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Single‐Walled Carbon Nanotubes as Scaffolds to Concentrate DNA for the Study of DNA–Protein Interactions
Author(s) -
Liu Zunfeng,
Galli Federica,
Waterreus WillemJan,
Meulenbroek Elisabeth,
Koning Roman I.,
Lamers Gerda E. M.,
Olsthoorn René C. L.,
Pannu Navraj,
Oosterkamp Tjerk. H.,
Koster Abraham J.,
Dame Remus T.,
Abrahams Jan Pieter
Publication year - 2012
Publication title -
chemphyschem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.016
H-Index - 140
eISSN - 1439-7641
pISSN - 1439-4235
DOI - 10.1002/cphc.201100896
Subject(s) - streptavidin , dna , carbon nanotube , chemistry , biophysics , tetramer , histone , escherichia coli , nanotechnology , biotin , biochemistry , materials science , biology , gene , enzyme
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.