title: Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing.
abstract: Genomic applications of DNA-binding molecules require an unbiased knowledge of their high affinity sites. We report the high-throughput analysis of pyrrole-imidazole polyamide DNA-binding specificity in a 10(12)-member DNA sequence library using affinity purification coupled with massively parallel sequencing. We find that even within this broad context, the canonical pairing rules are remarkably predictive of polyamide DNA-binding specificity. However, this approach also allows identification of unanticipated high affinity DNA-binding sites in the reverse orientation for polyamides containing β/Im pairs. These insights allow the redesign of hairpin polyamides with different turn units capable of distinguishing 5'-WCGCGW-3' from 5'-WGCGCW-3'. Overall, this study displays the power of high-throughput methods to aid the optimal targeting of sequence-specific minor groove binding molecules, an essential underpinning for biological and nanotechnological applications.
authors.affiliation: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA.
authors.forename: Jordan L
authors.initials: JL
authors.lastname: Meier
authors.forename: Abigail S
authors.initials: AS
authors.lastname: Yu
authors.forename: Ian
authors.initials: I
authors.lastname: Korf
authors.forename: David J
authors.initials: DJ
authors.lastname: Segal
authors.forename: Peter B
authors.initials: PB
authors.lastname: Dervan
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000235:genetics; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D007093:Imidazoles / Q000737:chemistry*; D009757:Nylons / Q000737:chemistry*; D011758:Pyrroles / Q000737:chemistry*
chemical_list: D007093:Imidazoles; D009757:Nylons; D011758:Pyrroles; C029899:imidazole; D004247:DNA