Real-time compaction of nanoconfined DNA by an intrinsically disordered macromolecular counterion
Journal article, 2020

We demonstrate how a recently developed nanofluidic device can be used to study protein-induced compaction of genome-length DNA freely suspended in solution. The protein we use in this study is the hepatitis C virus core protein (HCVcp), which is a positively charged, intrinsically disordered protein. Using nanofluidic devices in combination with fluorescence microscopy, we observe that protein-induced compaction preferentially begins at the ends of linear DNA. This observation would be difficult to make with many other single-molecule techniques, which generally require the DNA ends to be anchored to a substrate. We also demonstrate that this protein-induced compaction is reversible and can be dynamically modulated by exposing the confined DNA molecules to solutions containing either HCVcp (to promote compaction) or Proteinase K (to disassemble the compact nucleo-protein complex). Although the natural binding partner for HCVcp is genomic viral RNA, the general biophysical principles governing protein-induced compaction of DNA are likely relevant for a broad range of nucleic acid-binding proteins and their targets.

Nanofluidic device

Protein-DNA interaction

DNA condensation and compaction

Hepatitis C virus core protein

Macromolecular counterion

Intrinsically disordered protein


Rajhans Sharma

Chalmers, Biology and Biological Engineering, Chemical Biology

Sriram Kesarimangalam

Chalmers, Biology and Biological Engineering, Chemical Biology

Erik D. Holmstrom

University of Kansas

Fredrik Westerlund

Chalmers, Biology and Biological Engineering, Chemical Biology

Biochemical and Biophysical Research Communications

0006-291X (ISSN) 1090-2104 (eISSN)

Vol. 533 1 175-180

Areas of Advance

Nanoscience and Nanotechnology

Subject Categories

Biochemistry and Molecular Biology


Structural Biology





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