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Evaluation of two- and three-dimensional streptavidin binding platforms for surface plasmon resonance spectroscopy studies of DNA hybridization and protein-DNA binding.
Biosens Bioelectron. 2007 May 15; 22(11):2700-6.BB

Abstract

Surface plasmon resonance (SPR) spectroscopy has been used to study DNA assembly, DNA hybridization, and protein-DNA interactions on two streptavidin (SA) sensor chips. On one chip, SA molecules are immobilized on a biotin-exposed surface, forming an ordered two-dimensional (2D) SA monolayer. The other chip, BIAcore's SA chip, contains SA molecules immobilized within a three-dimensional (3D) carboxylated dextran matrix. Compared to the 2D chip, the 3D SA matrix allows for a slower immobilization rate of biotinylated DNA due to diffusion limitation in the dextran matrix, but with twice the amount of the immobilized DNA due to the greater number of reactive sites, which in turn enables a higher sensitivity for DNA hybridization detection. Interestingly, having a greater DNA probe dispersion in the 3D matrix does not induce a higher DNA hybridization efficiency. In a study of protein binding to immobilized DNA (estrogen receptor to estrogen response elements), aiming at assessing the DNA sequence dependent protein binding behavior, the 2D and 3D chips produce different binding characteristics. On the 2D chip, the protein binding exhibits a better selectivity to the specific sequences, regardless of binding stringency (e.g. salt concentration), whereas on the 3D chip, the liquid handling system needs to be optimized in order to minimize transport limitations and to detect small affinity differences. Through this study we demonstrate that the physicochemical structure of SPR chips affects the apparent binding behaviors of biomolecules. When interpreting SPR binding curves and selecting a sensor chip, these effects should be taken into account.

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Authors+Show Affiliations

Yang N
Department of Materials Science and Engineering, Massachusetts Institute of Technology, United States.
Su X
No affiliation info available
Tjong V
No affiliation info available
Knoll W
No affiliation info available

MeSH

Biosensing TechniquesDNADNA-Binding ProteinsIn Situ HybridizationOligonucleotide Array Sequence AnalysisProtein Array AnalysisSurface Plasmon Resonance

Pub Type(s)

Evaluation Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

17223028

Citation

Yang, Nan, et al. "Evaluation of Two- and Three-dimensional Streptavidin Binding Platforms for Surface Plasmon Resonance Spectroscopy Studies of DNA Hybridization and protein-DNA Binding." Biosensors & Bioelectronics, vol. 22, no. 11, 2007, pp. 2700-6.
Yang N, Su X, Tjong V, et al. Evaluation of two- and three-dimensional streptavidin binding platforms for surface plasmon resonance spectroscopy studies of DNA hybridization and protein-DNA binding. Biosens Bioelectron. 2007;22(11):2700-6.
Yang, N., Su, X., Tjong, V., & Knoll, W. (2007). Evaluation of two- and three-dimensional streptavidin binding platforms for surface plasmon resonance spectroscopy studies of DNA hybridization and protein-DNA binding. Biosensors & Bioelectronics, 22(11), 2700-6.
Yang N, et al. Evaluation of Two- and Three-dimensional Streptavidin Binding Platforms for Surface Plasmon Resonance Spectroscopy Studies of DNA Hybridization and protein-DNA Binding. Biosens Bioelectron. 2007 May 15;22(11):2700-6. PubMed PMID: 17223028.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Evaluation of two- and three-dimensional streptavidin binding platforms for surface plasmon resonance spectroscopy studies of DNA hybridization and protein-DNA binding. AU - Yang,Nan, AU - Su,Xiaodi, AU - Tjong,Vinalia, AU - Knoll,Wolfgang, Y1 - 2007/01/12/ PY - 2006/08/28/received PY - 2006/10/27/revised PY - 2006/11/10/accepted PY - 2007/1/16/pubmed PY - 2007/6/28/medline PY - 2007/1/16/entrez SP - 2700 EP - 6 JF - Biosensors & bioelectronics JO - Biosens Bioelectron VL - 22 IS - 11 N2 - Surface plasmon resonance (SPR) spectroscopy has been used to study DNA assembly, DNA hybridization, and protein-DNA interactions on two streptavidin (SA) sensor chips. On one chip, SA molecules are immobilized on a biotin-exposed surface, forming an ordered two-dimensional (2D) SA monolayer. The other chip, BIAcore's SA chip, contains SA molecules immobilized within a three-dimensional (3D) carboxylated dextran matrix. Compared to the 2D chip, the 3D SA matrix allows for a slower immobilization rate of biotinylated DNA due to diffusion limitation in the dextran matrix, but with twice the amount of the immobilized DNA due to the greater number of reactive sites, which in turn enables a higher sensitivity for DNA hybridization detection. Interestingly, having a greater DNA probe dispersion in the 3D matrix does not induce a higher DNA hybridization efficiency. In a study of protein binding to immobilized DNA (estrogen receptor to estrogen response elements), aiming at assessing the DNA sequence dependent protein binding behavior, the 2D and 3D chips produce different binding characteristics. On the 2D chip, the protein binding exhibits a better selectivity to the specific sequences, regardless of binding stringency (e.g. salt concentration), whereas on the 3D chip, the liquid handling system needs to be optimized in order to minimize transport limitations and to detect small affinity differences. Through this study we demonstrate that the physicochemical structure of SPR chips affects the apparent binding behaviors of biomolecules. When interpreting SPR binding curves and selecting a sensor chip, these effects should be taken into account. SN - 0956-5663 UR - https://www.unboundmedicine.com/medline/citation/17223028/Evaluation_of_two__and_three_dimensional_streptavidin_binding_platforms_for_surface_plasmon_resonance_spectroscopy_studies_of_DNA_hybridization_and_protein_DNA_binding_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0956-5663(06)00547-1 DB - PRIME DP - Unbound Medicine ER -