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Folding of two large nucleotide chains.

R Nussinov, G Pieczenik

    Journal of Theoretical Biology
    |February 7, 1984
    PubMed
    Summary

    The FOLD-A code predicts RNA and DNA folding. Applied to MS2 RNA and phi X 174 phage DNA, it reveals the phage genome

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    Area of Science:

    • Molecular Biology
    • Bioinformatics
    • Genomics

    Background:

    • The FOLD-A code was previously developed for predicting secondary structures of single-stranded nucleic acids.
    • Understanding nucleic acid folding is crucial for gene regulation and function.

    Purpose of the Study:

    • To apply the FOLD-A code to analyze the folding patterns of two specific long polynucleotide chains.
    • To investigate the secondary structure of the A protein gene from MS2 RNA.
    • To determine the folded structure of the entire single-stranded DNA genome of the bacteriophage phi X 174.

    Main Methods:

    • Utilizing the FOLD-A code algorithm for secondary structure prediction.
    • Analyzing the A protein gene sequence from MS2 RNA.
    • Analyzing the complete genome sequence of the phi X 174 phage.

    Main Results:

    • The FOLD-A code successfully predicted folding patterns for both MS2 RNA and phi X 174 phage DNA.
    • The predicted secondary structure for the phi X 174 phage single-stranded DNA forms a unique six-armed star configuration.
    • The origin of replication for phi X 174 phage is located at the center of this star structure.

    Conclusions:

    • The FOLD-A code is effective for predicting secondary structures in long viral RNA and DNA genomes.
    • The unique star-shaped folding of the phi X 174 phage genome may have implications for its replication mechanism.
    • This study provides insights into the complex structural organization of viral genetic material.

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