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Two-dimensional enzyme diffusion in laterally confined DNA monolayers

2011; Nature Portfolio; Volume: 2; Issue: 1 Linguagem: Inglês

10.1038/ncomms1296

2041-1723

Matteo Castronovo, Agnese Lucesoli, Pietro Parisse, Anastasia Kurnikova, Aseem Malhotra, Mario Grassi, Gabriele Grassi, Bruna Scaggiante, Loredana Casalis, G. Scoles,

RNA Interference and Gene Delivery

Addressing the effects of confinement and crowding on biomolecular function may provide insight into molecular mechanisms within living organisms, and may promote the development of novel biotechnology tools. Here, using molecular manipulation methods, we investigate restriction enzyme reactions with double-stranded (ds)DNA oligomers confined in relatively large (and flat) brushy matrices of monolayer patches of controlled, variable density. We show that enzymes from the contacting solution cannot access the dsDNAs from the top-matrix interface, and instead enter at the matrix sides to diffuse two-dimensionally in the gap between top- and bottom-matrix interfaces. This is achieved by limiting lateral access with a barrier made of high-density molecules that arrest enzyme diffusion. We put forward, as a possible explanation, a simple and general model that relates these data to the steric hindrance in the matrix, and we briefly discuss the implications and applications of this strikingly new phenomenon. Little is known about the effects of molecular crowding and confinement on biomolecule function. Castronovoet al. investigate the reactions of restriction enzymes with DNA confined in bushy matrices and find that the enzymes enter at the side of the matrix before diffusing two-dimensionally.