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Local variability and base sequence effects in DNA crystal structures.

D Bhattacharyya1, M Bansal

  • 1Molecular Biophysics Unit, Indian Institute of Science, Bangalore.

Journal of Biomolecular Structure & Dynamics
|December 1, 1990
PubMed
Summary
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Local doublet parameters effectively describe DNA structures, revealing sequence-dependent variations. Local helical parameters offer a magnified view, and basepair buckling influences local rise, showing sequence-specific stacking interactions in B-DNA.

Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Understanding sequence-dependent effects in DNA is crucial for deciphering its biological functions.
  • Local doublet parameters provide insights into the structural variations of DNA oligonucleotides.
  • Previous studies have highlighted the importance of local parameters in characterizing DNA conformation.

Purpose of the Study:

  • To evaluate the utility of local doublet and local helical parameters in describing A- and B-DNA oligonucleotide crystal structures.
  • To investigate the correlation between different local parameters and their relationship with DNA conformation.
  • To identify sequence-specific structural features and their underlying interactions.

Main Methods:

  • Utilized the NUPARM algorithm to calculate local doublet and local helical parameters from DNA crystal structures.

Related Experiment Videos

  • Compared NUPARM-derived parameters with those from the NEWHELIX90 program.
  • Analyzed correlations between various local parameters, including local rise, roll, twist, and buckle.
  • Examined sequence-dependent variations in these parameters for A- and B-DNA forms.

    • Main Results:

    • Both local doublet and local helical parameters adequately describe oligonucleotide structures, with helical parameters providing a magnified view.
    • NUPARM and NEWHELIX90 parameter values are comparable for undistorted DNA fragments.
    • Local rise along the z-axis is strongly correlated with basepair buckling, and this relationship holds for both A- and B-DNA.
    • Specific basepair sequences in B-DNA exhibit characteristic local rise values, indicating intrinsic stacking interactions.
    • B-DNA oligonucleotides show limited roll angles, while local twist varies significantly; CA/TG sequences display distinct geometric preferences.

    Conclusions:

    • Local doublet and helical parameters are effective tools for analyzing sequence-dependent DNA structural variations.
    • Basepair buckling significantly influences local rise, suggesting a mechanism for structural adaptation.
    • Intrinsic base-stacking interactions dictate sequence-specific structural features in DNA.
    • The observed structural variations are largely independent of DNA crystallinity and data quality.