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Related Experiment Videos

How flexible are fleximer nucleobases? A computational study.

Alma B Bardon1, Stacey D Wetmore

  • 1Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick E4L 1G8, Canada.

The Journal of Physical Chemistry. A
|July 15, 2006
PubMed
Summary

Modified purines called fleximers exhibit high flexibility due to rotation around carbon-carbon bonds. Their hydrogen-bonding properties mimic natural purines, suggesting potential in biochemical applications.

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Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Biochemistry

Background:

  • Modified purines, termed fleximers, feature separated imidazole and pyrimidine rings linked by a carbon-carbon bond.
  • Understanding the conformational flexibility and binding properties of these modified nucleobases is crucial for their potential applications.

Purpose of the Study:

  • To investigate the potential energy surface for rotation around the carbon-carbon bonds in guanosine, adenosine, and inosine fleximers.
  • To evaluate the influence of different ring connectivities and the presence of a ribose moiety on fleximer conformation and flexibility.
  • To assess the hydrogen-bonding capabilities of fleximers in comparison to natural purines.

Main Methods:

  • Density functional theory (DFT) calculations were employed to study the potential energy surfaces.

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  • Calculations were performed on fleximer nucleobases both with and without the ribose sugar moiety.
  • Binding energies of fleximer-pyrimidine pairs were computed to assess hydrogen-bonding interactions.

    • Main Results:

    • A planar arrangement of imidazole and pyrimidine rings is favored in isolated fleximer nucleobases, with low rotational barriers (<40 kJ mol(-1)).
    • Fleximers demonstrate hydrogen-bonding properties comparable to natural purines.
    • The inclusion of the ribose moiety can favor nonplanar ring orientations and alter rotational barriers depending on the specific fleximer structure and connectivity.

    Conclusions:

    • Fleximers are highly flexible molecules with conformational properties influenced by both intrinsic structure and the presence of a sugar group.
    • The studied fleximers possess hydrogen-bonding characteristics similar to natural purines.
    • Several fleximer connectivities show promise for biochemical applications requiring flexible nucleobases.