Methods and apparatus for single molecule sequencing using energy transfer detection
First Claim
1. A method for generating an energy transfer signal comprising the steps of:
- (a) contacting (i) a modified polymerase linked to an energy transfer donor moiety with (ii) a nucleic acid molecule and with (iii) at least one type of a nucleotide having an energy transfer acceptor moiety;
(b) incorporating the nucleotide into the nucleic acid molecule using the polymerase, wherein the incorporating includes (i) forming a nucleotide cleavage product; and
(ii) generating an energy transfer signal through energy transfer between the donor moiety and the acceptor moiety; and
(c) detecting the energy transfer signal, wherein the detecting is not performed in a waveguide, wherein the at least one type of nucleotide includes 4-10 phosphate groups, and wherein and the modified polymerase includes one or more amino acid substitutions which reduce the rate of polymerase dissociation from a nucleotide cleavage product relative to a polymerase lacking the one or more amino acid substitutions, wherein the modified polymerase comprises the amino acid sequence of SEQ ID NO;
1 having histidine at position 370 substituted with glycine, threonine, serine, lysine, arginine, alanine, glutamine, tryptophan, tyrosine, or phenylalanine.
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Abstract
Provided herein are systems and methods for nucleotide incorporation reactions. The systems comprise polymerases having altered nucleotide incorporation kinetics and are linked to an energy transfer donor moiety, and nucleotide molecules linked with at least one energy transfer acceptor moiety. The donor and acceptor moieties undergo energy transfer when the polymerase and nucleotide are proximal to each other during nucleotide binding and/or nucleotide incorporation. As the donor and acceptor moieties undergo energy transfer, they generate an energy transfer signal which can be associated with nucleotide binding or incorporation. Detecting a time sequence of the generated signals, or the change in the signals, can be used to determine the order of the incorporated nucleotides, and can therefore be used to deduce the sequence of the target molecule.
118 Citations
22 Claims
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1. A method for generating an energy transfer signal comprising the steps of:
- (a) contacting (i) a modified polymerase linked to an energy transfer donor moiety with (ii) a nucleic acid molecule and with (iii) at least one type of a nucleotide having an energy transfer acceptor moiety;
(b) incorporating the nucleotide into the nucleic acid molecule using the polymerase, wherein the incorporating includes (i) forming a nucleotide cleavage product; and
(ii) generating an energy transfer signal through energy transfer between the donor moiety and the acceptor moiety; and
(c) detecting the energy transfer signal, wherein the detecting is not performed in a waveguide, wherein the at least one type of nucleotide includes 4-10 phosphate groups, and wherein and the modified polymerase includes one or more amino acid substitutions which reduce the rate of polymerase dissociation from a nucleotide cleavage product relative to a polymerase lacking the one or more amino acid substitutions, wherein the modified polymerase comprises the amino acid sequence of SEQ ID NO;
1 having histidine at position 370 substituted with glycine, threonine, serine, lysine, arginine, alanine, glutamine, tryptophan, tyrosine, or phenylalanine. - View Dependent Claims (5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22)
- (a) contacting (i) a modified polymerase linked to an energy transfer donor moiety with (ii) a nucleic acid molecule and with (iii) at least one type of a nucleotide having an energy transfer acceptor moiety;
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2. A method for generating an energy transfer signal comprising the steps of:
- (a) contacting (i) a modified polymerase linked to an energy transfer donor moiety with (ii) a nucleic acid molecule and with (iii) at least one type of a hexaphosphate nucleotide having an energy transfer acceptor moiety;
(b) incorporating the hexaphosphate nucleotide into the nucleic acid molecule using the polymerase, wherein the incorporating includes (i) forming a nucleotide cleavage product; and
(ii) generating an energy transfer signal through energy transfer between the donor moiety and the acceptor moiety; and
(c) detecting the energy transfer signal, wherein the detecting is not performed in a waveguide, wherein and the modified polymerase includes one or more amino acid substitutions which reduce the rate of polymerase dissociation from a nucleotide cleavage product relative to a polymerase lacking the one or more amino acid substitutions, wherein the modified polymerase comprises the amino acid sequence of SEQ ID NO;
1 having histidine at position 370 substituted with glycine, threonine, serine, lysine, arginine, alanine, glutamine, tryptophan, tyrosine, or phenylalanine.
- (a) contacting (i) a modified polymerase linked to an energy transfer donor moiety with (ii) a nucleic acid molecule and with (iii) at least one type of a hexaphosphate nucleotide having an energy transfer acceptor moiety;
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3. A method for generating an energy transfer signal comprising the steps of:
- (a) contacting (i) a modified polymerase linked to an energy transfer donor moiety with (ii) a target nucleic acid molecule which is base-paired with a polymerization initiation site having a terminal 3′
OH group and with (iii) at least one type of a nucleotide having an energy transfer acceptor moiety;
(b) incorporating the nucleotide onto the terminal 3′
OH group using the polymerase, wherein the incorporating includes (i) forming a nucleotide cleavage product; and
(ii) generating an energy transfer signal through energy transfer between the donor moiety and the acceptor moiety; and
(c) detecting the energy transfer signal, wherein the detecting is not performed in a waveguide, wherein the at least one type of nucleotide includes 4-10 phosphate groups, and wherein and the modified polymerase includes one or more amino acid substitutions which reduce the rate of polymerase dissociation from a nucleotide cleavage product relative to a polymerase lacking the one or more amino acid substitutions, wherein the modified polymerase comprises the amino acid sequence of SEQ ID NO;
1 having histidine at position 370 substituted with glycine, threonine, serine, lysine, arginine, alanine, glutamine, tryptophan, tyrosine, or phenylalanine.
- (a) contacting (i) a modified polymerase linked to an energy transfer donor moiety with (ii) a target nucleic acid molecule which is base-paired with a polymerization initiation site having a terminal 3′
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4. A method for generating an energy transfer signal comprising the steps of:
- (a) contacting (i) a modified polymerase linked to an energy transfer donor moiety with (ii) a target nucleic acid molecule which is base-paired with a polymerization initiation site having a terminal 3′
OH group and with (iii) at least one type of a hexaphosphate nucleotide having an energy transfer acceptor moiety;
(b) incorporating the hexaphosphate nucleotide onto the terminal 3′
OH group using the polymerase, wherein the incorporating includes (i) forming a nucleotide cleavage product; and
(ii) generating an energy transfer signal through energy transfer between the donor moiety and the acceptor moiety; and
(c) detecting the energy transfer signal, wherein the detecting is not performed in a waveguide, wherein and the modified polymerase includes one or more amino acid substitutions which reduce the rate of polymerase dissociation from a nucleotide cleavage product relative to a polymerase lacking the one or more amino acid substitutions, wherein the modified polymerase comprises the amino acid sequence of SEQ ID NO;
1 having histidine at position 370 substituted with glycine, threonine, serine, lysine, arginine, alanine, glutamine, tryptophan, tyrosine, or phenylalanine.
- (a) contacting (i) a modified polymerase linked to an energy transfer donor moiety with (ii) a target nucleic acid molecule which is base-paired with a polymerization initiation site having a terminal 3′
Specification