title: Two-dimensional enzyme diffusion in laterally confined DNA monolayers.
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.
authors.affiliation: Department of Biology, Temple University, 1900 North 12th Street, Philadelphia, Philadelphia 19122, USA. matteo.castronovo@temple.edu
authors.forename: Matteo
authors.initials: M
authors.lastname: Castronovo
authors.forename: Agnese
authors.initials: A
authors.lastname: Lucesoli
authors.forename: Pietro
authors.initials: P
authors.lastname: Parisse
authors.forename: Anastasia
authors.initials: A
authors.lastname: Kurnikova
authors.forename: Aseem
authors.initials: A
authors.lastname: Malhotra
authors.forename: Mario
authors.initials: M
authors.lastname: Grassi
authors.forename: Gabriele
authors.initials: G
authors.lastname: Grassi
authors.forename: Bruna
authors.initials: B
authors.lastname: Scaggiante
authors.forename: Loredana
authors.initials: L
authors.lastname: Casalis
authors.forename: Giacinto
authors.initials: G
authors.lastname: Scoles
mesh_terms: D004247:DNA / Q000737:chemistry*; D004262:DNA Restriction Enzymes / Q000737:chemistry*; D004058:Diffusion; D013499:Surface Properties
chemical_list: D004247:DNA; D004262:DNA Restriction Enzymes