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

The Analyst ◽  
2020 ◽  
Vol 145 (12) ◽  
pp. 4254-4259
Author(s):  
Qingqing Zhang ◽  
Tong Yang ◽  
Guoxiang Zheng ◽  
Heng Gao ◽  
Chenxiao Yan ◽  
...  
Keyword(s):  
Quadruplex Structure ◽  
G Quadruplex ◽  
Quadruplex Formation

A guanine-rich sequence containing three G-tracts adopts a tetramolecular G-quadruplex structure (4erG4) rather than G-triplex (G3) folding.

scholarly journals The Effects of Molecular Crowding on the Structure and Stability of G-Quadruplexes with an Abasic Site

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Takeshi Fujimoto ◽  
Shu-ichi Nakano ◽  
Daisuke Miyoshi ◽  
Naoki Sugimoto
Keyword(s):  
Site Effects ◽  
Enthalpy Change ◽  
Molecular Crowding ◽  
Abasic Site ◽  
Structure And Stability ◽  
Quadruplex Structure ◽  
Abasic Sites ◽  
Crowding Effects ◽  
G Quadruplex ◽  
Quadruplex Formation

Both cellular environmental factors and chemical modifications critically affect the properties of nucleic acids. However, the structure and stability of DNA containing abasic sites under cell-mimicking molecular crowding conditions remain unclear. Here, we investigated the molecular crowding effects on the structure and stability of the G-quadruplexes including a single abasic site. Structural analysis by circular dichroism showed that molecular crowding by PEG200 did not affect the topology of the G-quadruplex structure with or without an abasic site. Thermodynamic analysis further demonstrated that the degree of stabilization of the G-quadruplex by molecular crowding decreased with substitution of an abasic site for a single guanine. Notably, we found that the molecular crowding effects on the enthalpy change for G-quadruplex formation had a linear relationship with the abasic site effects depending on its position. These results are useful for predicting the structure and stability of G-quadruplexes with abasic sites in the cell-mimicking conditions.

Characterization of the G-quadruplex structure of a catalytic DNA with peroxidase activity

Biopolymers ◽  
2009 ◽  
Vol 91 (5) ◽  
pp. 331-339 ◽  
Author(s):  
De-Ming Kong ◽  
Li-Li Cai ◽  
Jun-Hong Guo ◽  
Jing Wu ◽  
Han-Xi Shen
Keyword(s):  
Peroxidase Activity ◽  
Quadruplex Structure ◽  
G Quadruplex ◽  
Catalytic Dna

A multi-functional guanine derivative for studying the DNA G-quadruplex structure

The Analyst ◽  
2017 ◽  
Vol 142 (21) ◽  
pp. 4083-4088 ◽  
Author(s):  
Takumi Ishizuka ◽  
Pei-Yan Zhao ◽  
Hong-Liang Bao ◽  
Yan Xu
Keyword(s):  
Fluorescent Probe ◽  
Living Cells ◽  
Quadruplex Structure ◽  
G Quadruplex ◽  
Quadruplex Formation

A multi-functional guanine derivative, 8FG, as a G-quadruplex stabilizer, a fluorescent probe for the detection of G-quadruplex formation, and a 19F sensor for the observation of the G-quadruplex in vitro and in living cells.

scholarly journals A novel G-quadruplex motif in the Human MET promoter region

2017 ◽  
Vol 37 (6) ◽  
Author(s):  
Jing Yan ◽  
Deming Zhao ◽  
Liping Dong ◽  
Shuang Pan ◽  
Fengjin Hao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Regulation ◽  
Luciferase Assay ◽  
Klenow Fragment ◽  
Regulate Gene Expression ◽  
Physiological Conditions ◽  
Quadruplex Structure ◽  
G Quadruplex ◽  
Quadruplex Formation

It is known that the guanine-rich strands in proto-oncogene promoters can fold into G-quadruplex structures to regulate gene expression. An intramolecular parallel G-quadruplex has been identified in MET promoter. It acts as a repressor in regulating MET expression. However, the full guanine-rich region in MET promoter forms a hybrid parallel/antiparallel G-quadruplex structure under physiological conditions, which means there are some antiparallel and hybrid parallel/antiparallel G-quadruplex structures in this region. In the present study, our data indicate that g3-5 truncation adopts an intramolecular hybrid parallel/antiparallel G-quadruplex under physiological conditions in vitro. The g3-5 G-quadruplex structure significantly stops polymerization by Klenow fragment in K+ buffer. Furthermore, the results of circular dichroism (CD) spectra and polymerase stop assay directly demonstrate that the G-quadruplex structure in g3-5 fragment can be stabilized by the G-quadruplex ligand TMPyP4 (5,10,15,20-tetra-(N-methyl-4-pyridyl) porphine). But the dual luciferase assay indicates TMPyP4 has no effect on the formation of g3-5 G-quadruplex in HepG2 cells. The findings in the present study will enrich our understanding of the G-quadruplex formation in proto-oncogene promoters and the mechanisms of gene expression regulation.

Characterization of G-quadruplex formation in the ARID1A promoter

2020 ◽  
Vol 147 ◽  
pp. 750-761 ◽  
Author(s):  
Ting Yan ◽  
Bo Zhao ◽  
Qiong Wu ◽  
Wenmeng Wang ◽  
Jinming Shi ◽  
...  
Keyword(s):  
G Quadruplex ◽  
Quadruplex Formation
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