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Characterization of intermolecular G-quadruplex formation over intramolecular G-triplex for DNA containing three G-tracts.

Authors
  • Zhang, Qingqing1
  • Yang, Tong1
  • Zheng, Guoxiang2
  • Gao, Heng1
  • Yan, Chenxiao1
  • Zheng, Xiong1
  • Zhou, Xiaoshun1
  • Shao, Yong1
  • 1 Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China. [email protected] , (China)
  • 2 Undergraduate Teaching Department, Zhejiang Normal University, Jinhua 321004, Zhejiang, China. , (China)
Type
Published Article
Journal
The Analyst
Publisher
The Royal Society of Chemistry
Publication Date
Jun 15, 2020
Volume
145
Issue
12
Pages
4254–4259
Identifiers
DOI: 10.1039/d0an00791a
PMID: 32478785
Source
Medline
Language
English
License
Unknown

Abstract

G-triplex (G3) has been recognized as a popular intermediate during the folding of G-quadruplex (G4). This has raised interest to anticipate the ultimate formation of G3 by shortening the G4-forming oligonucleotides with the remaining three G-tracts. Some G3 structures have been validated and their stability has been found to be affected by the loop sequences similar to G4s. In this work, however, we first found that an intermolecular parallel G4 structure was preferred in K+ for the oligonucleotide 5'-TGGGTAGGGCGGG-3' (DZ3) containing only three G-tracts. We screened auramine O (AO) as the appropriate fluorophore with a molecular rotor feature to target this G4 structure. AO bound with DZ3 in a 1 : 4 ratio, as confirmed by isothermal titration calorimetry experiments, suggesting the formation of a tetramolecular G4 structure (4erG4). The excimer emission from the labelled pyrene and the DNA melting behavior at various pHs in the presence of Ag+ proved the formation of the 4erG4 structure rather than the prevalent intramolecular G3 folding. This work demonstrates that one should be cautious while putatively predicting a G3 structure from an oligonucleotide containing three G-tracts.

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