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Abstract 2D nanoslit devices, where two crystals with atomically flat surfaces are separated by only a few nanometers, have attracted considerable attention because their tunable control over the confinement allows for the discovery of unusual transport behavior of gas, water, and ions. Here, the passage of double‐stranded DNA molecules is studied through nanoslits fabricated from exfoliated 2D materials, such as graphene or hexagonal boron nitride, and the DNA polymer behavior is examined in this tight confinement. Two types of events are observed in the ionic current: long current blockades that signal DNA translocation and short spikes where DNA enters the slits but withdraws. DNA translocation events exhibit three distinct phases in their current‐blockade traces—loading, translation, and exit. Coarse‐grained molecular dynamics simulation allows the different polymer configurations of these phases to be identified. DNA molecules, including folds and knots in their polymer structure, are observed to slide through the slits with near‐uniform velocity without noticeable frictional interactions of DNA with the confining graphene surfaces. It is anticipated that this new class of 2D‐nanoslit devices will provide unique ways to study polymer physics and enable lab‐on‐a‐chip biotechnology.
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Role of DNA–DNA sliding friction and nonequilibrium dynamics in viral genome ejection and packaging
Abstract Many viruses eject their DNA via a nanochannel in the viral shell, driven by internal forces arising from the high-density genome packing. The speed of DNA exit is controlled by friction forces that limit the molecular mobility, but the nature of this friction is unknown. We introduce a method to probe the mobility of the tightly confined DNA by measuring DNA exit from phage phi29 capsids with optical tweezers. We measure extremely low initial exit velocity, a regime of exponentially increasing velocity, stochastic pausing that dominates the kinetics and large dynamic heterogeneity. Measurements with variable applied force provide evidence that the initial velocity is controlled by DNA–DNA sliding friction, consistent with a Frenkel–Kontorova model for nanoscale friction. We confirm several aspects of the ejection dynamics predicted by theoretical models. Features of the pausing suggest that it is connected to the phenomenon of ‘clogging’ in soft matter systems. Our results provide evidence that DNA–DNA friction and clogging control the DNA exit dynamics, but that this friction does not significantly affect DNA packaging.
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- Award ID(s):
- 1716219
- PAR ID:
- 10431622
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Nucleic Acids Research
- Volume:
- 51
- Issue:
- 15
- ISSN:
- 0305-1048
- Page Range / eLocation ID:
- p. 8060-8069
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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