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Related Experiment Videos

A Hoogsteen base pair embedded in undistorted B-DNA.

Jun Aishima1, Rossitza K Gitti, Joyce E Noah

  • 1Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185, USA.

Nucleic Acids Research
|December 6, 2002
PubMed
Summary

A Hoogsteen base pair was found in normal B-DNA, challenging previous understanding. Protein binding appears to stabilize this unusual DNA structure, suggesting a new role in cellular processes.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • Hoogsteen base pairs are typically found in distorted DNA or near drug binding sites.
  • Their presence in unmodified, undistorted B-DNA is rare and not well understood.

Purpose of the Study:

  • To investigate the occurrence and formation of Hoogsteen base pairs in unmodified B-DNA.
  • To explore the role of protein binding in stabilizing Hoogsteen base pairs within DNA.

Main Methods:

  • X-ray crystallography of a protein-DNA complex (MATalpha2 homeodomain bound to DNA) at 2.1 Å resolution.
  • Nuclear Magnetic Resonance (NMR) studies of free DNA.
  • Molecular dynamics simulations of the protein-DNA complex.

Main Results:

Related Experiment Videos

  • A Hoogsteen base pair (syn adenine with anti thymine) was observed within undistorted B-DNA in the crystal structure.
  • NMR studies showed no Hoogsteen base pair formation in free DNA.
  • Molecular dynamics simulations supported the role of non-specifically bound protein in favoring Hoogsteen base pair formation.

Conclusions:

  • Protein binding can favor the transition from Watson-Crick to Hoogsteen base pairs in DNA.
  • Hoogsteen base pairs may play a previously unrecognized role in fundamental cellular processes like transcription and replication.