ExoChew: An exonuclease technique to generate single-stranded DNA libraries

Abstract

Although DNA in the genome is double-stranded, single-stranded DNA is generated during various processes including DNA replication and repair. Some single-stranded DNAs can form noncanonical structures. Various proteins bind to the single-stranded DNAs site-specifically and/or structure-specifically to regulate various DNA transactions. Because of the transient nature of single-stranded DNAs in the cell, current in vivo techniques may not reveal all such sequences, structures, and protein-DNA complexes. To explore such sequences and structures genome-wide, it is necessary to generate single-stranded DNA libraries. Current in vitro methods involve heat denaturation of libraries of double-stranded DNA fragments followed by cooling to prevent reannealing; however, a significant amount of DNA can reanneal to regenerate double-stranded DNAs. In ExoChew method, double-stranded DNA fragment libraries are enzymatically converted to single-stranded DNA libraries. Genomic DNA is sonicated to generate pools of double-stranded DNA fragments of required size. Each pool of double-stranded DNA fragments is then treated with either T7 exonuclease or E. coli exonuclease III. which recognize and cleave double-stranded DNA from 5 ends or 3 ends, generating single-stranded DNA pools, respectively. The enzymatically generated single-stranded DNA pools can be used for genome-wide studies of protein-DNA interactions and structural studies of DNA.