Hairpin loop method for double strand polynucleotide sequencing using transmembrane pores
First Claim
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1. A method of sequencing a target polynucleotide using an apparatus comprising:
- (i) a chamber comprising an aqueous solution and a membrane separating the chamber into two compartments, wherein a transmembrane nanopore is present in the membrane; and
(ii) electrodes connected to the two compartments, the method comprising;
(a) providing in the solution (i) a construct comprising a double stranded, target polynucleotide, wherein a single stranded leader polynucleotide is linked to one end of the double stranded, target polynucleotide, and a hairpin loop links the two strands of the target polynucleotide at the opposite end of the target polynucleotide; and
(ii) a polynucleotide binding protein that is a polymerase or a helicase that binds the construct;
(b) applying a voltage across the electrodes sufficient to cause the construct to move, in a single stranded form, through the nanopore, wherein under the applied voltage the polynucleotide binding protein simultaneously controls the rate of movement of the target polynucleotide through the nanopore and separates the two strands of the target polynucleotide to generate the single stranded form; and
(c) measuring the current passing through the nanopore as the construct moves through the nanopore in the order of (1) one strand of the target polynucleotide, (2) the hairpin loop, and (3) the other strand of the target polynucleotide, and sequencing the target polynucleotide based on the measured current.
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Abstract
The invention relates to a new method of sequencing a double stranded target polynucleotide. The two strands of the double stranded target polynucleotide are linked by a bridging moiety. The two strands of the target polynucleotide are separated using a polynucleotide binding protein and the target polynucleotide is sequenced using a transmembrane pore.
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16 Claims
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1. A method of sequencing a target polynucleotide using an apparatus comprising:
- (i) a chamber comprising an aqueous solution and a membrane separating the chamber into two compartments, wherein a transmembrane nanopore is present in the membrane; and
(ii) electrodes connected to the two compartments, the method comprising;(a) providing in the solution (i) a construct comprising a double stranded, target polynucleotide, wherein a single stranded leader polynucleotide is linked to one end of the double stranded, target polynucleotide, and a hairpin loop links the two strands of the target polynucleotide at the opposite end of the target polynucleotide; and
(ii) a polynucleotide binding protein that is a polymerase or a helicase that binds the construct;(b) applying a voltage across the electrodes sufficient to cause the construct to move, in a single stranded form, through the nanopore, wherein under the applied voltage the polynucleotide binding protein simultaneously controls the rate of movement of the target polynucleotide through the nanopore and separates the two strands of the target polynucleotide to generate the single stranded form; and (c) measuring the current passing through the nanopore as the construct moves through the nanopore in the order of (1) one strand of the target polynucleotide, (2) the hairpin loop, and (3) the other strand of the target polynucleotide, and sequencing the target polynucleotide based on the measured current. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15)
- (i) a chamber comprising an aqueous solution and a membrane separating the chamber into two compartments, wherein a transmembrane nanopore is present in the membrane; and
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16. A method of sequencing a target polynucleotide using an apparatus comprising:
- (i) a chamber comprising an aqueous solution and a membrane separating the chamber into two compartments, wherein a transmembrane nanopore is present in the membrane; and
(ii) electrodes connected to the two compartments, the method comprising;(a) providing a single stranded polynucleotide comprising two strands of a double stranded, target polynucleotide, wherein the two strands of the target polynucleotide are linked at one end of the target polynucleotide by a polynucleotide linker; (b) synthesising a complement of the single stranded polynucleotide of step (a), such that the single stranded polynucleotide of step (a) and the complement form a double stranded polynucleotide; (c) providing in the solution (i) a construct comprising the double stranded polynucleotide of step (b), wherein a single stranded leader polynucleotide is linked to one end of the double stranded polynucleotide and a hairpin loop links the two strands of the double stranded polynucleotide at the opposite end of the double stranded polynucleotide; and
(ii) a polynucleotide binding protein that is a polymerase or a helicase that binds the construct;(d) applying a voltage across the electrodes sufficient to cause the construct to move, in a single stranded form, through the nanopore, wherein under the applied voltage the polynucleotide binding protein simultaneously controls the rate of movement of the double stranded polynucleotide of step (b) through the transmembrane nanopore and separates the two strands of the double stranded polynucleotide of step (b) to generate the single stranded form; and (e) measuring the current passing through the nanopore as the construct moves through the nanopore in the order of (1) the single stranded polynucleotide of step (a), (2) the hairpin loop, and (3) the complement of step (b), and sequencing the target polynucleotide based on the measured current.
- (i) a chamber comprising an aqueous solution and a membrane separating the chamber into two compartments, wherein a transmembrane nanopore is present in the membrane; and
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