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Related Experiment Videos

Structural and combinatorial constraints on base pairing in large nucleotide sequences.

R Nussinov, G Pieczenik

    Journal of Theoretical Biology
    |February 7, 1984
    PubMed
    Summary

    This study introduces FOLD-A, a computer code designed to predict the base-paired structures of long RNA and DNA molecules. It efficiently searches for low-energy configurations, addressing complex folding challenges.

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    MASS: multiple structural alignment by secondary structures.

    Bioinformatics (Oxford, England)·2003

    Area of Science:

    • Computational Biology
    • Molecular Biology
    • Bioinformatics

    Background:

    • Predicting nucleic acid secondary structures is crucial for understanding their function.
    • Folding long RNA and single-stranded DNA presents significant computational challenges due to combinatorial complexity.
    • Existing methods may struggle with very long sequences and identifying optimal low-energy configurations.

    Purpose of the Study:

    • To develop and describe a computational tool for predicting base-paired structures in long nucleic acid sequences.
    • To address the constraints and combinatorial problems associated with folding long RNA and DNA.
    • To identify low-energy configurations for these molecules.

    Main Methods:

    • Development of a computer code named FOLD-A.

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  • Implementation of an algorithm designed for base pairing foldings of very long sequence chains.
  • Utilizing the algorithm to search for thermodynamically stable (low-energy) configurations.

    • Main Results:

    • The FOLD-A code is capable of performing base pairing foldings on very long sequence chains.
    • The algorithm effectively searches for and identifies low-energy configurations.
    • The accompanying paper details applications to specific biological systems.

    Conclusions:

    • FOLD-A provides a viable computational approach for predicting secondary structures of long RNA and DNA.
    • The tool addresses key challenges in nucleic acid folding prediction.
    • This work facilitates further research into the structure-function relationships of large nucleic acid molecules.