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International Conference on Mathematical Biology and

Annual Meeting of The Society for Mathematical Biology,

July 27-30, 2009

University of British Columbia, Vancouver

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Program

Poster PS31B
Laleh Samii
Simon Fraser University
Title “Studying the biased motion and motor properties of molecular spiders on a 1D track”
Abstract The purpose of our work is to understand how “molecular spiders” function. Molecular spiders are synthetic molecular walkers where each leg consists of a deoxyribozyme, a single-stranded DNA catalyst. The deoxyribozyme leg interacts with its substrate, a partially complementary ssDNA, through binding and cleavage. Experimental studies suggest the motion of the spider is biased towards uncleaved substrates (Pei et al., 2005). Inspired by experimental results for molecular spiders, we perform Monte Carlo simulation studies of a bipedal spider moving with an inchworm (IW) or a hand-over-hand (HOH) stepping mechanism on a 1D lattice. Each lattice site represents the substrate to be cleaved and can be in one of two states: cleaved or uncleaved. Binding, unbinding and substrate cleavage by the enzyme are controlled by rate constants in a simple kinetic model for the interaction of a deoxyribozyme leg with its substrate. The transitions between these biochemical states are Markovian processes and use the Gillespie algorithm to numerically simulate our kinetic model. This algorithm determines which transition in our kinetic model is going to take place first and how long this transition takes. We focus on the following central issues for the molecular spider: (a) the biased motion of IW and HOH spiders; (b) the effect of track properties on biased motion; (c) the memory effect (role of conversion of substrate to product by cleavage); (d) the processivity (number of cleavage events before spider detachment); (e) the mechanochemical coupling of IW and HOH spiders; and (f) the force-velocity relationship for molecular spiders. Our investigation shows that the biased motion of spiders depends on track properties as well as on stepping mechanisms. In addition, a “memory effect” or cleavage of the substrate plays a significant role in the biased motion of spiders.
CoauthorsLaleh Samii, Heiner Linke, Martin J. Zuckermann,Nancy R. Forde
LocationWoodward Lobby (Wednesday-Thursday)