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Int. J. Mol. Sci. 2016, 17(2), 211; doi:10.3390/ijms17020211

The Effect of Small Cosolutes that Mimic Molecular Crowding Conditions on the Stability of Triplexes Involving Duplex DNA

1
Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, Barcelona 08034, Spain
2
Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, Barcelona 08034, Spain
3
Department of Food, Environmental and Nutritional Sciences (DEFENS), Section of Chemical and Biomolecular Sciences, University of Milan, Via Celoria 2, Milan 20133, Italy
4
Department of Analytical Chemistry, University of Barcelona, Martí i Franquès, 1-11, Barcelona 08028, Spain
*
Author to whom correspondence should be addressed.
Academic Editor: Malcolm D´Souza
Received: 2 October 2015 / Revised: 20 January 2016 / Accepted: 27 January 2016 / Published: 5 February 2016
(This article belongs to the Special Issue Solution Chemical Kinetics)
View Full-Text   |   Download PDF [1084 KB, uploaded 5 February 2016]   |  

Abstract

Triplex stability is studied in crowding conditions using small cosolutes (ethanol, acetonitrile and dimethylsulfoxide) by ultraviolet (UV), circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopies. The results indicate that the triplex is formed preferentially when the triplex forming oligonucleotide (TFO) is RNA. In addition, DNA triplexes (D:D·D) are clearly less stable in cosolute solutions while the stability of the RNA triplexes (R:D·D) is only slightly decreased. The kinetic of triplex formation with RNA-TFO is slower than with DNA-TFO and the thermal stability of the triplex is increased with the salt concentration in EtOH-water solutions. Accordingly, RNA could be considered a potential molecule to form a stable triplex for regulatory purposes in molecular crowding conditions. View Full-Text
Keywords: molecular crowding; triplex forming oligonucleotide (TFO); DNA; RNA; cosolute; thermal stability molecular crowding; triplex forming oligonucleotide (TFO); DNA; RNA; cosolute; thermal stability
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Aviñó, A.; Mazzini, S.; Gargallo, R.; Eritja, R. The Effect of Small Cosolutes that Mimic Molecular Crowding Conditions on the Stability of Triplexes Involving Duplex DNA. Int. J. Mol. Sci. 2016, 17, 211.

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