Table of Contents
Journal of Amino Acids
Volume 2012 (2012), Article ID 816032, 19 pages
http://dx.doi.org/10.1155/2012/816032
Review Article

Real-Time Analysis of Specific Protein-DNA Interactions with Surface Plasmon Resonance

Department of Chemistry, Bielefeld University, P.O. Box 100131, 33501 Bielefeld, Germany

Received 24 August 2011; Accepted 7 November 2011

Academic Editor: Alice Vrielink

Copyright © 2012 Markus Ritzefeld and Norbert Sewald. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Several proteins, like transcription factors, bind to certain DNA sequences, thereby regulating biochemical pathways that determine the fate of the corresponding cell. Due to these key positions, it is indispensable to analyze protein-DNA interactions and to identify their mode of action. Surface plasmon resonance is a label-free method that facilitates the elucidation of real-time kinetics of biomolecular interactions. In this article, we focus on this biosensor-based method and provide a detailed guide how SPR can be utilized to study binding of proteins to oligonucleotides. After a description of the physical phenomenon and the instrumental realization including fiber-optic-based SPR and SPR imaging, we will continue with a survey of immobilization methods. Subsequently, we will focus on the optimization of the experiment, expose pitfalls, and introduce how data should be analyzed and published. Finally, we summarize several interesting publications of the last decades dealing with protein-DNA and RNA interaction analysis by SPR.