Abstract: The present invention provides a method of detecting the presence of a nucleotide sequence within a double-stranded DNA in a sample comprising: a. digesting the double-stranded DNA with an exonuclease which converts at least a portion of the double-stranded DNA to single-stranded DNA; b. hybridizing the single-stranded DNA with i) a first nucleic acid probe adapted with a moiety which can be captured to a solid support, and ii) a second nucleic acid probe labeled with a detectable moiety which can hybridize with the single-stranded DNA adjacent the hybridized first nucleic acid probe; c. ligating the hybridized first and second nucleic acid probes; d. capturing the moiety on the first nucleic acid probe hybridized to the DNA to the solid support; e. denaturing the ligated first and second nucleic acid probes from the hybridized single-stranded DNA; f. removing uncaptured labeled probe; and, g.