scholarly journals Effects of Central Loop Length and Metal Ions on the Thermal Stability of G-Quadruplexes

Molecules ◽  
2019 ◽  
Vol 24 (10) ◽  
pp. 1863 ◽  
Author(s):  
Fengjin Hao ◽  
Yushu Ma ◽  
Yifu Guan
Keyword(s):  
Thermal Stability ◽  
Stability Analysis ◽  
Difference Spectrum ◽  
Loop Length ◽  
Rna Sequences ◽  
Quadruplex Structure ◽  
G Quadruplex ◽  
The Stability ◽  
Central Loop ◽  
Uv Melting

The central loop of G-quadruplex molecular beacons is a key element to sense target DNA or RNA sequences. In this study, circular dichroism spectroscopy (CD), thermal difference spectrum (TDS), non-denatured non-denaturing gel electrophoresis, and thermal stability analysis were used to investigate the effect of the central loop length on G-quadruplex features. Two series of G-quadruplexes, AG3TTAG3-(TTA)n-G3TTAG3T (n = 1–8) (named TTA series) and AG3TTTG3-(TTA)n-G3TTTG3T (n = 1–8) (named TTT series) were examined in K+ and Na+ solutions, respectively. CD and TDS spectral data indicated that TTA series adopted an antiparallel G-quadruplex structure in Na+ solution and a hybrid G-quadruplex structure in K+ solution respectively. TTT series exhibited a hybrid G-quadruplex structure in both Na+ and K+ solutions. UV melting curves indicated that the stability of G-quadruplex in both series was reduced by the elongation of central loop. Thermal stability analysis concluded that the G-quadruplex destabilization with long central loop is an entropy-driven process due to more flexible and longer central loops.

The Effect of Temperature on the Interaction of Phenanthroline-based Ligands with G-quadruplex: In Silico Viewpoint

2019 ◽  
Vol 22 (8) ◽  
pp. 546-554
Author(s):  
Mohadeseh Bazoobandi ◽  
Mohammad R. Bozorgmehr ◽  
Ali Mahmoudi ◽  
Ali Morsali
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Low Temperatures ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Effect Of Temperature ◽  
Quadruplex Structure ◽  
G Quadruplex ◽  
The Stability ◽  
Increasing Temperature

Aim and Objective: The stability of the G-quadruplex structure can increase its activity in telomerase inhibiting cancer cells. In this study, a molecular dynamics simulation method was used to study the effect of three phenanthroline-based ligands on the structure of G-quadruplex at the temperatures of 20, 40, 60 and 80°C. Materials and Methods: RMSD values and frequency of calculated RMSD in the presence and absence of ligands show that ligands cause the relative stability of the G-quadruplex, particularly at low temperatures. The calculation of hydrogen bonds in Guanine-tetrads in three different quadruplex sheets shows that the effect of ligands on the sheets is not the same so that the bottom sheet of G-quadruplex is most affected by the ligands at high temperatures, and the Guaninetetrads in this sheet are far away. Conformation factor was calculated as a measure of ligands binding affinity for each of the G-quadruplex residues. Results: The results show that the studied ligands interact more with the G-quadruplex than loop areas, although with increasing temperature, the binding area also includes the G-quadruplex sheets. The contribution of each of the residues involved in the G-quadruplex binding area with ligands was also calculated. Conclusion: The calculations performed are consistent with the previous experimental observations that can help to understand the molecular mechanism of the interaction of phenanthroline and its derivatives with quadruplex.

scholarly journals Duplex formation in a G-quadruplex bulge

2020 ◽  
Vol 48 (18) ◽  
pp. 10567-10575 ◽  
Author(s):  
Thi Quynh Ngoc Nguyen ◽  
Kah Wai Lim ◽  
Anh Tuân Phan
Keyword(s):  
Base Pair ◽  
Solution Structure ◽  
Biological Significance ◽  
Consensus Definition ◽  
Quadruplex Structure ◽  
G Quadruplex ◽  
Structural Details ◽  
The Stability ◽  
Definition Of ◽  
Duplex Formation

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.

scholarly journals Short loop length and high thermal stability determine genomic instability induced by G‐quadruplex‐forming minisatellites

2015 ◽  
Vol 34 (12) ◽  
pp. 1718-1734 ◽  
Author(s):  
Aurèle Piazza ◽  
Michael Adrian ◽  
Frédéric Samazan ◽  
Brahim Heddi ◽  
Florian Hamon ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Genomic Instability ◽  
High Thermal Stability ◽  
Loop Length ◽  
Short Loop ◽  
G Quadruplex

Stability Analysis of the Nanjung Water Diversion Twin Tunnels based on Convergence Measurement

2019 ◽  
Vol 1 (1) ◽  
pp. 49-60
Author(s):  
Simon Heru Prassetyo ◽  
Ganda Marihot Simangunsong ◽  
Ridho Kresna Wattimena ◽  
Made Astawa Rai ◽  
Irwandy Arif ◽  
...  
Keyword(s):  
Stability Analysis ◽  
Convergence Rate ◽  
Critical Strain ◽  
Convergence Rates ◽  
Strain Analysis ◽  
Water Diversion ◽  
Tunnel Face ◽  
Tunnel Stability ◽  
The Stability ◽  
Twin Tunnels

This paper focuses on the stability analysis of the Nanjung Water Diversion Twin Tunnels using convergence measurement. The Nanjung Tunnel is horseshoe-shaped in cross-section, 10.2 m x 9.2 m in dimension, and 230 m in length. The location of the tunnel is in Curug Jompong, Margaasih Subdistrict, Bandung. Convergence monitoring was done for 144 days between February 18 and July 11, 2019. The results of the convergence measurement were recorded and plotted into the curves of convergence vs. day and convergence vs. distance from tunnel face. From these plots, the continuity of the convergence and the convergence rate in the tunnel roof and wall were then analyzed. The convergence rates from each tunnel were also compared to empirical values to determine the level of tunnel stability. In general, the trend of convergence rate shows that the Nanjung Tunnel is stable without any indication of instability. Although there was a spike in the convergence rate at several STA in the measured span, that spike was not replicated by the convergence rate in the other measured spans and it was not continuous. The stability of the Nanjung Tunnel is also confirmed from the critical strain analysis, in which most of the STA measured have strain magnitudes located below the critical strain line and are less than 1%.

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