Single-walled carbon nanotubes as scaffolds to concentrate DNA for the study of DNA-protein interactions

Liu, Zunfeng and Galli, Federica and Waterreus, Willem-Jan and Meulenbroek, Elisabeth and Koning, Roman I. and Lamers, Gerda E. M. and Olsthoorn, René C. L. and Pannu, Navraj and Oosterkamp, Tjerk H. and Koster, Abraham J. and Dame, Remus T. and Abrahams, Jan Pieter. (2012) Single-walled carbon nanotubes as scaffolds to concentrate DNA for the study of DNA-protein interactions. ChemPhysChem, 13 (6). pp. 1569-1575.

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Genomic DNA in bacteria exists in a condensed state, which exhibits different biochemical and biophysical properties from a dilute solution. DNA was concentrated on streptavidin-covered single-walled carbon nanotubes (Strep-SWNTs) through biotin-streptavidin interactions. We reasoned that confining DNA within a defined space through mechanical constraints, rather than by manipulating buffer conditions, would more closely resemble physiological conditions. By ensuring a high streptavidin loading on SWNTs of about 1 streptavidin tetramer per 4 nm of SWNT, we were able to achieve dense DNA binding. DNA is bound to Strep-SWNTs at a tunable density and up to as high as 0.5 mg mL(-1) in solution and 29 mg mL(-1) on a 2D surface. This platform allows us to observe the aggregation behavior of DNA at high concentrations and the counteracting effects of HU protein (a histone-like protein from Escherichia coli strain U93) on the DNA aggregates. This provides an in vitro model for studying DNA-DNA and DNA-protein interactions at a high DNA concentration.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Structural Biology & Biophysics > Nano-diffraction of Biological Specimen (Abrahams)
UniBasel Contributors:Abrahams, Jan Pieter
Item Type:Article, refereed
Article Subtype:Research Article
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:06 Nov 2020 07:53
Deposited On:06 Nov 2020 07:53

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