Derivation of nearest-neighbor DNA parameters in magnesium from single molecule experiments
Author
Huguet Casades, Josep Maria
Ribezzi-Crivellari, Marco
Valim Bizarro, Cristiano
Ritort, Felix
Publication date
2017ISSN
0305-1048
Abstract
DNA hybridization is an essential molecular reaction in biology with many applications. The nearest-neighbor (NN) model for nucleic acids predicts DNA thermodynamics using energy values for the different base pair motifs. These values have been derived from melting experiments in monovalent and divalent salt and applied to predict melting temperatures of oligos within a few degrees. However, an improved determination of the NN energy values and their salt dependencies in magnesium is still needed for current biotechnological applications seeking high selectivity in the hybridization of synthetic DNAs. We developed a methodology based on single molecule unzipping experiments to derive accurate NN energy values and initiation factors for DNA. A new set of values in magnesium is derived, which reproduces unzipping data and improves melting temperature predictions for all available oligo lengths, in a range of temperature and salt conditions where correlation effects between the magnesium bound ions are weak. The NN salt correction parameters are shown to correlate to the GC content of the NN motifs. Our study shows the power of single-molecule force spectroscopy assays to unravel novel features of nucleic acids such as sequence-dependent salt corrections.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
57 - Biological sciences in general
Keywords
Biologia
Biología
Biology
Pages
10
Publisher
Oxford University Press
Collection
45; 22
Is part of
Nucleic Acids Research
Citation
Huguet Casades, Josep Maria; Ribezzi-Crivellari, Marco; Valim Bizarro, Cristiano [et al.]. Derivation of nearest-neighbor DNA parameters in magnesium from single molecule experiments. Nucleic Acids Research, 2017, 45(22), p. 12921–12931. Disponible en: <https://academic.oup.com/nar/article/45/22/12921/4643374?login=true>. Fecha de acceso: 15 mar. 2024. DOI: 10.1093/nar/gkx1161
This item appears in the following Collection(s)
- Ciències Bàsiques [65]
Rights
© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by-nc/4.0/