scholarly journals A Sequence-Independent Analysis of the Loop Length Dependence of Intramolecular RNA G-Quadruplex Stability and Topology

Biochemistry ◽  
2011 ◽  
Vol 50 (33) ◽  
pp. 7251-7258 ◽  
Author(s):  
Amy Y. Q. Zhang ◽  
Anthony Bugaut ◽  
Shankar Balasubramanian
Keyword(s):  
Loop Length ◽  
Length Dependence ◽  
And Topology ◽  
Independent Analysis ◽  
G Quadruplex

scholarly journals G-quadruplex conformation and dynamics are determined by loop length and sequence

2014 ◽  
Vol 42 (12) ◽  
pp. 8106-8114 ◽  
Author(s):  
Ramreddy Tippana ◽  
Weikun Xiao ◽  
Sua Myong
Keyword(s):  
Loop Length ◽  
G Quadruplex

G-Quadruplex DNA Assemblies: Loop Length, Cation Identity, and Multimer Formation†

2008 ◽  
Vol 130 (31) ◽  
pp. 10208-10216 ◽  
Author(s):  
Nicolas Smargiasso ◽  
Frédéric Rosu ◽  
Wei Hsia ◽  
Pierre Colson ◽  
Erin Shammel Baker ◽  
...  
Keyword(s):  
Loop Length ◽  
Quadruplex Dna ◽  
G Quadruplex

Non-ideal Loop-Length-Dependence of Phase Noise in OEOs

2009 ◽  
Author(s):  
Olukayode Okusaga ◽  
Weimin Zhou ◽  
Etgar Levy ◽  
Moshe Horowitz ◽  
Gary Carter ◽  
...  
Keyword(s):  
Phase Noise ◽  
Loop Length ◽  
Length Dependence

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

scholarly journals Topological impact of noncanonical DNA structures on Klenow fragment of DNA polymerase

2017 ◽  
Vol 114 (36) ◽  
pp. 9605-9610 ◽  
Author(s):  
Shuntaro Takahashi ◽  
John A. Brazier ◽  
Naoki Sugimoto
Keyword(s):  
Dna Polymerase ◽  
Mixed Type ◽  
Klenow Fragment ◽  
Polymorphic Region ◽  
Dna Templates ◽  
Dna Structures ◽  
Dna Polymerization ◽  
And Topology ◽  
G Quadruplex ◽  
The Stability

Noncanonical DNA structures that stall DNA replication can cause errors in genomic DNA. Here, we investigated how the noncanonical structures formed by sequences in genes associated with a number of diseases impacted DNA polymerization by the Klenow fragment of DNA polymerase. Replication of a DNA sequence forming an i-motif from a telomere, hypoxia-induced transcription factor, and an insulin-linked polymorphic region was effectively inhibited. On the other hand, replication of a mixed-type G-quadruplex (G4) from a telomere was less inhibited than that of the antiparallel type or parallel type. Interestingly, the i-motif was a better inhibitor of replication than were mixed-type G4s or hairpin structures, even though all had similar thermodynamic stabilities. These results indicate that both the stability and topology of structures formed in DNA templates impact the processivity of a DNA polymerase. This suggests that i-motif formation may trigger genomic instability by stalling the replication of DNA, causing intractable diseases.

Unimolecular antiparallel G-quadruplex folding topology of 2′–5′-isoTBA sequences remains unaltered by loop composition

2015 ◽  
Vol 13 (48) ◽  
pp. 11696-11703 ◽  
Author(s):  
Manisha N. Aher ◽  
Namrata D. Erande ◽  
Moneesha Fernandes ◽  
Vaijayanti A. Kumar
Keyword(s):  
Loop Length ◽  
G Quadruplex

Unlike 3′–5′-linked TBA, the 2′–5′-linked isoTBA formed only unimolecular antiparallel G-quadruplexes independent of loop length.

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.

Implication of the solvent effect, metal ions and topology in the electronic structure and hydrogen bonding of human telomeric G-quadruplex DNA

2016 ◽  
Vol 18 (31) ◽  
pp. 21573-21585 ◽  
Author(s):  
Lokendra Poudel ◽  
Nicole F. Steinmetz ◽  
Roger H. French ◽  
V. Adrian Parsegian ◽  
Rudolf Podgornik ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Electronic Structure ◽  
Metal Ions ◽  
Density Functional ◽  
Three Dimensional ◽  
Functional Study ◽  
Quadruplex Dna ◽  
And Topology ◽  
G4 Dna ◽  
G Quadruplex

First-principles density functional study elucidating the effects of solvent, metal ions and topology on the electronic structure and hydrogen bonding of 12 well-designed three dimensional G-quadruplex (G4-DNA) models.

scholarly journals Solution Structure of a MYC Promoter G-Quadruplex with 1:6:1 Loop Length

ACS Omega ◽  
2019 ◽  
Vol 4 (2) ◽  
pp. 2533-2539 ◽  
Author(s):  
Jonathan Dickerhoff ◽  
Buket Onel ◽  
Luying Chen ◽  
Yuwei Chen ◽  
Danzhou Yang
Keyword(s):  
Solution Structure ◽  
Loop Length ◽  
G Quadruplex
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