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Spatial configuration of deoxyribotrinucleoside diphosphates in aqueous solution

D M Cheng, M M Dhingra, R H Sarma

    Nucleic Acids Research
    |November 1, 1978
    PubMed
    Summary

    Nuclear magnetic resonance (NMR) spectroscopy revealed deoxyribotrinucleoside diphosphates (dNTPs) like d-TpTpT and d-TpTpC maintain their structure in solution. These DNA building blocks conserve intrinsic features when forming longer DNA chains.

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    Area of Science:

    • Biochemistry
    • Molecular Biology
    • Structural Biology

    Background:

    • Deoxyribotrinucleoside diphosphates (dNTPs) are essential DNA building blocks.
    • Understanding their conformational dynamics is crucial for DNA replication and repair mechanisms.

    Purpose of the Study:

    • To investigate the detailed conformational features and dynamics of d-TpTpT and d-TpTpC.
    • To determine if monomers and dimers retain their intrinsic properties within trimers.

    Main Methods:

    • Nuclear magnetic resonance (NMR) spectroscopy was employed.
    • Experiments were conducted at 20°C and 80°C in aqueous solution.

    Main Results:

    • NMR parameters indicated high similarity between trimers and their constituent monomers/dimers.

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  • Conformational properties are conserved upon incorporation into oligomers.
  • Model building suggested specific spatial configurations for distant shieldings.

    • Conclusions:

    • Deoxyribotrinucleoside diphosphates (d-TpTpT, d-TpTpC) maintain their conformational integrity in solution.
    • Monomers and dimers conserve intrinsic features within these DNA trimers.
    • Specific bulged-out configurations may explain observed NMR signals.