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Sedimentation Velocity Ultracentrifugation Analysis for Hydrodynamic Characterization of G-Quadruplex Structures

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G-Quadruplex DNA

Part of the book series: Methods in Molecular Biology ((MIMB,volume 608))

Abstract

Analytical ultracentrifugation (AUC) is a powerful technique for the characterization of hydrodynamic and thermodynamic properties. The intent of this article is to demonstrate the utility of sedimentation velocity (SV) studies to obtain hydrodynamic information for G-quadruplex (GQ) systems and to provide insights into one part of this process, namely, data analysis of existing SV data. An array of data analysis software is available, mostly written and continually developed by established researchers in the AUC field, with particularly rapid advances in the analysis of SV data. Each program has its own learning curve, and this article is intended as a resource in the data analysis process for beginning researchers in the field. We discuss the application of three of the most commonly used data analysis programs, DCDT+, Sedfit, and SedAnal, to the interpretation of SV data obtained in our laboratory on two GQ systems.

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Abbreviations

AUC:

Analytical ultracentrifugation

CD:

Circular dichroism

D:

Translational diffusion coefficient

SV:

Sedimentation velocity

SE:

Sedimentation equilibrium

s:

Sedimentation coefficient

s20,w :

Sedimentation coefficient corrected to a temperature of 20°C and to the density and viscosity of pure water

S:

Svedberg unit equal to 10−13 s

M:

Molecular weight

\( \bar v \) :

Partial specific volume

\( \rho \) :

Density

GQ:

G-quadruplex

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Acknowledgments

We thank Jack Correia for countless helpful discussions. This work was supported by National Cancer Institute grant CA35635 to J.B.C.

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Authors and Affiliations

  1. James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA

    Nichola C. Garbett, Chongkham S. Mekmaysy & Jonathan B. Chaires

Authors
  1. Nichola C. Garbett
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  2. Chongkham S. Mekmaysy
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  3. Jonathan B. Chaires
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Corresponding author

Correspondence to Jonathan B. Chaires .

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  1. Medical Research, Stowers Institute for, East 50th Street 1000, Kansas City, 64110, U.S.A.

    Peter Baumann

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Garbett, N.C., Mekmaysy, C.S., Chaires, J.B. (2010). Sedimentation Velocity Ultracentrifugation Analysis for Hydrodynamic Characterization of G-Quadruplex Structures. In: Baumann, P. (eds) G-Quadruplex DNA. Methods in Molecular Biology, vol 608. Humana Press. https://doi.org/10.1007/978-1-59745-363-9_7

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  • DOI: https://doi.org/10.1007/978-1-59745-363-9_7

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