Single-Walled Carbon Nanotubes as Scaffolds to Concentrate DNA for the Study of DNA–Protein Interactions

Authors

  • Dr. Zunfeng Liu,

    Corresponding author
    1. Gorlaeus Laboratory, Leiden Institute of Chemistry, Leiden University, 2300RA Leiden (The Netherlands), Fax: (+31) 071 527 4357
    • Gorlaeus Laboratory, Leiden Institute of Chemistry, Leiden University, 2300RA Leiden (The Netherlands), Fax: (+31) 071 527 4357
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  • Dr. Federica Galli,

    1. Leiden Institute of Physics, Leiden University, 2333CA Leiden (The Netherlands)
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  • Dr. Willem-Jan Waterreus,

    1. Gorlaeus Laboratory, Leiden Institute of Chemistry, Leiden University, 2300RA Leiden (The Netherlands), Fax: (+31) 071 527 4357
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  • Dr. Elisabeth Meulenbroek,

    1. Gorlaeus Laboratory, Leiden Institute of Chemistry, Leiden University, 2300RA Leiden (The Netherlands), Fax: (+31) 071 527 4357
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  • Dr. Roman I. Koning,

    1. Department of Molecular Cell Biology Section Electron Microscopy, Leiden University Medical Center, 2300 RC Leiden (The Netherlands)
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  • Dr. Gerda E. M. Lamers,

    1. Institute Biology,Leiden University, 2333 BE Leiden (The Netherlands)
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  • Dr. René C. L. Olsthoorn,

    1. Gorlaeus Laboratory, Leiden Institute of Chemistry, Leiden University, 2300RA Leiden (The Netherlands), Fax: (+31) 071 527 4357
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  • Prof. Navraj Pannu,

    1. Gorlaeus Laboratory, Leiden Institute of Chemistry, Leiden University, 2300RA Leiden (The Netherlands), Fax: (+31) 071 527 4357
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  • Prof. Tjerk. H. Oosterkamp,

    1. Leiden Institute of Physics, Leiden University, 2333CA Leiden (The Netherlands)
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  • Prof. Abraham J. Koster,

    1. Department of Molecular Cell Biology Section Electron Microscopy, Leiden University Medical Center, 2300 RC Leiden (The Netherlands)
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  • Dr. Remus T. Dame,

    Corresponding author
    1. Gorlaeus Laboratory, Leiden Institute of Chemistry, Leiden University, 2300RA Leiden (The Netherlands), Fax: (+31) 071 527 4357
    • Gorlaeus Laboratory, Leiden Institute of Chemistry, Leiden University, 2300RA Leiden (The Netherlands), Fax: (+31) 071 527 4357
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  • Prof. Jan Pieter Abrahams

    Corresponding author
    1. Gorlaeus Laboratory, Leiden Institute of Chemistry, Leiden University, 2300RA Leiden (The Netherlands), Fax: (+31) 071 527 4357
    • Gorlaeus Laboratory, Leiden Institute of Chemistry, Leiden University, 2300RA Leiden (The Netherlands), Fax: (+31) 071 527 4357
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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 (StrepSWNTs) 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 StrepSWNTs 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.

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