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Article

Tracking Topological and Electronic Effects on the Folding and Stability of Guanine-Deficient RNA G-Quadruplexes, Engineered with a New Computational Tool for De Novo Quadruplex Folding

1
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
2
Faculty of Chemistry, Biological & Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
3
Faculty of Chemical and Process Engineering, Warsaw University of Technology, Waryńskiego 1, 00-645 Warsaw, Poland
4
Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
5
Molecure SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
*
Author to whom correspondence should be addressed.
Academic Editor: Mark Andrew White
Int. J. Mol. Sci. 2022, 23(19), 10990; https://doi.org/10.3390/ijms231910990
Received: 29 July 2022 / Revised: 9 September 2022 / Accepted: 13 September 2022 / Published: 20 September 2022
(This article belongs to the Section Molecular Informatics)
The initial aim of this work was to elucidate the mutual influence of different single-stranded segments (loops and caps) on the thermodynamic stability of RNA G-quadruplexes. To this end, we used a new NAB-GQ-builder software program, to construct dozens of two-tetrad G-quadruplex topologies, based on a designed library of sequences. Then, to probe the sequence–morphology–stability relationships of the designed topologies, we performed molecular dynamics simulations. Their results provide guidance for the design of G-quadruplexes with balanced structures, and in turn programmable physicochemical properties for applications as biomaterials. Moreover, by comparative examinations of the single-stranded segments of three oncogene promoter G-quadruplexes, we assess their druggability potential for future therapeutic strategies. Finally, on the basis of a thorough analysis at the quantum mechanical level of theory on a series of guanine assemblies, we demonstrate how a valence tautomerism, triggered by a coordination of cations, initiates the process of G-quadruplex folding, and we propose a sequential folding mechanism, otherwise dictated by the cancellation of the dipole moments on guanines. View Full-Text
Keywords: RNA G-quadruplex folding; RNA—cation interactions; valence tautomerism; de novo RNA modelling; RNA G-quadruplex stabilization RNA G-quadruplex folding; RNA—cation interactions; valence tautomerism; de novo RNA modelling; RNA G-quadruplex stabilization
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MDPI and ACS Style

Göç, Y.B.; Poziemski, J.; Smolińska, W.; Suwała, D.; Wieczorek, G.; Niedzialek, D. Tracking Topological and Electronic Effects on the Folding and Stability of Guanine-Deficient RNA G-Quadruplexes, Engineered with a New Computational Tool for De Novo Quadruplex Folding. Int. J. Mol. Sci. 2022, 23, 10990. https://doi.org/10.3390/ijms231910990

AMA Style

Göç YB, Poziemski J, Smolińska W, Suwała D, Wieczorek G, Niedzialek D. Tracking Topological and Electronic Effects on the Folding and Stability of Guanine-Deficient RNA G-Quadruplexes, Engineered with a New Computational Tool for De Novo Quadruplex Folding. International Journal of Molecular Sciences. 2022; 23(19):10990. https://doi.org/10.3390/ijms231910990

Chicago/Turabian Style

Göç, Yavuz Burak, Jakub Poziemski, Weronika Smolińska, Dominik Suwała, Grzegorz Wieczorek, and Dorota Niedzialek. 2022. "Tracking Topological and Electronic Effects on the Folding and Stability of Guanine-Deficient RNA G-Quadruplexes, Engineered with a New Computational Tool for De Novo Quadruplex Folding" International Journal of Molecular Sciences 23, no. 19: 10990. https://doi.org/10.3390/ijms231910990

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