Abstract
Stochastic resonance (SR) is a well-known phenomenon in dynamical systems. It consists of the amplification and optimization of the response of a system assisted by stochastic (random or probabilistic) noise. Here we carry out the first experimental study of SR in single DNA hairpins which exhibit cooperatively transitions from folded to unfolded configurations under the action of an oscillating mechanical force applied with optical tweezers. By varying the frequency of the force oscillation, we investigate the folding and unfolding kinetics of DNA hairpins in a periodically driven bistable free-energy potential. We measure several SR quantifiers under varied conditions of the experimental setup such as trap stiffness and length of the molecular handles used for single-molecule manipulation. We find that a good quantifier of the SR is the signal-to-noise ratio (SNR) of the spectral density of measured fluctuations in molecular extension of the DNA hairpins. The frequency dependence of the SNR exhibits a peak at a frequency value given by the resonance-matching condition. Finally, we carry out experiments on short hairpins that show how SR might be useful for enhancing the detection of conformational molecular transitions of low SNR.Received 14 March 2012DOI:https://doi.org/10.1103/PhysRevX.2.031012This article is available under the terms of the Creative Commons Attribution 3.0 License. Further distribution of this work must maintain attribution to the author(s) and the published article’s title, journal citation, and DOI.Published by the American Physical Society
Highlights
All nonlinear systems that exhibit stochastic noise are susceptible to undergoing stochastic resonance (SR)
In order to extract the signal from the background noise, we define the output signal (OS), the background noise (BN), and the signal-to-noise ratio (SNR) as [12], OS 1⁄4 lim Z osþÁ SðÞd; (2)
If we increase by 20-fold the length of the handles (528 bp and 874 bp at each flanking side) while keeping the trap stiffness constant, trap 1⁄4 70 pN=m, we find that the resonance frequency shifts to a larger value for the long handles (Fig. 3)
Summary
All nonlinear systems that exhibit stochastic (random or probabilistic) noise are susceptible to undergoing stochastic resonance (SR). Beyond affecting thermal and thermally assisted noise, temperature modifies the shape of the molecular free-energy landscape Another tunable parameter such as the oscillation frequency of an applied force might be more appropriate for studying SR in biomolecules. Our primary aim in this work is to perform a systematic study of SR in single molecules exhibiting bistable dynamics, rather than using SR as a useful tool to determine the kinetic properties of DNA hairpins. These can be estimated by using other much less time-consuming methods (e.g., by directly analyzing hopping traces). VIII, we summarize our conclusions and discuss situations in which SR might be a useful technique
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