Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors
File(s)rupture_ACSNano (1).pdf (4.04 MB)
Accepted version
Author(s)
Mosayebi, M
Louis, AA
Doye, JPK
Ouldridge, TE
Type
Journal Article
Abstract
The rupture of double-stranded DNA under stress is a key process in biophysics
and nanotechnology. In this article, we consider the shear-induced rupture of short DNA
duplexes, a system that has been given new importance by recently designed force sensors
and nanotechnological devices. We argue that rupture must be understood as an activated
process, where the duplex state is metastable and the strands will separate in a finite time
that depends on the duplex length and the force applied. Thus, the critical shearing force
required to rupture a duplex depends strongly on the time scale of observation. We use simple
models of DNA to show that this approach naturally captures the observed dependence of
the force required to rupture a duplex within a given time on duplex length. In particular, this
critical force is zero for the shortest duplexes, before rising sharply and then plateauing in the
long length limit. The prevailing approach, based on identifying when the presence of each
additional base pair within the duplex is thermodynamically unfavorable rather than allowing for metastability, does not predict a time-scale-dependent
critical force and does not naturally incorporate a critical force of zero for the shortest duplexes. We demonstrate that our findings have important
consequences for the behavior of a new force-sensing nanodevice, which operates in a mixed mode that interpolates between shearing and unzipping.
At a fixed time scale and duplex length, the critical force exhibits a sigmoidal dependence on the fraction of the duplex that is subject to shearing.
and nanotechnology. In this article, we consider the shear-induced rupture of short DNA
duplexes, a system that has been given new importance by recently designed force sensors
and nanotechnological devices. We argue that rupture must be understood as an activated
process, where the duplex state is metastable and the strands will separate in a finite time
that depends on the duplex length and the force applied. Thus, the critical shearing force
required to rupture a duplex depends strongly on the time scale of observation. We use simple
models of DNA to show that this approach naturally captures the observed dependence of
the force required to rupture a duplex within a given time on duplex length. In particular, this
critical force is zero for the shortest duplexes, before rising sharply and then plateauing in the
long length limit. The prevailing approach, based on identifying when the presence of each
additional base pair within the duplex is thermodynamically unfavorable rather than allowing for metastability, does not predict a time-scale-dependent
critical force and does not naturally incorporate a critical force of zero for the shortest duplexes. We demonstrate that our findings have important
consequences for the behavior of a new force-sensing nanodevice, which operates in a mixed mode that interpolates between shearing and unzipping.
At a fixed time scale and duplex length, the critical force exhibits a sigmoidal dependence on the fraction of the duplex that is subject to shearing.
Date Issued
2015-12-01
Date Acceptance
2015-11-17
Citation
ACS Nano, 2015, 9 (12), pp.11993-12003
ISSN
1936-086X
Publisher
American Chemical Society
Start Page
11993
End Page
12003
Journal / Book Title
ACS Nano
Volume
9
Issue
12
Copyright Statement
This document is the Accepted Manuscript version of a Published Work that appeared in final form in ACS Nano, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://dx.doi.org/10.1021/acsnano.5b04726
Subjects
Science & Technology
Physical Sciences
Technology
Chemistry, Multidisciplinary
Chemistry, Physical
Nanoscience & Nanotechnology
Materials Science, Multidisciplinary
Chemistry
Science & Technology - Other Topics
Materials Science
DNA nanotechnology
force spectroscopy
non-equilibrium chemistry
molecular simulation
coarse-grained modeling
DOUBLE HELIX
HYBRIDIZATION KINETICS
SINGLE
DYNAMICS
STRANDS
THERMODYNAMICS
DENATURATION
DISPLACEMENT
SPECTROSCOPY
DEPENDENCE
Publication Status
Published