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Constructing Free Energy Landscapes of Nucleic Acid Hairpin Unfolding

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DNA Nanotechnology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1811))

Abstract

Single nucleic acid molecules form hairpins that may stabilize secondary and tertiary structures as well as perform enzymatic and other chemical functions. Considerable progress has been made in the effort to understand the contributions of various factors to the stability of a given hairpin sequence. For a given sequence, it is possible to compute both the most likely structural arrangements and their associated free energies over a range of experimental conditions. However, there are many observed hairpin irregularities for which the energies and function are not well understood. Here we examine the irregular RNA Transactivation Response (TAR) hairpin from the HIV-1 genome. Using single molecule optical tweezers, the hairpin is force unfolded, revealing the overall unfolding free energy and the character of the transition state. These measurements allow the construction of a simple energy landscape from unfolding measurements, which can be directly compared to a theoretical landscape. This method is easily adapted to other structures, including the effects of noncanonical bases and even ligand binding.

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Acknowledgments

This work was supported by grants NIH GM072462 and NSF MCB-1243883 to M.C.W.

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Authors and Affiliations

  1. Department of Physics, Northeastern University, Boston, MA, USA

    Micah J. McCauley & Mark C. Williams

  2. Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA

    Ioulia Rouzina

Authors
  1. Micah J. McCauley
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  2. Ioulia Rouzina
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  3. Mark C. Williams
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Corresponding author

Correspondence to Mark C. Williams .

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Editors and Affiliations

  1. Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy

    Giampaolo Zuccheri

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McCauley, M.J., Rouzina, I., Williams, M.C. (2018). Constructing Free Energy Landscapes of Nucleic Acid Hairpin Unfolding. In: Zuccheri, G. (eds) DNA Nanotechnology. Methods in Molecular Biology, vol 1811. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8582-1_21

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  • DOI: https://doi.org/10.1007/978-1-4939-8582-1_21

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8581-4

  • Online ISBN: 978-1-4939-8582-1

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