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[Deoxyribonucleic acid sequence effects on molecular structure].

S Fujii

    Yakugaku Zasshi : Journal of the Pharmaceutical Society of Japan
    |May 1, 1989
    PubMed
    Summary
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    DNA structure is not fixed, varying with base sequence and environment. Studies reveal unique oligonucleotide conformations and propose models for DNA bending and base-pairing using advanced computational and experimental methods.

    Area of Science:

    • Molecular Biology
    • Structural Biology
    • Biophysics

    Context:

    • Deoxyribonucleic acid (DNA) exhibits polymorphism influenced by base sequence and environmental factors.
    • Understanding DNA conformational variations is crucial for deciphering its biological functions.
    • Oligonucleotides serve as model systems to investigate sequence-dependent DNA properties.

    Purpose:

    • To investigate base sequence-dependent conformational properties of synthesized oligonucleotides.
    • To propose possible DNA structures in solution using molecular dynamics (MD) simulations.
    • To elucidate DNA bending mechanisms and base-pairing schemes through combined experimental and computational approaches.

    Summary:

    • X-ray analysis and physico-chemical techniques reveal unique conformational characteristics of oligonucleotides, particularly those with adenine or adenine-thymine tracts.

    Related Experiment Videos

  • Molecular dynamics (MD) simulations, integrated with nuclear magnetic resonance (NMR) data, propose a junction-model for DNA bending.
  • MD calculations provide models consistent with NMR evidence for inosine-adenine base-pairing in B-DNA, highlighting sequence-dependent preferences for anti/anti and anti/syn forms.
  • Oligonucleotides with cyclonucleosides in a high-anti glycosidic conformation adopt left-handed double-helical structures, with models proposed via energy minimization.

    • Impact:

    • Provides insights into the structural plasticity of DNA and its sequence-dependent variations.
    • Advances the understanding of DNA bending and base-pairing, critical for DNA-protein interactions and genetic regulation.
    • Demonstrates the utility of combining experimental techniques (X-ray, NMR) with computational methods (MD) for structural biology research.
    • Contributes to the development of models for novel DNA structures, including left-handed helices.