A method for preparing and analyzing a target analyte, the method comprising: a) providing a double-stranded DNA template having a first and a second DNA strand, each DNA strand having a 5' end and a 3' end, b) contacting the double-stranded DNA template with a nicking endonuclease to form a nick at a sequence-specific nicking location on the first DNA strand, c) conducting a base extension reaction on the first DNA strand along a corresponding region of the second DNA strand, said reaction starting at the nick and progressing toward the 3' end of the first DNA strand to thereby form a single-stranded flap on the double-stranded DNA template adjacent to the sequence-specific nicking location, to thereby prepare the target analyte, d) coating the double-stranded DNA template and the single-stranded flap with a binding moiety that enhances electrical detection of the double-stranded DNA template and the single-stranded flap, to thereby prepare the target analyte, wherein the binding moiety comprises one or more proteins selected from the group consisting of RecA, T4 gene 32 protein, f1 geneV protein, human replication protein A, Pf3 single-stranded binding protein, adenovirus DNA binding protein, and E. coli single-stranded binding protein; and e) monitoring changes in an electrical property across a channel as the target analyte is translocated therethrough, wherein the channel comprises either a nano-channel having a width selected from 10nm to 1μm, a depth selected from 10nm to 1μm and a length selected from 1μm to 10 cm, or a micro-channel having a width selected from 1μm to 25μm, a depth selected from 200nm to 5μm and a length selected from 1μm to 10 cm, and a pair of electromotive electrodes is connected to a voltage source and positioned in spaced apart relationship in the channel, and a pair of detector electrodes is positioned perpendicular to the channel in a spaced apart relationship that is laterally offset along the length of the channel to define a detection volume and the pair of detector electrodes is connected to a detector, the electrical property in the detection volume between the pair of detector electrodes is monitored, wherein the changes in the electrical property being indicative of double-stranded regions of the target analyte and of the single-stranded flap regions. a) providing a double-stranded DNA template having a first and a second DNA strand, each DNA strand having a 5' end and a 3' end, b) contacting the double-stranded DNA template with a nicking endonuclease to form a nick at a sequence-specific nicking location on the first DNA strand, c) conducting a base extension reaction on the first DNA strand along a corresponding region of the second DNA strand, said reaction starting at the nick and progressing toward the 3' end of the first DNA strand to thereby form a single-stranded flap on the double-stranded DNA template adjacent to the sequence-specific nicking location, to thereby prepare the target analyte, d) coating the double-stranded DNA template and the single-stranded flap with a binding moiety that enhances electrical detection of the double-stranded DNA template and the single-stranded flap, to thereby prepare the target analyte, wherein the binding moiety comprises one or more proteins selected from the group consisting of RecA, T4 gene 32 protein, f1 geneV protein, human replication protein A, Pf3 single-stranded binding protein, adenovirus DNA binding protein, and E. coli single-stranded binding protein; and e) monitoring changes in an electrical property across a channel as the target analyte is translocated therethrough, wherein the channel comprises either a nano-channel having a width selected from 10nm to 1μm, a depth selected from 10nm to 1μm and a length selected from 1μm to 10 cm, or a micro-channel having a width selected from 1μm to 25μm, a depth selected from 200nm to 5μm and a length selected from 1μm to 10 cm, and a pair of electromotive electrodes is connected to a voltage source and positioned in spaced apart relationship in the channel, and a pair of detector electrodes is positioned perpendicular to the channel in a spaced apart relationship that is laterally offset along the length of the channel to define a detection volume and the pair of detector electrodes is connected to a detector, the electrical property in the detection volume between the pair of detector electrodes is monitored, wherein the changes in the electrical property being indicative of double-stranded regions of the target analyte and of the single-stranded flap regions.