Method and apparatus for determining the sequence of polynucleotides
First Claim
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1. An apparatus for determining the sequence of a nucleic acid, comprising:
- a fabricated substrate comprising at least one alignment path having a nucleic acid binding surface;
a scanning microscope for scanning along said alignment path to provide an output signal representative of the position of each labeled base in said nucleic acid sequence;
a data processor for processing the signal to provide an output signal representative of the sequence of said nucleic acid.
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Abstract
Methods for determining the sequence of a polynucleotide are described. The method utilizes a novel apparatus. Linearly oriented nucleic acids are scanned by scanning tunneling microscopy, and the presence of base specific labels determined. The information is compiled for different labels, and the data sets combined to provide the full nucleotide sequence.
262 Citations
16 Claims
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1. An apparatus for determining the sequence of a nucleic acid, comprising:
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a fabricated substrate comprising at least one alignment path having a nucleic acid binding surface; a scanning microscope for scanning along said alignment path to provide an output signal representative of the position of each labeled base in said nucleic acid sequence; a data processor for processing the signal to provide an output signal representative of the sequence of said nucleic acid. - View Dependent Claims (2, 3, 4, 11, 12, 13, 14, 15)
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5. A method for determining the nucleotide sequence of a DNA, the method comprising:
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(1)(A) preparing purified, linear single-stranded DNA, wherein said DNA comprises a label distinguishable by scanning microscopy (SXM) specific for one base species; (B) aligning said DNA on a fabricated substrate comprising at least one alignment path having a nucleic acid binding surface; (C) scanning said aligned DNA by STM; (D) recording the position of said label along said aligned DNA to provide a base sequence-data set; (2) repeating steps (A) to (D) with a label specific for each nucleoside base; and (3) compiling each of said base sequence-data sets to provide a complete sequence data set, wherein said data set describes the position of each nucleotide in the sequence of said DNA. - View Dependent Claims (6, 7, 8, 9, 10)
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16. An apparatus for determining the sequence of a nucleic acid, comprising:
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a fabricated substrate comprising at least one alignment path having a nucleic acid binding surface, wherein said substrate is formed from a base material selected from the group consisting of crystalline silicon, germanium, and III-V compounds, said base material having a root mean surface number of less than about 5 angstroms; a scanning microscope for scanning along said alignment path to provide an output signal representative of the position of each labeled base in said nucleic acid sequence; a data processor for processing the signal to provide an output signal representative of the sequence of said nucleic acid.
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Specification