Patent ID: 7202037

Claim:
A method of detecting base stacking perturbations in a duplex nucleic acid sequence associated with protein binding to the duplex nucleic acid sequence, comprising: a) contacting a first single stranded derivatized nucleic acid sequence, wherein the first single stranded nucleic acid sequence contains a protein binding sequence and an electrochemical probe binding sequence, with a second single stranded nucleic acid sequence to form a duplex, wherein the second single stranded nucleic acid sequence is hybridized to a monolayer of first single stranded nucleic acid sequences on an electrode, wherein the monolayer is prepared by first attaching a double stranded nucleic acid sequence comprising the first single stranded nucleic acid sequence to the electrode, and dehybridizing the double stranded nucleic acid sequence, such that the first single stranded nucleic acid sequence remains attached to the electrode, and wherein a hybrid of the first single stranded nucleic acid sequence and the second single stranded sequence form a duplex-modified film; b) adding an electrochemical probe to the duplex modified film, wherein the electrochemical probe binds to the electrochemical probe binding sequence of the first single stranded nucleic acid sequence; c) adding a protein to the duplex-modified film, wherein the protein binds to the protein binding sequence of the first single stranded nucleic acid sequence; and d) measuring a difference in reduction of the electrical current or charges of the electrochemical probe between the duplex-modified film of step (c) and a control duplex-modified film without protein, wherein the difference in the electrical current or charge from the duplex not having the bound protein compared to the duplex having the bound protein is indicative of the presence or absence of one or more base stacking perturbations in the duplex.