Functionalized head-to-head hairpin polyamides: synthesis, double-stranded DNA-binding activity and affinity

Bioorg Med Chem Lett. 2005 Aug 15;15(16):3720-4. doi: 10.1016/j.bmcl.2005.05.106.

Abstract

A series of 4 functionalized head-to-head-linked hairpin oligo(N-methylpyrrole) carboxamides with different linkers have been synthesized. Their ability to bind double-stranded DNA and sequence specificity were compared and the apparent Kd values of their DNA complexes were determined. These compounds, particularly those with iminodiacetic linkers, revealed a high affinity for DNA (Kd = 4.5-4.8 x 10(-9) M) and sequence specific recognition of 9-10 base pairs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Binding Sites
  • DNA / chemical synthesis
  • DNA / chemistry*
  • DNA / metabolism*
  • HIV* / genetics
  • Heparin / chemical synthesis*
  • Heparin / metabolism*
  • Humans
  • Molecular Sequence Data
  • Molecular Structure
  • Nucleic Acid Conformation
  • Nylons / chemical synthesis*
  • Nylons / metabolism*
  • Proviruses / chemistry
  • Proviruses / genetics

Substances

  • Nylons
  • Heparin
  • DNA