side chains of the first and second cysteine residues are covalently connected by a linker, thereby topologically encircling the template nucleic acid.
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Abstract
Provided are compositions comprising recombinant polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for sequencing RNA or RNA/DNA templates. Polymerases that topologically encircle the template nucleic acid are provided. Also provided are methods of using such polymerases to make a DNA or to sequence a template comprising RNA.
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16 Claims
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1. A reaction mixture comprising a polymerase enzyme complex comprising a polymerase enzyme and a template nucleic acid that is bound to the polymerase,
wherein the polymerase is a recombinant Φ - 29-type polymerase, which recombinant polymerase comprises an amino acid sequence that is at least 80% identical to SEQ ID NO;
1 or at least 80% identical to SEQ ID NO;
2, and which recombinant polymerase comprises a) a first cysteine residue at position V19 and a second cysteine residue at position N409, b) a first cysteine residue at position D84 and a second cysteine residue at position E418, c) a first cysteine residue at position N409 and a second cysteine residue at position V568, or d) a first cysteine residue at position A83 and a second cysteine residue at position E420, wherein identification of positions is relative to SEQ ID NO;
1,wherein the side chains of the first and second cysteine residues are covalently connected by a linker, thereby topologically encircling the template nucleic acid. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 15, 16)
- 29-type polymerase, which recombinant polymerase comprises an amino acid sequence that is at least 80% identical to SEQ ID NO;
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12. A method for sequencing a nucleic acid template comprising:
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providing a polymerase enzyme complex comprising a polymerase enzyme, a template nucleic acid that is bound to the polymerase, and optionally a primer hybridized to the template nucleic acid, wherein the polymerase is a recombinant Φ
29-type polymerase, which recombinant polymerase comprises an amino acid sequence that is at least 80% identical to SEQ ID NO;
1 or at least 80% identical to SEQ ID NO;
2, and which recombinant polymerase comprises a) a first cysteine residue at position V19 and a second cysteine residue at position N409, b) a first cysteine residue at position D84 and a second cysteine residue at position E418, c) a first cysteine residue at position N409 and a second cysteine residue at position V568, or d) a first cysteine residue at position A83 and a second cysteine residue at position E420, wherein identification of positions is relative to SEQ ID NO;
1, wherein the side chains of the first and second cysteine residues are covalently connected by a linker, thereby topologically encircling the template nucleic acid, wherein the polymerase enzyme complex is immobilized on a surface;adding sequencing reagents in contact with the surface comprising reagents for carrying out nucleic acid synthesis including one or more labeled nucleotide analogs; and determining the sequential addition of nucleotide residues to a nucleic acid strand complementary to a strand of the template nucleic acid by observing the interaction of the labeled nucleotide analogs with the polymerase enzyme complex.
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13. A system for sequencing nucleic acids comprising:
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a chip comprising a plurality of polymerase enzyme complexes bound thereto, each polymerase enzyme complex individually optically resolvable, each polymerase enzyme complex comprising a polymerase enzyme, a template nucleic acid that is bound to the polymerase, and optionally a primer hybridized to the template nucleic acid, wherein the polymerase is a recombinant Φ
29-type polymerase, which recombinant polymerase comprises an amino acid sequence that is at least 80% identical to SEQ ID NO;
1 or at least 80% identical to SEQ ID NO;
2, and which recombinant polymerase comprises a) a first cysteine residue at position V19 and a second cysteine residue at position N409, b) a first cysteine residue at position D84 and a second cysteine residue at position E418, c) a first cysteine residue at position N409 and a second cysteine residue at position V568, or d) a first cysteine residue at position A83 and a second cysteine residue at position E420, wherein identification of positions is relative to SEQ ID NO;
1, wherein the side chains of the first and second cysteine residues are covalently connected by a linker, thereby topologically encircling the template;sequencing reagents in contact with the surface comprising reagents for carrying out nucleic acid synthesis including one or more labeled nucleotide analogs; an illumination system for illuminating the polymerase enzyme complexes; an optical detection system for detecting fluorescence from the labeled nucleotide analogs while they are interacting with the polymerase enzyme complexes; and a computer for analyzing the signals detected by the detection system to determine the sequential addition of nucleotide residues to a nucleic acid strand complementary to a strand of the template nucleic acid.
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Specification