Apparatus and methods for kinetic analysis and determination of nucleic acid sequences

Abstract

A system for determining nucleic acid sequences, including (a) an array of nucleic acid features; (b) a fluidic apparatus configured to deliver sequencing reagents, including polymerases and nucleotides, to the array; (c) a detector configured to obtain pre-equilibrium kinetic measurements from the array at a resolution that distinguishes individual nucleic acid features; (d) a control module having instructions for (i) directing the fluidic apparatus to deliver the sequencing reagents to the array, and (ii) directing the detection apparatus to obtain the kinetic measurements; and (e) an analysis module having instructions for (i) processing the kinetic measurements to determine binding of the polymerase molecules to the nucleic acid features at several pre-equilibrium time points, thereby determining a transient state of the polymerase molecules at the nucleic acid features, and (ii) identifying nucleic acid features that correctly incorporate the nucleotide molecules based on the transient state of the polymerase molecules.

Description

[0001]This application is based on, and claims the benefit of, U.S. Provisional Application No. 61 / 578,684, filed Dec. 21, 2011, which is incorporated herein by reference in its entirety.BACKGROUND[0002]This disclosure relates generally to detection and characterization of nucleic acids. More specifically this disclosure relates to determining the sequences of nucleic acids.[0003]One's genome provides a blue print for predicting many inherent predispositions such as one's likes and dislikes, talents, susceptibility to disease and responsiveness to therapeutic drugs. The human genome contains a sequence of over 3 billion nucleotides and it is the differences in just a fraction of those nucleotides that determines unique characteristics of an individual. The research community is making impressive strides in unraveling the link between genomic sequence and the living structures they encode. However, a more complete understanding will require that tens-of-thousands or millions of genom...

AI Technical Summary

Benefits of technology

This patent describes a method and system for identifying and distinguishing nucleotide sequences of different nucleic acid molecules. The method involves mixing multiple nucleic acid molecules with polymerase molecules and nucleotide molecules, attached to a surface in the form of an array of nucleic acid features. The polymerase molecules are then allowed to attach to the nucleic acid features and form transient states, resulting in a unique binding pattern for each nucleic acid molecule. By identifying which nucleic acid features have correctly incorporated nucleotide molecules, the method can distinguish the nucleotide sequences of different nucleic acid molecules. The system includes an array of nucleic acid features, a fluidic apparatus for delivering sequencing reagents, a detection apparatus for obtaining kinetic measurements, and an analysis module for processing the kinetic measurements to determine the transient state of the polymerase molecules and identify the nucleic acid features that correctly incorporated nucleotide molecules. Overall, this patent provides a reliable and efficient method for identifying and characterizing nucleotide sequences of different nucleic acid molecules.

Problems solved by technology

Several commercial sequencing platforms are available, and although they provide an accurate tool for sequencing on the scale of entire genomes, they are still prohibitively expensive for wide deployment across large populations of individuals.

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