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.

Hybridization of G-Quadruplex-Forming Peptide Nucleic Acids to Guanine-Rich DNA Templates Inhibits DNA Polymerase η Extension

Biochemistry ◽  
2014 ◽  
Vol 53 (32) ◽  
pp. 5315-5322 ◽  
Author(s):  
Connor T. Murphy ◽  
Anisha Gupta ◽  
Bruce A. Armitage ◽  
Patricia L. Opresko
Keyword(s):  
Nucleic Acids ◽  
Dna Polymerase ◽  
Peptide Nucleic Acids ◽  
Dna Templates ◽  
G Quadruplex

scholarly journals New Modified Deoxythymine with Dibranched Tetraethylene Glycol Stabilizes G-Quadruplex Structures

Molecules ◽  
2020 ◽  
Vol 25 (3) ◽  
pp. 705
Author(s):  
Hisae Tateishi-Karimata ◽  
Tatsuya Ohyama ◽  
Takahiro Muraoka ◽  
Shigenori Tanaka ◽  
Kazushi Kinbara ◽  
...  
Keyword(s):  
Tetraethylene Glycol ◽  
Dna Structures ◽  
Dna Oligonucleotides ◽  
Loop Region ◽  
Promising Therapeutic Approach ◽  
G Quadruplex ◽  
Molecular Dynamics Calculations ◽  
Dna Materials ◽  
The Stability ◽  
Oligoethylene Glycols

Methods for stabilizing G-quadruplex formation is a promising therapeutic approach for cancer treatment and other biomedical applications because stable G-quadruplexes efficiently inhibit biological reactions. Oligo and polyethylene glycols are promising biocompatible compounds, and we have shown that linear oligoethylene glycols can stabilize G-quadruplexes. Here, we developed a new modified deoxythymine with dibranched or tribranched tetraethylene glycol (TEG) and incorporated these TEG-modified deoxythymines into a loop region that forms an antiparallel G-quadruplex. We analyzed the stability of the modified G-quadruplexes, and the results showed that the tribranched TEG destabilized G-quadruplexes through entropic contributions, likely through steric hindrance. Interestingly, the dibranched TEG modification increased G-quadruplex stability relative to the unmodified DNA structures due to favorable enthalpic contributions. Molecular dynamics calculations suggested that dibranched TEG interacts with the G-quadruplex through hydrogen bonding and CH-π interactions. Moreover, these branched TEG-modified deoxythymine protected the DNA oligonucleotides from degradation by various nucleases in human serum. By taking advantage of the unique interactions between DNA and branched TEG, advanced DNA materials can be developed that affect the regulation of DNA structure.

5′-Derivatives of oligonucleotides as primers of DNA polymerization catalyzed by AMV reverse transcriptase and Klenow fragment of DNA polymerase 1

FEBS Letters ◽  
1991 ◽  
Vol 281 (1-2) ◽  
pp. 111-113 ◽  
Author(s):  
I.A. Lokhova ◽  
G.A. Nevinsky ◽  
T.S. Godovikova ◽  
E.M. Ivanova ◽  
A.A. Koshkin ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Dna Polymerase ◽  
Klenow Fragment ◽  
Dna Polymerization ◽  
Derivatives Of

Label-free simple fluorescence assay of DNA polymerase using the G-quadruplex structure

2016 ◽  
Vol 8 (2) ◽  
pp. 275-279 ◽  
Author(s):  
Seyeon Kim ◽  
Jongback Gang
Keyword(s):  
Enzymatic Activity ◽  
Dna Polymerase ◽  
Fluorescence Assay ◽  
Label Free ◽  
Klenow Fragment ◽  
Quadruplex Structure ◽  
G Quadruplex

In this study, the G-quadruplex structure was used to detect the enzymatic activity and inhibition of the Klenow fragment exo−(KF−) in the presence ofN-methylmesoporphyrin IX (NMM) which binds specifically to the G-quadruplex.

scholarly journals DNA G-quadruplexes for native mass spectrometry in potassium: a database of validated structures in electrospray-compatible conditions

2021 ◽  
Author(s):  
Anirban Ghosh ◽  
Eric Largy ◽  
Valérie Gabelica
Keyword(s):  
Mass Spectrometry ◽  
Drug Targets ◽  
Native Mass Spectrometry ◽  
Drug Binding ◽  
Quadruplex Dna ◽  
Dna Structures ◽  
Nmr Structures ◽  
G Quadruplex ◽  
Screening Assays

Abstract G-quadruplex DNA structures have become attractive drug targets, and native mass spectrometry can provide detailed characterization of drug binding stoichiometry and affinity, potentially at high throughput. However, the G-quadruplex DNA polymorphism poses problems for interpreting ligand screening assays. In order to establish standardized MS-based screening assays, we studied 28 sequences with documented NMR structures in (usually ∼100 mM) potassium, and report here their circular dichroism (CD), melting temperature (Tm), NMR spectra and electrospray mass spectra in 1 mM KCl/100 mM trimethylammonium acetate. Based on these results, we make a short-list of sequences that adopt the same structure in the MS assay as reported by NMR, and provide recommendations on using them for MS-based assays. We also built an R-based open-source application to build and consult a database, wherein further sequences can be incorporated in the future. The application handles automatically most of the data processing, and allows generating custom figures and reports. The database is included in the g4dbr package (https://github.com/EricLarG4/g4dbr) and can be explored online (https://ericlarg4.github.io/G4_database.html).

scholarly journals The new investigation of the stability of mixed type additive-quartic functional equations in non-Archimedean spaces

2020 ◽  
Vol 53 (1) ◽  
pp. 174-192
Author(s):  
Anurak Thanyacharoen ◽  
Wutiphol Sintunavarat
Keyword(s):  
Functional Equation ◽  
Normed Space ◽  
Functional Equations ◽  
Mixed Type ◽  
Additive Group ◽  
Ulam Stability ◽  
Quartic Functional Equation ◽  
The Stability

AbstractIn this article, we prove the generalized Hyers-Ulam stability for the following additive-quartic functional equation:f(x+3y)+f(x-3y)+f(x+2y)+f(x-2y)+22f(x)+24f(y)=13{[}f(x+y)+f(x-y)]+12f(2y),where f maps from an additive group to a complete non-Archimedean normed space.

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