A method for sequencing a nucleic acid template comprising: providing a substrate having an upper solution above the substrate and a lower solution below the substrate, the substrate comprising a nanopore connecting the upper solution and lower solution, the nanopore sized to pass a single strand of a nucleic acid; providing a voltage across the nanopore to produce a measurable current flow through the nanopore; controlling the rate of translocation of a single stranded portion of the nucleic acid template through the nanopore with a translocating enzyme that is associated with the nucleic acid template under reaction conditions whereby the translocating enzyme and the reaction conditions are selected such that the translocating enzyme exhibits two kinetic steps wherein each of the kinetic steps has a rate constant, and the ratio of the rate constants of the kinetic steps is from 10:1 to 1:10; measuring the current through the nanopore over time as the nucleic acid template is translated through the nanopore; and determining the sequence of a portion of the nucleic acid template as it translates through the nanopore using the measured current over time. view more

The method of claim 1 wherein the translocating enzyme comprises a polymerase, an exonuclease, or a helicase.

The method of claim 1 wherein the substrate comprises an array of nanopores.

A method of determining a nucleotide sequence of a region of interest in a polynucleotide, the method comprising: introducing a polynucleotide comprising a region of interest to a sequence analysis system comprising a nanopore in a membrane, wherein the polynucleotide comprises a double-stranded portion comprising complementary strands of the region of interest; applying a voltage across the membrane; monitoring variations in ionic current through the nanopore of the sequence analysis system during enzyme chaperone-regulated passage of the polynucleotide through the nanopore; analyzing the monitored variations in ionic current to obtain nucleotide sequence information for the polynucleotide, wherein the nucleotide sequence information comprises redundant sequence information for the region of interest, wherein the redundant sequence information comprises the nucleotide sequence of the complementary strands; and determining a consensus sequence for the region of interest based on the redundant sequence information. view more

The method of claim 1, wherein the nanopore comprises a protein channel.

The method of claim 8, wherein the complementary strands are linked by a linker comprising a nucleotide.

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A method for sequencing template nucleic acids comprising: a) providing a device comprising an array of nanopores a in contact with a solution, the solution comprising a plurality of template nucleic acids above the nanopore; b) providing a voltage across the nanopores, whereby, for one or more nanopore in the array, a template nucleic acid is translocated through the nanopore, wherein the translocation rate through the nanopore is enzymatically controlled; c) measuring an electrical signal which has a value that varies for at least N monomeric units of the template nucleic acid in the nanopore, wherein the measuring is performed as a function of time while the template nucleic acid translocates through the nanopore, wherein N is three or greater; and d) determining the sequence of the template nucleic acid using the measured electrical signal from step (c) by performing a process including comparing the electrical signal from step (c) to calibration information that accounts for the electrical signal for 4 to the N sequence combinations. view more

The method of claim 1 wherein the at least N monomeric units comprise 5-mers.

The method of claim 1 wherein the device substrate comprises a semiconductor chip comprising an array of nanopores.

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