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Emergent Properties and Functions of Nanoconfined Nucleic Acid Architectures

  • Chapter
RNA and DNA Diagnostics

Part of the book series: RNA Technologies ((RNATECHN))

Abstract

The facile ability of DNA to self-assemble has enabled the creation of complex architectures with diverse functions on surfaces or in solution. This approach provides a powerful design tool for the development of nanoscale devices with transformative applications in multiple areas, including the detection of complex biomolecules, drug delivery, and in situ biomolecular synthesis. However, little is known of the effect of confinement on the function of complex nucleic acid architectures, which exhibit unanticipated behaviors that presumably reflect high-level molecular crowding. In this chapter, we review selected recent studies that describe the application and atypical behaviors of nanoconfined nucleic acids, in particular with respect to hybridization, denaturation, conformation, stability, and enzyme accessibility. We argue that the novel behavior of dense nucleic acid arrays naturally emerge as a result of immobilization and reduction in spatial degrees of freedom. We summarize by emphasizing the need for basic physical–chemical studies of dense nucleic acid architectures, involving an interplay of experimental and theoretical approaches, in order to effectively guide the successful technological development of nucleic acid nanodevices.

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Acknowledgments

Studies in the authors’ laboratories were supported in part by the College of Science and Technology of Temple University (A.W.N., S.K.R., V.C., and M.C.), the NIH (RO1-GM56772) (A.W.N), and the European Research Council (Grant ERC Ideas 2010 n. 269051-Monalisa’s Quidproquo) (A.S., L.C., and M.C.).

Competing Financial Interests

The authors declare no competing financial interests.

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Authors and Affiliations

  1. Department of Biology, Temple University, 1900 North 12th Street, Philadelphia, PA, 19122, USA

    Allen W. Nicholson, Shiv K. Redhu, Vincenzo Carnevale & Matteo Castronovo

  2. Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, PA, 19122, USA

    Allen W. Nicholson

  3. Ph.D. School of Nanotechnology, University of Trieste, Trieste, Italy

    Alex Stopar & Lucia Coral

  4. Department of Biological and Medical Sciences, University of Udine, Piazzale Kolbe 4, Udine, Italy

    Alex Stopar & Lucia Coral

  5. Institute for Computational Molecular Science, Temple University, 1925 North 12th Street, Philadelphia, PA, 19122, USA

    Vincenzo Carnevale

  6. Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe 2, 33100, Udine, Italy

    Matteo Castronovo

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  1. Allen W. Nicholson
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  2. Shiv K. Redhu
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  3. Alex Stopar
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  4. Lucia Coral
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  5. Vincenzo Carnevale
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  6. Matteo Castronovo
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Correspondence to Matteo Castronovo .

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Editors and Affiliations

  1. Free University of Berlin Institute of Chemistry/Biochemistry, Thielallee 63, Berlin, Germany

    Volker A. Erdmann

  2. Nanobiomedical Center, Adam Mickiewicz University, Umultowska 85 Poznań, Poland

    Stefan Jurga

  3. Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Z. Noskowskiego 12/14 Poznań, Poland

    Jan Barciszewski

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Nicholson, A.W., Redhu, S.K., Stopar, A., Coral, L., Carnevale, V., Castronovo, M. (2015). Emergent Properties and Functions of Nanoconfined Nucleic Acid Architectures. In: Erdmann, V., Jurga, S., Barciszewski, J. (eds) RNA and DNA Diagnostics. RNA Technologies. Springer, Cham. https://doi.org/10.1007/978-3-319-17305-4_9

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