A nanofluidic device for real-time visualization of DNA–protein interactions on the single DNA molecule level
Journal article, 2019

Single DNA molecule techniques have revolutionized our understanding of DNA-protein interactions. Traditional techniques for such studies have the major drawback that the DNA molecule studied is attached to a bead or a surface. Stretching of DNA molecules in nanofluidic channels has enabled single-molecule studies of DNA-protein interactions without the need of tethering the molecule to a foreign entity. This in turn allows for studying reactions along the whole extension of the molecule, including the free DNA ends. However, existing studies either rely on measurements where all components are mixed before introduction into the nanochannels or where passive diffusion brings the reagents to the confined DNA molecule. We here present a new generation of nanofluidic devices, where active exchange of the local environment within the nanofluidic channel is possible, while keeping the DNA molecule stretched and in confinement. To demonstrate the functionality of this novel device we added different analytes, such as SDS, spermidine and DNase I, to YOYO-1 stained DNA and studied the response in real time. We also performed a FRET-based reaction, where two different analytes were added sequentially to the same DNA molecule. We believe that this design will enable in situ mapping of complex biochemical processes, involving multiple proteins and cofactors, on single DNA molecules as well as other biomacromolecules.


Robin Öz

Chalmers, Biology and Biological Engineering, Chemical Biology

Sriram Kesarimangalam

Chalmers, Biology and Biological Engineering, Chemical Biology

Fredrik Westerlund

Chalmers, Biology and Biological Engineering, Chemical Biology


2040-3364 (ISSN)

Vol. 11 4 2071-2078

Areas of Advance

Nanoscience and Nanotechnology (SO 2010-2017, EI 2018-)

Subject Categories

Physical Chemistry


Theoretical Chemistry





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