Abstract
Biosensor-surface plasmon resonance (SPR) technology has emerged as a powerful label-free approach for the study of nucleic acid interactions in real time. The method provides simultaneous equilibrium and kinetic characterization for biomolecular interactions with low sample requirements and without the need for external probes. A detailed and practical guide for protein–DNA interaction analyses using biosensor-SPR methods is presented. Details of SPR technology and basic fundamentals are described with recommendations on the preparation of the SPR instrument, sensor chips and samples, experimental design, quantitative and qualitative data analyses and presentation. A specific example of the interaction of a transcription factor with DNA is provided with results evaluated by both kinetic and steady-state SPR methods.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Homola J (2008) Surface plasmon resonance sensors for detection of chemical and biological species. Chem Rev 108:462–493
Rich RL, Myszka DG (2000) Advances in surface plasmon resonance biosensor analysis. Curr Opin Biotechnol 11:54–61
Wilson WD (2002) Analyzing biomolecular interactions. Science 295:2103–2105
Piliarik M, Vaisocherova H, Homola J (2009) Surface plasmon resonance biosensing. In: Rasooly A, Herold KE (eds) Methods in molecular biology, vol 503. Humana, New York, pp 65–88
Davis TM, Wilson WD (2001) Surface plasmon resonance biosensor analysis of RNA-small molecule interactions. Methods Enzymol 340:22–51
Papalia GA, Giannetti AM, Arora N, Myszka DG (2008) Thermodynamic characterization of pyrazole and azaindole derivatives binding to p38 mitogen-activated protein kinase using Biacore T100 technology and van’t Hoff analysis. Anal Biochem 383:255–264
Liu Y, Wilson WD (2010) Quantitative analysis of small molecule-nucleic acid interactions with a biosensor surface and surface plasmon resonance detection. In: Fox KR (ed) Methods in molecular biology, vol 613. Humana, New York, pp 1–23
Nanjunda R, Munde M, Liu Y, Wilson WD (2011) Real-time monitoring of nucleic acid interactions with biosensor-surface plasmon resonance. In: Wanunu M, Tor Y (eds) Methods for studying nucleic acid/drug interactions. CRC, Boca Raton, pp 91–122
He X, Coombs D, Myszka DG, Goldstein B (2006) A theoretical and experimental study of competition between solution and surface receptors for ligand in a Biacore flow cell. Bull Math Biol 68:1125–1150
Bondeson K, Frostellkarlsson A, Fagerstam L, Magnusson G (1993) Lactose repressor-operator DNA interactions: kinetic analysis by a surface plasmon resonance biosensor. Anal Biochem 214:245–251
Goeddel DV, Yansura DG, Caruthers MH (1977) Binding of synthetic lactose operator DNAs to lactose represessors. Proc Natl Acad Sci U S A 74:3292–3296
Davis TM, Wilson WD (2000) Determination of the refractive index increments of small molecules for correction of surface plasmon resonance data. Anal Biochem 284:348–353
Degnan BM, Degnan SM, Naganuma T, Morse DE (1993) The ETS multigene family is conserved throughout the metazoa. Nucleic Acids Res 21:3479–3484
Oikawa T, Yamada T (2003) Molecular biology of the Ets family of transcription factors. Gene 303:11–34
Sharrocks AD (2001) The ETS-domain transcription factor family. Nat Rev Mol Cell Biol 2:827–837
Sementchenko VI, Watson DK (2000) Ets target genes: past, present and future. Oncogene 19:6533–6548
Hsu T, Trojanowska M, Watson DK (2004) Ets proteins in biological control and cancer. J Cell Biochem 91:896–903
Gilliland DG (2001) The diverse role of the ETS family of transcription factors in cancer. Clin Cancer Res 7:451–453
Oikawa T (2004) ETS transcription factors: possible targets for cancer therapy. Cancer Sci 95:626–633
Galang CK, Muller WJ, Foos G, Oshima RG, Hauser CA (2004) Changes in the expression of many Ets family transcription factors and of potential target genes in normal mammary tissue and tumors. J Biol Chem 279:11281–11292
Wei G-H, Badis G, Berger MF, Kivioja T, Palin K, Enge M et al (2010) Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J 29:2147–2160
Hollenhorst PC, McIntosh LP, Graves BJ (2011) Genomic and biochemical insights into the specificity of ETS transcription factors. In: Kornberg RD, Raetz CRH, Rothman JE, Thorner JW (eds). Annu Rev Biochem 80:437–471
DeKoter RP, Singh H (2000) Regulation of B lymphocyte and macrophage development by graded expression of PU.1. Science 288:1439–1441
Ross IL, Yue X, Ostrowski MC, Hume DA (1998) Interaction between PU.1 and another Ets family transcription factor promotes macrophage-specific basal transcription initiation. J Biol Chem 273:6662–6669
Kopp JL, Wilder PJ, Desler M, Kim JH, Hou J, Nowling T et al (2004) Unique and selective effects of five Ets family members, Elf3, Ets1, Ets2, PEA3, and PU.1, on the promoter of the type II transforming growth factor-beta receptor gene. J Biol Chem 279:19407–19420
Pham TH, Minderjahn J, Schmidl C, Hoffmeister H, Schmidhofer S, Chen W et al (2013) Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1. Nucleic Acids Res 41:6391–6402
Munde M, Poon GM, Wilson WD (2013) Probing the electrostatics and pharmacological modulation of sequence-specific binding by the DNA-binding domain of the ETS family transcription factor PU.1: a binding affinity and kinetics investigation. J Mol Biol 425:1655–1669
Poon GM (2012) Sequence discrimination by DNA-binding domain of ETS family transcription factor PU.1 is linked to specific hydration of protein-DNA interface. J Biol Chem 287:18297–18307
Poon GM (2012) DNA binding regulates the self-association of the ETS domain of PU.1 in a sequence-dependent manner. Biochemistry 51:4096–4107
Myszka DG (2000) Kinetic, equilibrium, and thermodynamic analysis of macromolecular interactions with BIACORE. Methods Enzymol 323:325–340
Nguyen B, Tanious FA, Wilson WD (2007) Biosensor-surface plasmon resonance: quantitative analysis of small molecule-nucleic acid interactions. Methods 42:150–161
Tanious FA, Nguyen B, Wilson WD (2008) Biosensor-surface plasmon resonance methods for quantitative analysis of biomolecular interactions. In: Correia JJ, Detrich HW (eds). Methods Cell Biol 84:53–77
Karlsson R (1999) Affinity analysis of non-steady-state data obtained under mass transport limited conditions using BIAcore technology. J Mol Recognit 12:285–292
Eisenbeis CF, Singh H, Storb U (1993) PU-1 is a component of a multiprotein complex which binds an essential site in the murine immunoglobulin lambda-2-4 enhancer. Mol Cell Biol 13:6452–6461
Poon GM, Gross P, Macgregor RB (2002) The sequence-specific association of the ETS domain of murine PU.1 with DNA exhibits unusual energetics. Biochemistry 41:2361–2371
Poon GM, Macgregor RB (2003) Base coupling in sequence-specific site recognition by the ETS domain of murine PU.1. J Mol Biol 328:805–819
Myszyka DG (1999) Improving biosensor analysis. J Mol Recognit 12:279–284
Acknowledgments
We gratefully thank the NIH (GM111749) and the NSF (MCB1411502) for the support for biosensor-SPR studies on DNA complexes, and the Georgia Research Alliance for funding of the Biacore instruments. We thank Carol Wilson for manuscript proofreading.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Wang, S., Poon, G.M.K., Wilson, W.D. (2015). Quantitative Investigation of Protein–Nucleic Acid Interactions by Biosensor Surface Plasmon Resonance. In: Leblanc, B., Rodrigue, S. (eds) DNA-Protein Interactions. Methods in Molecular Biology, vol 1334. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2877-4_20
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2877-4_20
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2876-7
Online ISBN: 978-1-4939-2877-4
eBook Packages: Springer Protocols