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NMR structure of a parallel-stranded DNA duplex at atomic resolution.

V Rani Parvathy1, Sukesh R Bhaumik, Kandala V R Chary

  • 1Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India.

Nucleic Acids Research
|March 28, 2002
PubMed
Summary

DNA dodecamers form stable parallel-stranded duplexes due to C:C+ clamps, challenging antiparallel DNA structures. These findings offer new insights into DNA structural polymorphism.

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural DNA Research

Background:

  • Antiparallel DNA duplexes are the canonical structure.
  • Parallel DNA structures are less common and their formation mechanisms are not fully understood.
  • DNA dodecamers offer a model system to study DNA structural transitions.

Purpose of the Study:

  • To design and characterize DNA dodecamers capable of forming parallel-stranded duplexes.
  • To investigate the structural stability and properties of parallel DNA duplexes.
  • To elucidate the molecular basis for parallel duplex formation over antiparallel structures.

Main Methods:

  • Oligonucleotide synthesis and design with specific A:T and C:C+ sequences.
  • Spectroscopic analyses including UV-Vis, Circular Dichroism (CD), and Infrared (IR) spectroscopy.

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  • Nuclear Magnetic Resonance (NMR) spectroscopy for structural elucidation.
  • Molecular dynamics (MD) simulations under NMR constraints.

    • Main Results:

    • Designed DNA dodecamers (d(CCATAATTTACC) and d(CCTATTAAATCC)) form stable parallel-stranded duplexes in aqueous solution at 1:1 stoichiometry.
    • Formation of parallel duplexes is driven by C:C+ clamps at the ends and mismatches in the antiparallel orientation.
    • The parallel duplex is stable at neutral and acidic pH, exhibiting cooperative melting at higher temperatures.
    • Structural analysis revealed anti conformation of nucleotides, reverse Watson-Crick A:T base pairing, and specific base-stacking interactions.
    • Molecular dynamics simulations provided an atomic-resolution 3D structure, showing B-DNA-like torsional angles but distinct base stacking and helicoid parameters.

    Conclusions:

    • Specific DNA sequences can be engineered to favor parallel-stranded duplex formation.
    • C:C+ base pairing plays a crucial role in stabilizing parallel DNA structures.
    • The study provides a detailed structural and dynamic characterization of a novel parallel DNA duplex, expanding the understanding of DNA structural diversity.