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Related Experiment Videos

Eco RI* specificity and hydrogen bonding.

J M Rosenberg, P Greene

    DNA (Mary Ann Liebert, Inc.)
    |January 1, 1982
    PubMed
    Summary
    This summary is machine-generated.

    Eco RI endonuclease normally recognizes a specific DNA sequence but exhibits altered Eco RI* specificity under non-standard conditions. This altered specificity is explained by retained hydrogen bonds, primarily in the DNA

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    Area of Science:

    • Molecular Biology
    • Biochemistry
    • Genetics

    Background:

    • Eco RI endonuclease typically recognizes the specific inverted repeat sequence GAATTC.
    • Under non-standard conditions, Eco RI exhibits relaxed specificity, known as Eco RI* specificity, recognizing various DNA sequences.
    • Understanding the molecular basis of this altered specificity is crucial for enzyme function studies.

    Purpose of the Study:

    • To elucidate the sequence recognition rules governing Eco RI* specificity.
    • To develop a model explaining how Eco RI* recognizes alternative DNA sequences.
    • To identify the DNA structural features involved in Eco RI* recognition.

    Main Methods:

    • Analysis of hydrolysis rates at known Eco RI* recognition sites.
    • Development of hierarchical models for base preferences at each position.

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  • Comparison of Eco RI* recognition with standard Eco RI binding models.

    • Main Results:

    • Established hierarchical preferences for base recognition at each position under Eco RI* conditions: G>A>T>C (position 1), A>[G,C]>T (positions 2 & 3), and their complements.
    • Proposed a model where Eco RI* specificity arises from the random replacement of standard hydrogen bonds with water.
    • Identified retained hydrogen bonds as key determinants of sequence recognition within the established hierarchies.
    • Located Eco RI recognition points within the DNA major groove.

    Conclusions:

    • Eco RI* specificity is quantitatively predictable using hierarchical base preferences.
    • The number of retained hydrogen bonds dictates sequence recognition under non-standard conditions.
    • Eco RI interacts with DNA primarily through its major groove.