Patent ID: 7323313

Claim:
A method for identifying a plurality of pairs of interacting proteins wherein a pair of interacting proteins comprises a first test protein and a second test protein, wherein the first and second test proteins interact with each other in a cell, the method comprising the steps of: a) providing a cDNA library; b) providing a plurality of a first plasmid comprising a coding sequence for a DNA binding domain of a transcription activator, a first recombinase recognition site, a first selectable marker, a first Type II S restriction site and a first inserted cDNA encoding a first test protein; c) providing a plurality of a second plasmid comprising a coding sequence for a transcription activation domain of the transcription activator, a second recombinase recognition site, a second selectable marker and a second Type II S restriction site, and a second inserted cDNA encoding a second test protein, wherein the first and second recombinase recognition sites may be identical or distinct and the first and second Type II S restriction sites may be identical or distinct; d) introducing the first and second plasmids from b) and c) into the same cell; e) inducing the expression of the recombinase to recombine the first and second introduced plasmids; f) isolating and digesting the recombined plasmids with a Type II S restriction enzyme to obtain restriction fragments and ligating the restriction fragments to a universal adapter to provide a pool of digested fragments flanked by universal adapter sequences; g) forming concatamers from the pool of digested fragments and sequencing the concatamers to determine the identity of the plurality of pairs of interacting proteins.