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

Ritzefeld M, Sewald N (2012)
Journal of Amino Acids 2012: 1-19.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Abstract / Bemerkung
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.
Erscheinungsjahr
2012
Zeitschriftentitel
Journal of Amino Acids
Band
2012
Seite(n)
1-19
ISSN
2090-0104
eISSN
2090-0112
Page URI
https://pub.uni-bielefeld.de/record/2499315

Zitieren

Ritzefeld M, Sewald N. Real-Time Analysis of Specific Protein-DNA Interactions with Surface Plasmon Resonance. Journal of Amino Acids. 2012;2012:1-19.
Ritzefeld, M., & Sewald, N. (2012). Real-Time Analysis of Specific Protein-DNA Interactions with Surface Plasmon Resonance. Journal of Amino Acids, 2012, 1-19. doi:10.1155/2012/816032
Ritzefeld, Markus, and Sewald, Norbert. 2012. “Real-Time Analysis of Specific Protein-DNA Interactions with Surface Plasmon Resonance”. Journal of Amino Acids 2012: 1-19.
Ritzefeld, M., and Sewald, N. (2012). Real-Time Analysis of Specific Protein-DNA Interactions with Surface Plasmon Resonance. Journal of Amino Acids 2012, 1-19.
Ritzefeld, M., & Sewald, N., 2012. Real-Time Analysis of Specific Protein-DNA Interactions with Surface Plasmon Resonance. Journal of Amino Acids, 2012, p 1-19.
M. Ritzefeld and N. Sewald, “Real-Time Analysis of Specific Protein-DNA Interactions with Surface Plasmon Resonance”, Journal of Amino Acids, vol. 2012, 2012, pp. 1-19.
Ritzefeld, M., Sewald, N.: Real-Time Analysis of Specific Protein-DNA Interactions with Surface Plasmon Resonance. Journal of Amino Acids. 2012, 1-19 (2012).
Ritzefeld, Markus, and Sewald, Norbert. “Real-Time Analysis of Specific Protein-DNA Interactions with Surface Plasmon Resonance”. Journal of Amino Acids 2012 (2012): 1-19.

11 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Chitosan in Non-Viral Gene Delivery: Role of Structure, Characterization Methods, and Insights in Cancer and Rare Diseases Therapies.
Santos-Carballal B, Fernández Fernández E, Goycoolea FM., Polymers (Basel) 10(4), 2018
PMID: 30966479
Fiber Optic Surface Plasmon Resonance-Based Biosensor Technique: Fabrication, Advancement, and Application.
Liang G, Luo Z, Liu K, Wang Y, Dai J, Duan Y., Crit Rev Anal Chem 46(3), 2016
PMID: 27119268
Surface plasmon resonance: a label-free tool for cellular analysis.
Zeidan E, Kepley CL, Sayes C, Sandros MG., Nanomedicine (Lond) 10(11), 2015
PMID: 26080702
Production of pure and functional RNA for in vitro reconstitution experiments.
Edelmann FT, Niedner A, Niessing D., Methods 65(3), 2014
PMID: 24021718
Surface plasmon resonance for cell-based clinical diagnosis.
Yanase Y, Hiragun T, Ishii K, Kawaguchi T, Yanase T, Kawai M, Sakamoto K, Hide M., Sensors (Basel) 14(3), 2014
PMID: 24618778
Analysis of DNA interactions using single-molecule force spectroscopy.
Ritzefeld M, Walhorn V, Anselmetti D, Sewald N., Amino Acids 44(6), 2013
PMID: 23468137

96 References

Daten bereitgestellt von Europe PubMed Central.

Origins of specificity in protein-DNA recognition.
Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS., Annu. Rev. Biochem. 79(), 2010
PMID: 20334529
A new method for label-free imaging of biomolecular interactions
Li PY, Lin B, Gerstenmaier J, Cunningham BT., 0
Label-free screening of bio-molecular interactions.
Cooper MA., Anal Bioanal Chem 377(5), 2003
PMID: 12904946
Single-molecule experiments to elucidate the minimal requirement for DNA recognition by transcription factor epitopes.
Wollschlager K, Gaus K, Kornig A, Eckel R, Wilking SD, McIntosh M, Majer Z, Becker A, Ros R, Anselmetti D, Sewald N., Small 5(4), 2009
PMID: 19199332
Single-molecule experiments in synthetic biology: an approach to the affinity ranking of DNA-binding peptides.
Eckel R, Wilking SD, Becker A, Sewald N, Ros R, Anselmetti D., Angew. Chem. Int. Ed. Engl. 44(25), 2005
PMID: 15906400
Defining the thermodynamics of protein/DNA complexes and their components using micro-calorimetry
Crane-Robinson C, Dragan AI, Read CM., 2009
Survey of the year 2007 commercial optical biosensor literature.
Rich RL, Myszka DG., J. Mol. Recognit. 21(6), 2008
PMID: 18951413

AUTHOR UNKNOWN, 0
Surface plasmon resonance-based fiber optic sensors: Principle, probe designs, and some applications
Gupta BD, Verma RK., 2009
Fiber-optic sensors based on surface plasmon resonance: A comprehensive review
Sharma AK, Jha R, Gupta BD., 2007
Analysis of protein-DNA interactions using surface plasmon resonance.
Majka J, Speck C., Adv. Biochem. Eng. Biotechnol. 104(), 2007
PMID: 17290817

AUTHOR UNKNOWN, 0
Label-free analysis of biomolecular interactions using SPR imaging.
Kodoyianni V., BioTechniques 50(1), 2011
PMID: 21231920
A novel hydrogel matrix on gold surfaces in surface plasmon resonance sensors for fast and efficient covalent immobilization of ligands
Löfås S, Johnsson B., 1990
Specific capture of mammalian cells by cell surface receptor binding to ligand immobilized on gold thin films.
Peelen D, Kodoyianni V, Lee J, Zheng T, Shortreed MR, Smith LM., J. Proteome Res. 5(7), 2006
PMID: 16823965
Methods for site controlled coupling to carboxymethyldextran surfaces in surface plasmon resonance sensors
Löfås S, Johnsson B, Edstrom A., 1995

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 2008
Structure and DNA hybridization properties of mixed nucleic acid/maleimide-ethylene glycol monolayers.
Lee CY, Nguyen PC, Grainger DW, Gamble LJ, Castner DG., Anal. Chem. 79(12), 2007
PMID: 17492838
Surface plasmon resonance imaging of transcription factor proteins: interactions of bacterial response regulators with DNA arrays on gold films
Smith EA, Erickson MG, Ulijasz AT, Weisblum B, Corn RM., 2003
Covalent immobilization of recombinant fusion proteins with hAGT for single molecule force spectroscopy.
Kufer SK, Dietz H, Albrecht C, Blank K, Kardinal A, Rief M, Gaub HE., Eur. Biophys. J. 35(1), 2005
PMID: 16160825
Immobilization of proteins to biacore sensor chips using Staphylococcus aureus sortase A.
Clow F, Fraser JD, Proft T., Biotechnol. Lett. 30(9), 2008
PMID: 18414796
Self-directed and self-oriented immobilization of antibody by protein G-DNA conjugate.
Jung Y, Lee JM, Jung H, Chung BH., Anal. Chem. 79(17), 2007
PMID: 17668928
A surface plasmon resonance immunosensor based on the streptavidin-biotin complex.
Morgan H, Taylor DM., Biosens Bioelectron 7(6), 1992
PMID: 1515116
Immobilization chemistries suitable for use in the BIAcore surface plasmon resonance detector.
O'Shannessy DJ, Brigham-Burke M, Peck K., Anal. Biochem. 205(1), 1992
PMID: 1443550
The biotin-(strept)avidin system: principles and applications in biotechnology.
Diamandis EP, Christopoulos TK., Clin. Chem. 37(5), 1991
PMID: 2032315
Use of intein-mediated protein ligation strategies for the fabrication of functional protein arrays.
Chattopadhaya S, Abu Bakar FB, Yao SQ., Meth. Enzymol. 462(), 2009
PMID: 19632476
In vitro enzymatic biotinylation of recombinant fab fragments through a peptide acceptor tail.
Saviranta P, Haavisto T, Rappu P, Karp M, Lovgren T., Bioconjug. Chem. 9(6), 1998
PMID: 9815166
Detection of DNA sequences using biotinylated probes.
Woodhead JL, Figueiredo H, Malcolm AD., Methods Mol. Biol. 4(), 1988
PMID: 21424653
Reversible immobilization of proteins with streptavidin affinity tags on a surface plasmon resonance biosensor chip.
Li YJ, Bi LJ, Zhang XE, Zhou YF, Zhang JB, Chen YY, Li W, Zhang ZP., Anal Bioanal Chem 386(5), 2006
PMID: 17006676
Instruction for NeutrAvidin biotin-binding protein
AUTHOR UNKNOWN, 0
Blockade of vascular smooth muscle cell proliferation and intimal thickening after balloon injury by the sulfated oligosaccharide PI-88: phosphomannopentaose sulfate directly binds FGF-2, blocks cellular signaling, and inhibits proliferation.
Francis DJ, Parish CR, McGarry M, Santiago FS, Lowe HC, Brown KJ, Bingley JA, Hayward IP, Cowden WB, Campbell JH, Campbell GR, Chesterman CN, Khachigian LM., Circ. Res. 92(8), 2003
PMID: 12690039
Kinetic analysis of high-mobility-group proteins HMG-1 and HMG-I/Y binding to cholesterol-tagged DNA on a supported lipid monolayer.
Webster CI, Cooper MA, Packman LC, Williams DH, Gray JC., Nucleic Acids Res. 28(7), 2000
PMID: 10710428
Directed immobilization of DNA-binding proteins on a cognate DNA-modified chip surface.
Jeong EJ, Jeong YS, Park K, Yi SY, Ahn J, Chung SJ, Kim M, Chung BH., J. Biotechnol. 135(1), 2008
PMID: 18395923
Improving biosensor analysis.
Myszka DG., J. Mol. Recognit. 12(5), 1999
PMID: 10556875
Surface plasmon resonance (SPR) spectrometry as a tool to analyze nucleic acid-protein interactions in crude cellular extracts.
Ahmed FE, Wiley JE, Weidner DA, Bonnerup C, Mota H., Cancer Genomics Proteomics 7(6), 2010
PMID: 21156963

AUTHOR UNKNOWN, 0
Determination of interaction kinetic constants for HIV-1 protease inhibitors using optical biosensor technology.
Markgren PO, Lindgren MT, Gertow K, Karlsson R, Hamalainen M, Danielson UH., Anal. Biochem. 291(2), 2001
PMID: 11401294
Identification of MMP-12 inhibitors by using biosensor-based screening of a fragment library.
Nordstrom H, Gossas T, Hamalainen M, Kallblad P, Nystrom S, Wallberg H, Danielson UH., J. Med. Chem. 51(12), 2008
PMID: 18494455
The analysis of entire gene promoters by surface plasmon resonance.
Moyroud E, Reymond MC, Hames C, Parcy F, Scutt CP., Plant J. 59(5), 2009
PMID: 19453452

AUTHOR UNKNOWN, 2008
Investigating biomolecular interactions and binding properties using SPR biosensors
Navratilova I, Myszka DG., 2006
Extending the range of rate constants available from BIACORE: interpreting mass transport-influenced binding data.
Myszka DG, He X, Dembo M, Morton TA, Goldstein B., Biophys. J. 75(2), 1998
PMID: 9675161
Survey of the 1998 optical biosensor literature.
Myszka DG., J. Mol. Recognit. 12(6), 1999
PMID: 10611648

AUTHOR UNKNOWN, 1997
The salt dependence of DNA recognition by NF-kappaB p50: a detailed kinetic analysis of the effects on affinityand specificity.
Hart DJ, Speight RE, Cooper MA, Sutherland JD, Blackburn JM., Nucleic Acids Res. 27(4), 1999
PMID: 9927740
Detection of picomolar levels of interleukin-8 in human saliva by SPR
Yang CY, Brooks E, Li Y., 2005
Hepatocyte growth factor (HGF) in fecal samples: rapid detection by surface plasmon resonance
Nayeri F, Aili D, Nayeri T., 2005
Comment on: Rich and Myszka, Grading the commercial optical biosensor literature—Class of 2008: ’The Mighty Binders’. Journal of Molecular Recognition, vol. 23, pp. 1–64, 2010
Kenny PW., 2010
Response to grading of the commercial optical biosensor literature—class of 2008
Havard J., 2010
Scrubber 2.0 Tutorial
AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 1999
Kinetic analysis of interaction of BRCA1 tandem breast cancer c-terminal domains with phosphorylated peptides reveals two binding conformations.
Nomine Y, Botuyan MV, Bajzer Z, Owen WG, Caride AJ, Wasielewski E, Mer G., Biochemistry 47(37), 2008
PMID: 18717574
Detection of oligonucleotide systematic mismatches with a surface plasmon resonance sensor.
Milkani E, Morais S, Lambert CR, McGimpsey WG., Biosens Bioelectron 25(5), 2009
PMID: 19819685
Surface plasmon resonance study of PNA interactions with double-stranded DNA.
Ananthanawat C, Hoven VP, Vilaivan T, Su X., Biosens Bioelectron 26(5), 2010
PMID: 20580217
Heterocyclic diamidine interactions at AT base Pairs in the DNA minor groove: effects of heterocycle differences, DNA AT sequence and length
Liu Y, Collar CJ, Kumar A, Stephens CE, Boykin DW, Wilson WD., 2008
Study of protein-DNA interactions by surface plasmon resonance (real time kinetics)
Jost JP, Munch O, Andersson T., 1991
Lactose repressor-operator DNA interactions: kinetic analysis by a surface plasmon resonance biosensor.
Bondeson K, Frostell-Karlsson A, Fagerstam L, Magnusson G., Anal. Biochem. 214(1), 1993
PMID: 8250230
Analysis of the DNA-binding domain of Escherichia coli DnaA protein.
Blaesing F, Weigel C, Welzeck M, Messer W., Mol. Microbiol. 36(3), 2000
PMID: 10844646
Rapid coupling of Surface Plasmon Resonance (SPR and SPRi) and ProteinChip™ based mass spectrometry for the identification of proteins in nucleoprotein interactions
Bouffartigues E, Leh H, Anger-Leroy M, Rimsky S, Buckle M., 2007
Fiber optic SPR biosensing of DNA hybridization and DNA-protein interactions.
Pollet J, Delport F, Janssen KP, Jans K, Maes G, Pfeiffer H, Wevers M, Lammertyn J., Biosens Bioelectron 25(4), 2009
PMID: 19775884
Double recognition of oligonucleotide and protein in the detection of DNA methylation with surface plasmon resonance biosensors.
Pan S, Xu J, Shu Y, Wang F, Xia W, Ding Q, Xu T, Zhao C, Zhang M, Huang P, Lu S., Biosens Bioelectron 26(2), 2010
PMID: 20810273
A dual surface plasmon resonance assay for the determination of ribonuclease H activity.
Sipova H, Vaisocherova H, Stepanek J, Homola J., Biosens Bioelectron 26(4), 2010
PMID: 20829018
Real-time monitoring of solid-phase PCR using fiber-optic SPR.
Pollet J, Janssen KP, Knez K, Lammertyn J., Small 7(8), 2011
PMID: 21394905
Minor groove recognition is important for the transcription factor PhoB: a surface plasmon resonance study.
Ritzefeld M, Wollschlager K, Niemann G, Anselmetti D, Sewald N., Mol Biosyst 7(11), 2011
PMID: 21912786
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