It has been established that one or more large
double stranded DNA fragments (each 2,000 to 40,000 base pairs in size) can be captured and isolated from
genomic DNA fragments using sequence specific PNA hybridization probes. Compositions and methods for enrichment of a multiplicity of long
DNA sequences selected from the
genome of any
eukaryote are provided. Capture is performed using multiple PNA molecules with gamma-modified chiral backbones, comprising a mixture of neutral and positive
chemical groups. Two or more PNA probes with covalently bound haptens, preferably
biotin, target each
DNA domain of interest for capture, isolation, and subsequent sequencing analysis of the multiplicity of enriched targets, including
DNA methylation sequencing. The methods include enhancement of probe-DNA binding specificity through
single strand binding proteins (SSB).