Paper Citing NAMD - Abstract
McCullagh, Martin; Franco, Ignacio; Ratner, Mark A.; Schatz, George C.
DNA-Based Optomechanical Molecular Motor
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:3452-3459, MAR 16 2011
An azobenzene-capped DNA hairpin coupled to an AFM is presented as an optically triggered single-molecule motor. The photoinduced trans to cis isomerization of azobenzene affects both the overall length of the molecule and the ability of the DNA bases to hybridize. Using a combination of molecular dynamics simulations and free energy calculations the unfolding of both isomers along the O5'-O3' extension coordinate is monitored. The potentials of mean force (PMFs) along this coordinate indicate that there are two major differences induced by photoisomerization. The first is that the interbase hydrogen bond and stacking interactions are stable for a greater range of extensions in the trans system than in the cis system. The second difference is due to a decreased chain length of the cis isomer with respect to the trans isomer. These differences are exploited to extract work in optomechanical cycles. The disruption of the hairpin structure gives a maximum of 3.4 kcal mol(-1) of extractable work per cycle with an estimated maximum efficiency of 2.4%. Structure-function insights into the operation of this motor are provided, and the effect of the cantilever stiffness on the extractable work is characterized.
