Method and Apparatus for Rapid Nucleic Acid Sequencing

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.

1 - 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 μm. 
     
     
         158 . The apparatus of  claim 155 , wherein the array of reaction chambers comprises at least about 10 5  reaction chambers. 
     
     
         159 . The apparatus of  claim 155 , wherein an average center-to-center distance between adjacent FETs is less than 10 μm. 
     
     
         160 . The apparatus of  claim 155 , wherein the array of FETs comprises at least about 10 5  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.