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Calculation of Hydrodynamic Properties for G-Quadruplex Nucleic Acid Structures from in silico Bead Models

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Quadruplex Nucleic Acids

Part of the book series: Topics in Current Chemistry ((TOPCURRCHEM,volume 330))

Abstract

Nucleic acids enriched in guanine bases can adopt unique quadruple helical tertiary structures known as G-quadruplexes. G-quadruplexes have emerged as attractive drug targets as many G-quadruplex-forming sequences have been discovered in functionally critical sites within the human genome, including the telomere, oncogene promoters, and mRNA processing sites. A single G-quadruplex-forming sequence can adopt one of many folding topologies, often resulting in a lack of a single definitive atomic-level resolution structure for many of these sequences and a major challenge to the discovery of G-quadruplex-selective small molecule drugs. Low-resolution techniques employed to study G-quadruplex structures (e.g., CD spectroscopy) are often unable to discern between G-quadruplex structural ensembles, while high-resolution techniques (e.g., NMR spectroscopy) can be overwhelmed by a highly polymorphic system. Hydrodynamic bead modeling is an approach to studying G-quadruplex structures that could bridge the gap between low-resolution techniques and high-resolution molecular models. Here, we present a discussion of hydrodynamic bead modeling in the context of studying G-quadruplex structures, highlighting recent successes and limitations to this approach, as well as an example featuring a G-quadruplex structure formed from the human telomere. This example can easily be adapted to the investigation of any other G-quadruplex-forming sequences.

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Acknowledgments

We would like to acknowledge Dr. Robert D. Gray for useful discussions in the writing of this chapter. Molecular graphics images were produced using the UCSF Chimera package from the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIH P41 RR001081). This work was supported by NIH Grants CA35635 (J.B.C), GM077422 (J.B.C. and J.O.T) and University of Louisville grant, CTSPGP 20058 Award (J.B.C. and J.O.T).

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  1. Clinical and Translation Research Building, University of Louisville, 505 S. Hancock St, Louisville, KY, 40202, USA

    Huy T. Le, Robert Buscaglia, William L. Dean, Jonathan B. Chaires & John O. Trent

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  1. Huy T. Le
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  2. Robert Buscaglia
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  3. William L. Dean
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  4. Jonathan B. Chaires
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  5. John O. Trent
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Correspondence to John O. Trent .

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Editors and Affiliations

  1. James Graham Brown Cancer Center, University of Louisville, Louisville, 40202, New York, USA

    Jonathan B. Chaires

  2. , Department of Chemistry, University of Alamaba at Birmingham, 3rd Ave 1530, Birmingham, 35294-1240, Alaska, USA

    David Graves

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© 2012 Springer-Verlag Berlin Heidelberg

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Le, H.T., Buscaglia, R., Dean, W.L., Chaires, J.B., Trent, J.O. (2012). Calculation of Hydrodynamic Properties for G-Quadruplex Nucleic Acid Structures from in silico Bead Models. In: Chaires, J., Graves, D. (eds) Quadruplex Nucleic Acids. Topics in Current Chemistry, vol 330. Springer, Berlin, Heidelberg. https://doi.org/10.1007/128_2012_351

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