Stretching DNA to twice the normal length with single-molecule hydrodynamic trapping

Yan Jiang, Theodore Feldman, Julia A.M. Bakx, Darren Yang, Wesley P. Wong*

*Corresponding author for this work

Research output: Contribution to JournalArticleAcademicpeer-review


Single-molecule force spectroscopy has brought many new insights into nanoscale biology, from the functioning of molecular motors to the mechanical response of soft materials within the cell. To expand the single-molecule toolbox, we have developed a surface-free force spectroscopy assay based on a high-speed hydrodynamic trap capable of applying extremely high tensions for long periods of time. High-speed single-molecule trapping is enabled by a rigid and gas-impermeable microfluidic chip, rapidly and inexpensively fabricated out of glass, double-sided tape and UV-curable adhesive. Our approach does not require difficult covalent attachment chemistries, and enables simultaneous force application and single-molecule fluorescence. Using this approach, we have induced a highly extended state with twice the contour length of B-DNA in regions of partially intercalated double-stranded (dsDNA) by applying forces up to 250 pN. This highly extended state resembles the hyperstretched state of dsDNA, which was initially discovered as a structure fully intercalated by dyes under high tension. It has been hypothesized that hyperstretched DNA could also be induced without the aid of intercalators if high-enough forces were applied, which matches our observation. Combining force application with single-molecule fluorescence imaging is critical for distinguishing hyperstretched DNA from single-stranded DNA that can result from peeling. High-speed hydrodynamic trapping is a powerful yet accessible force spectroscopy method that enables the mechanics of biomolecules to be probed in previously difficult to access regimes.

Original languageEnglish
Pages (from-to)1780-1791
Number of pages12
JournalLab on a Chip
Issue number10
Publication statusPublished - 21 May 2020


We acknowledge help from the microfluidic prototyping facilities in Wyss Institute for Biologically Inspired Engineering on fabricating the microfluidic chip. We are also grateful to James Pelletier, the MIT Media Lab, and the Microfluidics Core Facility at Harvard Medical for their help in fabricating early versions of the microfluidic chip. This work was supported by the National Science Foundation Graduate Research Fellowship DGE-1144152 (D. Y.), NIH NIGMS R35 GM119537 (W. P. W.), and internal support from the Wyss Institute at Harvard.

FundersFunder number
Wyss Institute at Harvard
National Science FoundationDGE-1144152
National Institute of General Medical SciencesR35GM119537
MIT Media Lab


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