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Structure and conformation of helical nucleic acids: analysis program (SCHNAaP)

X J Lu1, M A El Hassan, C A Hunter

  • 1Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK.

Journal of Molecular Biology
|November 14, 1997
PubMed
Summary

SCHNAaP is a new program for analyzing nucleic acid structures, calculating helical parameters using rigorous methods. It handles various base pairs and provides detailed backbone and stacking analyses for structural classification.

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Chemistry

Background:

  • Accurate analysis of double-helical nucleic acid structures is crucial for understanding biological function.
  • Existing methods may lack comprehensiveness in parameter calculation and handling diverse base-pair types.

Purpose of the Study:

  • To introduce SCHNAaP, a versatile computational program for detailed analysis of nucleic acid structures.
  • To implement rigorous and reversible procedures for calculating local and global helical parameters.
  • To provide a comprehensive analysis including base-pairing, backbone conformation, and base-stacking.

Main Methods:

  • Utilized the Cambridge University Engineering Department Helix computation Scheme (CEHS) for local helical parameters.
  • Developed analogous procedures for global helical parameter determination.

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  • Incorporated analysis of mismatched base-pairs, modified bases, and sugar-phosphate backbone conformation.

    • Main Results:

    • SCHNAaP calculates a complete set of structural parameters conforming to the "Cambridge Accord."
    • The program generates standardized base-stacking diagrams for each dinucleotide step.
    • Nucleic acid structures are classified into polymorphic families (A/B, Z, W, R).

    Conclusions:

    • SCHNAaP offers a versatile and rigorous approach to nucleic acid structure analysis.
    • The program's comprehensive features facilitate detailed structural characterization and classification.
    • It supports the analysis of standard and non-standard nucleic acid forms.