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Predictive Binding Geometry of Ligands to DNA Minor Groove: Isohelicity and Hydrogen-Bonding Pattern

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Functional Analysis of DNA and Chromatin

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1094))

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Abstract

The interaction of drugs and dyes with nucleic acids, particularly when binding to DNA minor groove occurs, has increasing importance in biomedical sciences. This is due to the resulting biological activity and to the possibility of recognizing AT and GC base pairs. In such cases, DNA binding can be predicted if appropriate helical and hydrogen-bonding parameters are deduced from DNA models, and a simplified geometrical rule in the form of a stencil is then applied on computer-drawn molecules of interest. Relevant structure parameter values for minor groove binders are the length (4.6 < L < 5.4 Å) and angle (152 < σ < 156.5°) between three consecutive units, measured at the level of hydrogen donor or acceptor groups. Application of the stencil shows that predictive methods can aid in the design of new compounds, by checking the possible binding of isohelical sequence-specific ligands along the DNA minor groove.

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Acknowledgements

I thank A. Blázquez-Castro, J. Espada, and R.W. Horobin for valuable collaboration. This work was supported by a grant (CTQ2010-20870-C03-03) from the Ministerio de Ciencia e Innovación, Spain.

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Authors and Affiliations

  1. Department of Biology, Faculty of Sciences, Autonomous University of Madrid, Cantoblanco, Madrid, Spain

    Juan C. Stockert

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  1. Juan C. Stockert
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Editors and Affiliations

  1. Department of Biology, Autonomous University of Madrid Faculty of Sciences, Madrid, Spain

    Juan C. Stockert

  2. Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain

    Jesús Espada

  3. Department of Biology, Autonomous University of Madrid Faculty of Sciences, Madrid, Spain

    Alfonso Blázquez-Castro

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Stockert, J.C. (2014). Predictive Binding Geometry of Ligands to DNA Minor Groove: Isohelicity and Hydrogen-Bonding Pattern. In: Stockert, J., Espada, J., Blázquez-Castro, A. (eds) Functional Analysis of DNA and Chromatin. Methods in Molecular Biology, vol 1094. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-706-8_1

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  • DOI: https://doi.org/10.1007/978-1-62703-706-8_1

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-705-1

  • Online ISBN: 978-1-62703-706-8

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