The present invention provides new methods, employing a
nucleotide integrase, for cleaving single-stranded
RNA substrates, single-stranded
DNA substrates, and double- stranded
DNA substrates at specific sites and for inserting a
nucleic acid molecule into the cleaved substrate. One method uses a
nucleotide integrase to cleave one strand of a double-stranded
DNA substrate. The method comprises the steps of: providing a
nucleotide integrase comprising a
group II intron RNA having two hybridizing sequences that are capable of hybridizing with two
intron RNA binding sequences on the one strand of the DNA substrate, and a
group II-
intron encoded
protein which binds to a first sequence element of the substrate; and reacting the nucleotide integrase with the double-stranded DNA substrate under conditions that permit the nucleotide integrase to cleave the one strand of the DNA substrate and to insert the
group II intron RNA into the cleavage site. The method of cleaving both strands of a double-stranded DNA substrate comprises the steps of: providing a nucleotide integrase comprising a group II intron RNA having two hybridizing sequences that are capable of hybridizing with two intron RNA binding sequences on one strand of the substrate, and a group II-intron encoded
protein that is capable of binding to a first sequence element and to a second sequence element in the recognition site of the substrate; and reacting the nucleotide integrase with the double-stranded DNA substrate such that the nucleotide integrase cleaves both strands of the DNA substrate and inserts the group II intron RNA into the cleavage site of the one strand. The method for cleaving a single-stranded
nucleic acid substrate comprises the steps of: providing a nucleotide integrase having two hybridizing sequences that are capable of hybridizing with two intron RNA-binding sequences on the single-stranded substrate, and a group II intron encoded
protein; and reacting the nucleotide integrase with the single stranded
nucleic acid substrate for a time and at a temperature sufficient to allow the nucleotide integrase to cleave the substrate and to attach the group II intron
RNA molecule thereto.