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Effects of Central Loop Length and Metal Ions on the Thermal Stability of G-Quadruplexes

Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
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Author to whom correspondence should be addressed.
Molecules 2019, 24(10), 1863; https://doi.org/10.3390/molecules24101863
Received: 14 April 2019 / Revised: 4 May 2019 / Accepted: 7 May 2019 / Published: 15 May 2019
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Abstract

The central loop of G-quadruplex molecular beacons is a key element to sense target DNA or RNA sequences. In this study, circular dichroism spectroscopy (CD), thermal difference spectrum (TDS), non-denatured non-denaturing gel electrophoresis, and thermal stability analysis were used to investigate the effect of the central loop length on G-quadruplex features. Two series of G-quadruplexes, AG3TTAG3-(TTA)n-G3TTAG3T (n = 1–8) (named TTA series) and AG3TTTG3-(TTA)n-G3TTTG3T (n = 1–8) (named TTT series) were examined in K+ and Na+ solutions, respectively. CD and TDS spectral data indicated that TTA series adopted an antiparallel G-quadruplex structure in Na+ solution and a hybrid G-quadruplex structure in K+ solution respectively. TTT series exhibited a hybrid G-quadruplex structure in both Na+ and K+ solutions. UV melting curves indicated that the stability of G-quadruplex in both series was reduced by the elongation of central loop. Thermal stability analysis concluded that the G-quadruplex destabilization with long central loop is an entropy-driven process due to more flexible and longer central loops. View Full-Text
Keywords: G-quadruplex; central loop length; thermal stability; entropy-driven; ionic effect G-quadruplex; central loop length; thermal stability; entropy-driven; ionic effect
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Hao, F.; Ma, Y.; Guan, Y. Effects of Central Loop Length and Metal Ions on the Thermal Stability of G-Quadruplexes. Molecules 2019, 24, 1863.

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