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Structural models for non-helical DNA.

G Yagil, J L Sussman

    The EMBO Journal
    |July 1, 1986
    PubMed
    Summary
    This summary is machine-generated.

    Structural modeling reveals two non-helical DNA models with low energy requirements, suggesting a role for these unwound DNA structures in gene regulation. These findings explore alternative DNA conformations beyond the classical B-DNA form.

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    Area of Science:

    • Molecular Biology
    • Structural Bioinformatics
    • Biophysics

    Background:

    • Classical B DNA is the predominant double-stranded helical DNA form.
    • Alternative DNA structures exist and are implicated in gene regulation.
    • Understanding the energetic landscape of DNA structural transitions is crucial.

    Purpose of the Study:

    • To investigate the energetic feasibility of transforming B DNA into unwound, double-stranded DNA structures.
    • To model and characterize regular non-helical DNA conformations.
    • To assess the potential biological relevance of these alternative DNA structures.

    Main Methods:

    • Employed structural modeling techniques, including CORELS for idealization and EREF for energy minimization.
    • Generated two regular non-helical DNA models (N1 and N2) with conventional base pairing and stacking.

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  • Analyzed backbone dihedral angles and calculated energy differences compared to B DNA.

    • Main Results:

    • Two regular non-helical DNA models (N1 and N2) were generated, characterized by no net rotation between base pairs.
    • Specific backbone dihedral angles, notably P-O5'-C5'-C4', adopted unprecedented domains (g+ or g-).
    • Energy differences per nucleotide were 6.6 kcal/mol for N1 and 3.4 kcal/mol for N2, indicating relatively low energetic costs.

    Conclusions:

    • The low energy requirements for the N1 and N2 models support their potential existence in biological systems.
    • Non-helical DNA structures may contribute to alternative DNA conformations observed in regulatory regions of genes.
    • These findings expand our understanding of DNA structural diversity and its functional implications.