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Solution structure of a quinomycin bisintercalator-DNA complex

H Chen1, D J Patel

  • 1Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons of Columbia University, New York, NY 10032.

Journal of Molecular Biology
|February 10, 1995
PubMed
Summary
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The quinomycin antibiotic UK-63052 (QN) bis-intercalates into DNA at specific sites, forming a complex with unique structural features. This study reveals the solution structure of the QN-DNA complex, highlighting its sequence specificity and comparing it to echinomycin.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Biology

Background:

  • Quinomycin antibiotics, like echinomycin, are known to bis-intercalate into DNA.
  • These antibiotics share a common scaffold featuring heterocyclic aromatic rings and a cyclic octadepsipeptide.

Purpose of the Study:

  • To determine the solution structure of the complex formed between quinomycin antibiotic UK-63052 (QN) and a DNA oligomer.
  • To elucidate the molecular interactions and sequence specificity governing QN-DNA complex formation.

Main Methods:

  • Nuclear Magnetic Resonance (NMR) spectroscopy.
  • Molecular dynamics simulations with intensity-based refinement.

Main Results:

  • The 3-hydroxy quinaldic acid rings of QN bis-intercalate into the DNA duplex at (A3-C4).(G5-T6) steps, causing unwinding.

Related Experiment Videos

  • The cyclic octadepsipeptide scaffold binds to the minor groove, with specific hydrogen bonds conferring sequence specificity.
  • The QN-DNA complex structure, featuring Watson-Crick base-pairs, is compared to the echinomycin-DNA crystal structure.

    • Conclusions:

    • The study provides detailed insights into the solution structure of the QN-DNA complex.
    • Specific intermolecular hydrogen bonds dictate the sequence-selective binding of QN to DNA.
    • Structural comparison with echinomycin highlights differences in DNA binding modes.