Nucleic acid hybridization is widely used for the specific capture of
complementary sequences from complex samples. It is useful for both analytical
methodologies, such as array hybridization (e.g. transcriptome analysis, genetic
variation analysis), and preparative strategies such as exome sequencing and
sequence-specific proteome capture and analysis (PICh, HyCCAPP). It has not
generally been possible to selectively elute particular captured subsequences,
however, as the conditions employed for disruption of a duplex can lack the
specificity needed to discriminate between different sequences. We show here
that it is possible to bind and selectively release multiple sets of sequences
by using toehold-mediated DNA branch migration. The strategy is illustrated for
simple mixtures of oligonucleotides, for the sequence-specific capture and
specific release of crosslinked yeast chromatin, and for the specific release of
oligonucleotides hybridized to DNA microarrays.