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Related Experiment Videos

Base sequence and helix structure variation in B and A DNA.

R E Dickerson

    Journal of Molecular Biology
    |May 25, 1983
    PubMed
    Summary

    DNA propeller twist relieves base-pair stacking but causes steric clashes. Sequence-derived functions accurately predict DNA helix parameter variations, aiding understanding of repressor-operator interactions.

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    The structure of a stable intermediate in the A <--> B DNA helix transition.

    Proceedings of the National Academy of Sciences of the United States of America·2000

    Area of Science:

    • Molecular Biology
    • Structural Biology
    • Biophysics

    Background:

    • Propeller twist in DNA base pairs enhances stacking interactions within a helix strand.
    • This twist can cause steric hindrance between purine bases on opposite DNA strands.

    Purpose of the Study:

    • To investigate mechanisms for relieving steric clashes caused by propeller twist in DNA.
    • To develop sequence-dependent functions for predicting local variations in DNA helix parameters.

    Main Methods:

    • Defined four sum functions (sigma 1-4) to calculate local variations in helix twist, base roll, torsion angle delta, and propeller twist based on DNA sequence.
    • Validated these functions against experimental data for B DNA, A DNA, and RNA/DNA hybrids.

    Main Results:

    • All four functions successfully predicted the behavior of B DNA.
    • Helix twist and base roll functions were applicable to A DNA.
    • The helix twist function showed limitations with RNA/DNA hybrids.
    • Sequence-derived functions closely matched observed helix parameter variations (correlation coefficients > 0.900).

    Conclusions:

    • Sequence-dependent DNA structural variations can be accurately predicted using simple sum functions.
    • These findings have implications for understanding protein-DNA interactions, such as repressor-operator binding.

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