A DNA aptamer which binds to and inhibits thrombin exhibits a new structural motif for DNA

Biochemistry. 1993 Mar 2;32(8):1899-904. doi: 10.1021/bi00059a003.

Abstract

The investigation of the three-dimensional structure of the DNA aptamer d(G1G2T3-T4G5G6T7G8T9G10G11T12T13G14G15) which binds to and inhibits thrombin has been carried out by NMR methods. This DNA exhibits a number of long-range NOEs between residues which are not adjacent in sequence, which allowed the determination of the novel tertiary structure adopted. This DNA adopts a highly compact, highly symmetrical structure which consists of two tetrads of guanosine base pairs and three loops. The residues of the tetrads alternate anti-syn-anti-syn. This novel structural motif for DNA may also be relevant to the structure of telomere DNA.

Publication types

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

MeSH terms

  • Base Sequence
  • DNA / chemistry
  • DNA / metabolism*
  • Hydrogen Bonding
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Denaturation
  • Oligodeoxyribonucleotides / chemistry
  • Oligodeoxyribonucleotides / metabolism*
  • Oligodeoxyribonucleotides / pharmacology
  • Protein Binding
  • Thrombin / antagonists & inhibitors
  • Thrombin / metabolism*

Substances

  • Oligodeoxyribonucleotides
  • DNA
  • Thrombin