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Two-dimensional enzyme diffusion in laterally confined DNA monolayers

Author

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  • Matteo Castronovo

    (Temple University, 1900 North 12th Street, Philadelphia, Philadelphia 19122, USA.
    Cluster in Biomolecular Medicine - CBM S.c.r.l, Area Science Park, S.S. 14 km 163.5, I-34149 Basovizza, Trieste, Italy.)

  • Agnese Lucesoli

    (Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 256, I-34136, Trieste, Italy.
    Italian Institute of Technology (IIT) - SISSA Unit
    Present addresses: Hospital San Salvatore, I-61121, Pesaro, Italy (A.L.); National Institute of Health, 49 Convent Drive, Bethesda, Maryland 20892, USA (A.K.); Centro Interdipartimentale di Medicina Rigenerativa (CIME), University of Udine, p.le Kolbe 4, 33100 Udine, Italy; Experimental and Clinical Pharmacology Unit, CRO-National Cancer Institute, Via Franco Gallini 2, I-33081 Aviano, Pordenone, Italy (G.S.).)

  • 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.
    Present addresses: Hospital San Salvatore, I-61121, Pesaro, Italy (A.L.); National Institute of Health, 49 Convent Drive, Bethesda, Maryland 20892, USA (A.K.); Centro Interdipartimentale di Medicina Rigenerativa (CIME), University of Udine, p.le Kolbe 4, 33100 Udine, Italy; Experimental and Clinical Pharmacology Unit, CRO-National Cancer Institute, Via Franco Gallini 2, I-33081 Aviano, Pordenone, Italy (G.S.).)

  • 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.
    Technological and Translational Sciences, University Hospital of Cattinara, I-34149, Trieste, Italy.)

  • Bruna Scaggiante

    (University of Trieste, Via L. Giorgeri 1, I-34127, Trieste, Italy.)

  • Loredana Casalis

    (Italian Institute of Technology (IIT) - SISSA Unit
    Sincrotrone Trieste S.C.p.A, S.S. 14 km 163.5, I-34149 Basovizza, Trieste, Italy.)

  • Giacinto Scoles

    (Temple University, 1900 North 12th Street, Philadelphia, Philadelphia 19122, USA.
    Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 256, I-34136, Trieste, Italy.
    Italian Institute of Technology (IIT) - SISSA Unit
    Sincrotrone Trieste S.C.p.A, S.S. 14 km 163.5, I-34149 Basovizza, Trieste, Italy.)

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.

Suggested Citation

  • Matteo Castronovo & Agnese Lucesoli & Pietro Parisse & Anastasia Kurnikova & Aseem Malhotra & Mario Grassi & Gabriele Grassi & Bruna Scaggiante & Loredana Casalis & Giacinto Scoles, 2011. "Two-dimensional enzyme diffusion in laterally confined DNA monolayers," Nature Communications, Nature, vol. 2(1), pages 1-10, September.
    • Handle: RePEc:nat:natcom:v:2:y:2011:i:1:d:10.1038_ncomms1296
    DOI: 10.1038/ncomms1296
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