Method and Apparatus for Rapid Nucleic Acid Sequencing

• US 20110281737A1
• Filed: 02/15/2011
• Published: 11/17/2011
• Est. Priority Date: 10/22/2008
• Status: Abandoned Application

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Huber, Martin, ROTHBERG, Jonathan M., Davidson, John F., van Oijen, Antoine M., Leamon, John H., Hinz, Wolfgang
• Application Number:
  US13/027,500
• Publication Number:
  US 20110281737A1
• Time in Patent Office: Days
• US Class Current: 506/2
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode
• CPC Class Codes: G01N 27/4145 specially adapted for biomolecules, e.g. gate electrode with immobilised receptors
• CPC Class Codes: G01N 27/4148 Integrated circuits therefor, e.g. fabricated by CMOS processing CMOS processing per se H01L21/82
• CPC Class Codes: H01L 21/82 to produce devices, e.g. integrated circuits, each consisting of a plurality of components

Abstract

Methods and apparatus relating to FET arrays including large FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.

Claims

1-154. -154. (canceled)

155. An apparatus for nucleic acid sequencing, comprising:

a) an array of reaction chambers coupled to an array of field effect transistors (FETs), wherein at least a portion of the reaction chambers having nicked nucleic acids disposed therein;

b) a fluidic distribution network configured to distribute into the array of reaction chambers a solution of known nucleotides, polymerase, and reaction constituents suitable for incorporating nucleotides in the nicked nucleic acids;

c) a detector configured to detect signals from the array of FETs generated in response to byproducts released into the portion of the reaction chambers having nicked nucleic acids by polymerase excision and incorporation activities as the known nucleotides are incorporated into the nicked nucleic acids; and

d) an assembler configured to receive signals from the detector and resolve the signals into nucleotide sequences associated with at least a portion of the nicked nucleic acids in the array of reaction chambers.

156. The apparatus of claim 155, wherein each of the reaction chambers in the array of reaction chambers has an average volume of less than or equal to 1 picoliter (pL).

157. The apparatus of claim 155, wherein an average center-to-center distance between adjacent reaction chambers is less than 10 μ

m.

158. The apparatus of claim 155, wherein the array of reaction chambers comprises at least about 10⁵ reaction chambers.

159. The apparatus of claim 155, wherein an average center-to-center distance between adjacent FETs is less than 10 μ

m.

160. The apparatus of claim 155, wherein the array of FETs comprises at least about 10⁵ FETs.

161. The apparatus of claim 155, wherein the nicked nucleic acids comprise concatemers of substantially identical nucleic acids.

162. The apparatus of claim 155, wherein the nicked nucleic acids are coupled to the reaction chambers.

163. The apparatus of claim 155, wherein the nicked nucleic acids are coupled to particles disposed in the reaction chambers.

164. The apparatus of claim 155, wherein the array of FETs comprises chemically-sensitive field effect transistors (chemFETs).

165. The apparatus of claim 155, wherein the array of FETs comprises ion-sensitive field effect transistors (ISFETs).

166. The apparatus of claim 155, wherein the byproducts of the incorporation activities comprise hydrogen ions.

167. The apparatus of claim 155, wherein the fluidic distribution network comprises a fluidic controller configured to sequentially distribute into the array of reaction chambers one or more solutions of different known nucleotides.

168. The apparatus of claim 155, wherein the solution further comprises a buffering inhibitor.

169. The apparatus of claim 168, wherein the buffering inhibitor is selected from the group consisting of a phospholipid, a sulfonic acid surfactant, a polyanionic electrolyte or a salt thereof, a polycationic electrolyte or a salt thereof, tetramethyl ammonium and a salt.

170. The apparatus of claim 169, wherein the buffering inhibitor comprises a combination of two or more different buffering inhibitors.