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Quantitative Analysis of Small Molecule–Nucleic Acid Interactions with a Biosensor Surface and Surface Plasmon Resonance Detection

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Book cover Drug-DNA Interaction Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 613))

Abstract

Surface plasmon resonance (SPR) technology with biosensor surfaces has become a widely-used tool for the study of nucleic acid interactions without any labeling requirements. The method provides simultaneous kinetic and equilibrium characterization of the interactions of biomolecules as well as small molecule-biopolymer binding. SPR monitors molecular interactions in real time and provides significant advantages over optical or calorimetic methods for systems with strong binding coupled to small spectroscopic signals and/or reaction heats. A detailed and practical guide for nucleic acid interaction analysis using SPR-biosensor methods is presented. Details of the SPR technology and basic fundamentals are described with recommendations on the preparation of the SPR instrument, sensor chips, and samples, as well as extensive information on experimental design, quantitative and qualitative data analysis and presentation. A specific example of the interaction of a minor-groove-binding agent with DNA is evaluated by both kinetic and steady-state SPR methods to illustrate the technique. Since the molecules that bind cooperatively to specific DNA sequences are attractive for many applications, a cooperative small molecule-DNA interaction is also presented.

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Acknowledgments

We very much thank the NIH for funding the research that has made this review possible and the Georgia Research Alliance for funding of Biacore instruments. We also very much thank Professor David W. Boykin and his coworkers (Georgia State University, Atlanta, GA, USA) for supplying DB293 and many other DNA and RNA binding agents for SPR studies as well as for helpful discussions.

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Authors and Affiliations

  1. Department of Chemistry, Georgia State University, Atlanta, GA, USA

    Yang Liu & W. David Wilson

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  1. Yang Liu
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  2. W. David Wilson
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Editors and Affiliations

  1. School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom

    Keith R. Fox

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Liu, Y., Wilson, W.D. (2010). Quantitative Analysis of Small Molecule–Nucleic Acid Interactions with a Biosensor Surface and Surface Plasmon Resonance Detection. In: Fox, K. (eds) Drug-DNA Interaction Protocols. Methods in Molecular Biology, vol 613. Humana Press. https://doi.org/10.1007/978-1-60327-418-0_1

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  • DOI: https://doi.org/10.1007/978-1-60327-418-0_1

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60327-417-3

  • Online ISBN: 978-1-60327-418-0

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