Active-electrode integrated biosensor array and methods for use thereof

Abstract

A method and device for performing DNA sequencing and extracting structural information from unknown nucleic acid strands. The device includes a microwell structure, where identical DNA strands are immobilized within the microwell structure on a surface of a micro-bead, an active electrode or a porous polymer. The device further includes a CMOS-integrated semiconductor integrated circuit, where the CMOS-integrated semiconductor integrated circuit includes metal layers on a silicon substrate, where the metal layers form an active electrode biosensor. In addition, a sensing electrode is formed by creating openings in a passivation layer of the CMOS-integrated semiconductor integrated circuit to hold a single bead, on which the DNA strands are immobilized.

1 . A system for assaying for a presence of a nucleic acid sequence in a nucleic acid sample, comprising:
 a chip comprising (i) a plurality of wells, wherein during use, an individual well of said plurality of wells comprises a porous polymer, a template nucleic acid molecule derived from said nucleic acid sample and reagents necessary for a polymerization reaction, and (ii) a sensor adjacent to said individual well, wherein said sensor detects signals indicative of said presence of said nucleic acid sequence in said template nucleic acid molecule; and   detection circuitry operatively coupled to said sensor, wherein said detection circuitry (i) detects said signals indicative of said presence of said nucleic acid sequence in said template nucleic acid molecule when said template nucleic acid molecule is subjected to said polymerization reaction under conditions that are sufficient to yield a nucleic acid strand that is complementary to said template nucleic acid molecule, and (ii) provides an output that is indicative of said presence of said nucleic acid sequence in said nucleic acid sample.   
     
     
         2 . The system of  claim 1 , wherein said sensor comprises a sensing electrode. 
     
     
         3 . The system of  claim 2 , wherein said sensor further comprises one or more metal layers disposed in an insulating layer adjacent to said sensing electrode. 
     
     
         4 . The system of  claim 1 , wherein said detection circuitry comprises an operational amplifier and a capacitor that is in a parallel configuration with respect to said operational amplifier. 
     
     
         5 . The system of  claim 1 , wherein during use, said template nucleic acid molecule is immobilized in said porous polymer. 
     
     
         6 . The system of  claim 1 , wherein said signals are indicative of an impedance at an interface between said sensor and said individual well. 
     
     
         7 . The system of  claim 1 , wherein said signals are indicative of a localized ionic current in said individual well during said polymerization reaction. 
     
     
         8 . The system of  claim 1 , wherein said signals are detected within a double layer in said individual well adjacent to said sensor. 
     
     
         9 . The system of  claim 1 , wherein said signals are indicative of a localized ionic current and interface impedance in said individual well during said polymerization reaction. 
     
     
         10 . The system of  claim 1 , wherein said plurality of wells comprises an additional well, wherein during use, said additional well comprises an additional template nucleic acid molecule derived from said nucleic acid sample.