title: Single-walled carbon nanotubes as scaffolds to concentrate DNA for the study of DNA-protein interactions.
abstract: 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.
authors.affiliation: Gorlaeus Laboratory, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands. liuz2@chem.leidenuniv.nl
authors.forename: Zunfeng
authors.initials: Z
authors.lastname: Liu
authors.forename: Federica
authors.initials: F
authors.lastname: Galli
authors.forename: Willem-Jan
authors.initials: WJ
authors.lastname: Waterreus
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Meulenbroek
authors.forename: Roman I
authors.initials: RI
authors.lastname: Koning
authors.forename: Gerda E M
authors.initials: GE
authors.lastname: Lamers
authors.forename: René C L
authors.initials: RC
authors.lastname: Olsthoorn
authors.forename: Navraj
authors.initials: N
authors.lastname: Pannu
authors.forename: Tjerk H
authors.initials: TH
authors.lastname: Oosterkamp
authors.forename: Abraham J
authors.initials: AJ
authors.lastname: Koster
authors.forename: Remus T
authors.initials: RT
authors.lastname: Dame
authors.forename: Jan Pieter
authors.initials: JP
authors.lastname: Abrahams
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry; D002352:Carrier Proteins / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry; D037742:Nanotubes, Carbon / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D002352:Carrier Proteins; D004268:DNA-Binding Proteins; D037742:Nanotubes, Carbon; D011506:Proteins; C040330:histone-like protein HU, bacteria; C452700:streptavidin-binding peptide; D004247:DNA