Two-dimensional enzyme diffusion in laterally confined DNA monolayers

Matteo Castronovo (), Agnese Lucesoli, Pietro Parisse, Anastasia Kurnikova, Aseem Malhotra, Mario Grassi, Gabriele Grassi, Bruna Scaggiante, Loredana Casalis and Giacinto Scoles
Additional contact information
Matteo Castronovo: Temple University, 1900 North 12th Street, Philadelphia, Philadelphia 19122, USA.
Agnese Lucesoli: Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 256, I-34136, Trieste, Italy.
Pietro Parisse: Sincrotrone Trieste S.C.p.A, S.S. 14 km 163.5, I-34149 Basovizza, Trieste, Italy.
Anastasia Kurnikova: Temple University, 1900 North 12th Street, Philadelphia, Philadelphia 19122, USA.
Aseem Malhotra: Temple University, 1900 North 12th Street, Philadelphia, Philadelphia 19122, USA.
Mario Grassi: University of Trieste, Via Valerio 6/4, I-34127, Trieste, Italy.
Gabriele Grassi: University of Trieste, Via L. Giorgeri 1, I-34127, Trieste, Italy.
Bruna Scaggiante: University of Trieste, Via L. Giorgeri 1, I-34127, Trieste, Italy.
Loredana Casalis: Italian Institute of Technology (IIT) - SISSA Unit
Giacinto Scoles: Temple University, 1900 North 12th Street, Philadelphia, Philadelphia 19122, USA.

Nature Communications, 2011, vol. 2, issue 1, 1-10

Abstract: Abstract 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.

Date: 2011
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:2:y:2011:i:1:d:10.1038_ncomms1296

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DOI: 10.1038/ncomms1296

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