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Open AccessArticle

Effects of Length and Loop Composition on Structural Diversity and Similarity of (G3TG3NmG3TG3) G-Quadruplexes

Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
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Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Molecules 2020, 25(8), 1779; https://doi.org/10.3390/molecules25081779
Received: 6 March 2020 / Revised: 9 April 2020 / Accepted: 9 April 2020 / Published: 13 April 2020
(This article belongs to the Special Issue Recent Advances of G-Quadruplexes In Vivo and In Vitro)
A G-rich sequence containing three loops to connect four G-tracts with each ≥2 guanines can possibly form G-quadruplex structures. Given that all G-quadruplex structures comprise the stacking of G-quartets, the loop sequence plays a major role on their folding topology and thermal stability. Here circular dichroism, NMR, and PAGE are used to study the effect of loop length and base composition in the middle loop, and a single base difference in loop 1 and 3 on G-quadruplex formation of (G3HG3NmG3HG3) sequences with and without flanking nucleotides, where H is T, A, or C and N is T, A, C, or G. In addition, melting curve for G-quadruplex unfolding was used to provide relatively thermal stability of G-quadruplex structure after the addition of K+ overnight. We further studied the effects of K+ concentration on their stability and found structural changes in several sequences. Such (G3HG3NmG3HG3) configuration can be found in a number of native DNA sequences. The study of structural diversity and similarity from these sequences may allow us to establish the correlation between model sequences and native sequences. Moreover, several sequences upon interaction with a G-quadruplex ligand, BMVC, show similar spectral change, implying that structural similarity is crucial for drug development. View Full-Text
Keywords: G-quadruplex; structural diversity; structural similarity; loop length; base composition; flanking nucleotide; quadruplex-duplex junction G-quadruplex; structural diversity; structural similarity; loop length; base composition; flanking nucleotide; quadruplex-duplex junction
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Li, J.; Chu, I.-T.; Yeh, T.-A.; Chen, D.-Y.; Wang, C.-L.; Chang, T.-C. Effects of Length and Loop Composition on Structural Diversity and Similarity of (G3TG3NmG3TG3) G-Quadruplexes. Molecules 2020, 25, 1779.

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