title: Multiplexed programmable release of captured DNA.
abstract: 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.
authors.affiliation: Department of Chemistry, University of Wisconsin at Madison, 1101 University Avenue, Madison, WI 53706 (USA).
authors.forename: Julia
authors.initials: J
authors.lastname: Kennedy-Darling
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Holden
authors.forename: Michael R
authors.initials: MR
authors.lastname: Shortreed
authors.forename: Lloyd M
authors.initials: LM
authors.lastname: Smith
mesh_terms: D004247:DNA / Q000378:metabolism*; D005456:Fluorescent Dyes / Q000737:chemistry; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D009841:Oligonucleotides / Q000737:chemistry / Q000378:metabolism; D012335:RNA, Ribosomal / Q000378:metabolism; D012341:RNA, Ribosomal, 5S / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction
chemical_list: D005456:Fluorescent Dyes; D009841:Oligonucleotides; D012335:RNA, Ribosomal; D012341:RNA, Ribosomal, 5S; C065039:RNA, ribosomal, 25S; D004247:DNA
keywords: DNA; microarrays; nucleic-acid hybridization; selective elution; toehold-mediated branch migration