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Title: Duplex formation in a G-quadruplex bulge
Authors: Ngoc Nguyen, Thi Quynh
Lim, Kah Wai
Phan, Anh Tuân
Keywords: Science::Chemistry
Issue Date: 2020
Source: Ngoc Nguyen, T. Q., Lim, K. W., & Phan, A. T. (2020). Duplex formation in a G-quadruplex bulge. Nucleic Acids Research, 48(18), 10567-10575. doi:10.1093/nar/gkaa738
Project: NRF-NRFI2017-09
Journal: Nucleic Acids Research
Abstract: Beyond the consensus definition of G-quadruplex-forming motifs with tracts of continuous guanines, G-quadruplexes harboring bulges in the G-tetrad core are prevalent in the human genome. Here, we study the incorporation of a duplex hairpin within a bulge of a G-quadruplex. The NMR solution structure of a G-quadruplex containing a duplex bulge was resolved, revealing the structural details of the junction between the duplex bulge and the G-quadruplex. Unexpectedly, instead of an orthogonal connection the duplex stem was observed to stack below the G-quadruplex forming a unique quadruplex-duplex junction. Breaking up of the immediate base pair step at the junction, coupled with a narrowing of the duplex groove within the context of the bulge, led to a progressive transition between the quadruplex and duplex segments. This study revealed that a duplex bulge can be formed at various positions of a G-quadruplex scaffold. In contrast to a non-structured bulge, the stability of a G-quadruplex slightly increases with an increase in the duplex bulge size. A G-quadruplex structure containing a duplex bulge of up to 33 nt in size was shown to form, which was much larger than the previously reported 7-nt bulge. With G-quadruplexes containing duplex bulges representing new structural motifs with potential biological significance, our findings would broaden the definition of potential G-quadruplex-forming sequences.
ISSN: 0305-1048
DOI: 10.1093/nar/gkaa738
Rights: © 2020 The Author(s). 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 (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Fulltext Permission: open
Fulltext Availability: With Fulltext
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