Design of artificial sequence-specific DNA bending ligands

Proc Natl Acad Sci U S A. 1996 Sep 3;93(18):9510-4. doi: 10.1073/pnas.93.18.9510.

Abstract

Proteins that bend DNA are important regulators of biological processes. Sequence-specific DNA bending ligands have been designed that bind two noncontiguous sites in the major groove and induce a bend in the DNA. An oligonucleotide containing pyrimidine segments separated by a central variable linker domain simultaneously binds by triple helix formation two 15-bp purine tracts separated by 10 bp. Bend angles of 61 degrees, 50 degrees, and 38 degrees directed towards the minor groove were quantitated by phasing analysis for linkers of four, five, and six T residues, respectively. The design and synthesis of nonnatural architectural factors may provide a new class of reagents for use in biology and human medicine.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Autoradiography
  • Base Sequence
  • Cross-Linking Reagents / chemical synthesis
  • Cross-Linking Reagents / pharmacology*
  • DNA / chemistry
  • DNA / drug effects*
  • DNA Footprinting
  • Deoxyribonuclease I / metabolism
  • Drug Design*
  • Humans
  • Molecular Sequence Data
  • Nucleic Acid Conformation / drug effects*
  • Oligonucleotides / chemical synthesis
  • Oligonucleotides / pharmacology*
  • Restriction Mapping

Substances

  • Cross-Linking Reagents
  • Oligonucleotides
  • DNA
  • Deoxyribonuclease I