Structural Aspects of Split G-Quadruplexes in Quadruplex-Duplex Hybrid Systems

Agustin, Dinda Fluor and Vianney, Yoanes Maria and Weisz, Klaus and Wahjudi, Mariana (2024) Structural Aspects of Split G-Quadruplexes in Quadruplex-Duplex Hybrid Systems. ChemistrySelect, 9 (4). e202304286/1-11. ISSN 2365-6549; E-ISSN 2365-6549

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Abstract

G-quadruplexes are secondary structures of nucleic acids increasingly employed for biological and also technological applications. Being of particular interest, a structural motif called quadruplex-duplex (QD) hybrid comprises both a G-quadruplex and duplex domain. Here, we attempted to engineer a bimolecular quadruplex-duplex hybrid through dual recognition of a receptor by a target strand with the simultaneous formation of both G-quadruplex and duplex structures. Three different constructs were designed for the G-quadruplex receptor, featuring either one, two, or three vacant sites. Addition of the target strand filled the vacancies when simultaneously hybridizing with flanking sequences to form a duplex as shown by NMR studies. Formed QD hybrid constructs either constitute an 11 : 1, 10 : 2, or 9 : 3 split G-quadruplex system. The 10 : 2 QD construct folds into a non-canonical V-loop topology. Remarkably, the latter also accommodates 5’-overhang residues of the target strand although suggested to impose a steric penalty. Formation of the duplex domain is demonstrated to be critical for the successful formation of the intact G-quadruplex domain. With the formation of a unique QD junction for detection, the constructs may constitute valuable tools for single strand capturing strategies.

Item Type:	Article
Subjects:	Q Science > Q Science (General)
Divisions:	Faculty of Technobiology > Department of Biology
Depositing User:	Ester Sri W. 196039
Date Deposited:	30 Jan 2024 03:07
Last Modified:	31 Jan 2024 06:18
URI:	http://repository.ubaya.ac.id/id/eprint/45828

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