Sequencing Nucleic Acid Polymers with Electron Microscopy

• US 20100267153A1
• Filed: 04/02/2010
• Published: 10/21/2010
• Est. Priority Date: 10/04/2007
• Status: Abandoned Application

• Current Assignee: Halcyon Molecular
• Original Assignee: Halcyon Molecular
• Inventors: Andregg, William, Andregg, Michael
• Application Number:
  US12/753,696
• Publication Number:
  US 20100267153A1
• Time in Patent Office: Days
• US Class Current: 436/94
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2565/601 being a microscope, e.g. atomic force microscopy [AFM]
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

This invention relates to using an electron microscope to sequence by direct inspection of labeled, stretched DNA. This method will have higher accuracy, lower cost, and longer read length than current DNA sequencing methods.

Claims

1-93. -93. (canceled)

94. A method of determining the sequence of 20 or more consecutive bases in a nucleic acid, the method comprising:

(a) providing a nucleic acid of 20 or more bases in length;

(b) imaging the nucleic acid by electron microscopy to obtain electron microscopy (EM) data; and

(c) determining the sequence of the nucleic acid from the EM data.

95. The method according to claim 94, wherein the method determines the sequence of 50 or more consecutive bases in the nucleic acid.

96. The method according to claim 95, wherein the method determines the sequence of 1,000 or more consecutive bases in the nucleic acid.

97. The method according to claim 95, wherein the method determines the sequence of 10,000 or more consecutive bases in the nucleic acid.

98. The method according to claim 95, wherein the method determines the sequence of 100,000 or more consecutive bases in the nucleic acid.

99. The method according to claim 95, wherein the method determines the sequence of 1,000,000 or more consecutive bases in the nucleic acid.

100. The method according to claim 94, wherein the nucleic acid sequence is obtained at a rate of at least 1,000 bases per second.

101. The method according to claim 94, wherein the EM data is obtained by transmission electron microscopy.

102. The method according to claim 100, wherein the imaging comprises imaging 10,000 or more bases per second

103. The method according to claim 94, wherein the nucleic acid has a pre-determined configuration.

104. The method according to claim 103, wherein the nucleic acid has a linear configuration with consistent base-to-base spacing.

105. The method according to claim 104, wherein the base-to-base spacing ranges from 3 to 7 Å

.

106. The method according to claim 105, wherein the providing step comprises:

a) introducing a nucleic acid binding tool into a fluid composition of the nucleic acid so that the nucleic acid binds to the nucleic acid binding tool;

b) removing the nucleic acid binding tool from the fluid so that the nucleic acid is stretched into space between an air/fluid interface and the nucleic acid binding tool; and

c) depositing the stretched nucleic acid onto a substrate.

107. The method according to claim 106, wherein the stretched nucleic acid is deposited onto the substrate using a shelf threading protocol.

108. The method according to claim 106, wherein the stretched nucleic acid is deposited onto the substrate using a gap threading protocol.

109. The method according to claim 94, wherein the nucleic acid is a contrast agent labeled nucleic acid.

110. The method according to claim 109, further comprising producing the contrast agent labeled nucleic acid by contacting the nucleic acid to be sequenced with a contrast agent that directly labels the nucleic acid to be sequenced to produce the contrast agent labeled nucleic acid.

111. The method according to claim 110, wherein the method comprises producing two or more different populations of differentially labeled nucleic acid sequences, wherein each of the different populations comprise nucleic acids of identical sequence.

112. The method according to 111, wherein the two or more different populations are labeled with the same label.

113. The method according to claim 110, wherein only a portion of the bases are labeled in the contrast agent labeled nucleic acid.

114. The method according to claim 110, wherein the contrast agent labeled nucleic acid is a labeled with a high-Z atom contrast agent.