Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing

Jordan L. Meier, Abigail S. Yu, Ian F Korf, David Segal, Peter B. Dervan

Research output: Contribution to journalArticlepeer-review

52 Scopus citations


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 1012-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.

Original languageEnglish (US)
Pages (from-to)17814-17822
Number of pages9
JournalJournal of the American Chemical Society
Issue number42
StatePublished - Oct 24 2012

ASJC Scopus subject areas

  • Chemistry(all)
  • Catalysis
  • Biochemistry
  • Colloid and Surface Chemistry


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