Synthetic genome readers target clustered binding sites across diverse chromatin states

Proc Natl Acad Sci U S A. 2016 Nov 22;113(47):E7418-E7427. doi: 10.1073/pnas.1604847113. Epub 2016 Nov 8.


Targeting the genome with sequence-specific DNA-binding molecules is a major goal at the interface of chemistry, biology, and precision medicine. Polyamides, composed of N-methylpyrrole and N-methylimidazole monomers, are a class of synthetic molecules that can be rationally designed to "read" specific DNA sequences. However, the impact of different chromatin states on polyamide binding in live cells remains an unresolved question that impedes their deployment in vivo. Here, we use cross-linking of small molecules to isolate chromatin coupled to sequencing to map the binding of two bioactive and structurally distinct polyamides to genomes directly within live H1 human embryonic stem cells. This genome-wide view from live cells reveals that polyamide-based synthetic genome readers bind cognate sites that span a range of binding affinities. Polyamides can access cognate sites within repressive heterochromatin. The occupancy patterns suggest that polyamides could be harnessed to target loci within regions of the genome that are inaccessible to other DNA-targeting molecules.

Keywords: COSMIC; chemical genomics; genome targeting; molecular recognition; polyamide.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Binding Sites
  • Cell Line
  • Chromatin / chemistry
  • Chromatin / genetics*
  • Cross-Linking Reagents
  • DNA / chemistry*
  • DNA / metabolism
  • Genome, Human
  • Human Embryonic Stem Cells / cytology
  • Humans
  • Nylons / metabolism*
  • Sequence Analysis, DNA / methods*
  • Small Molecule Libraries / chemistry


  • Chromatin
  • Cross-Linking Reagents
  • Nylons
  • Small Molecule Libraries
  • DNA