scholarly journals Crystallization and characterization of the thallium form of the Oxytricha nova G-quadruplex

2006 ◽  
Vol 34 (16) ◽  
pp. 4506-4514 ◽  
Author(s):  
Michelle L. Gill ◽  
Scott A. Strobel ◽  
J. Patrick Loria
Keyword(s):  
G Quadruplex ◽  
Oxytricha Nova

scholarly journals MoD-QM/MM Structural Refinement Method: Characterization of Hydrogen Bonding in the Oxytricha nova G-Quadruplex

2014 ◽  
Vol 10 (11) ◽  
pp. 5125-5135 ◽  
Author(s):  
Junming Ho ◽  
Michael B. Newcomer ◽  
Christina M. Ragain ◽  
Jose A. Gascon ◽  
Enrique R. Batista ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Structural Refinement ◽  
Refinement Method ◽  
G Quadruplex ◽  
Oxytricha Nova

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).

Characterization of Heme–DNA Complexes Composed of Some Chemically Modified Hemes and Parallel G-Quadruplex DNAs

Biochemistry ◽  
2015 ◽  
Vol 54 (49) ◽  
pp. 7168-7177 ◽  
Author(s):  
Yasuhiko Yamamoto ◽  
Masashi Kinoshita ◽  
Yuya Katahira ◽  
Haruna Shimizu ◽  
Yue Di ◽  
...  
Keyword(s):  
Dna Complexes ◽  
Chemically Modified ◽  
G Quadruplex

scholarly journals Characterization of a G-quadruplex from hepatitis B virus and its stabilization by binding TMPyP4, BRACO19 and PhenDC3

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Orsolya Réka Molnár ◽  
András Végh ◽  
Judit Somkuti ◽  
László Smeller
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Binding Constants ◽  
Temperature Stability ◽  
Cd Spectroscopy ◽  
Parallel Structure ◽  
Hybrid Form ◽  
B Virus ◽  
G Quadruplex

AbstractSpecific guanine rich nucleic acid sequences can form non-canonical structures, like the four stranded G-quadruplex (GQ). We studied the GQ-forming sequence (named HepB) found in the genome of the hepatitis B virus. Fluorescence-, infrared- and CD-spectroscopy were used. HepB shows a hybrid form in presence of K+, but Na+, Li+, and Rb+ induce parallel structure. Higher concentrations of metal ions increase the unfolding temperature, which was explained by a short thermodynamic calculation. Temperature stability of the GQ structure was determined for all these ions. Na+ has stronger stabilizing effect on HepB than K+, which is highly unusual. The transition temperatures were 56.6, 53.8, 58.5 and 54.4 °C for Na+, K+, Li+, and Rb+ respectively. Binding constants for Na+ and K+ were 10.2 mM and 7.1 mM respectively. Study of three ligands designed in cancer research for GQ targeting (TMPyP4, BRACO19 and PhenDC3) showed unequivocally their binding to HepB. Binding was proven by the increased stability of the bound form. The stabilization was higher than 20 °C for TMPyP4 and PhenDC3, while it was considerably lower for BRACO19. These results might have medical importance in the fight against the hepatitis B virus.

scholarly journals Biophysical Characterization of G-Quadruplex Recognition in the PITX1 mRNA by the Specificity Domain of the Helicase RHAU

PLoS ONE ◽  
2015 ◽  
Vol 10 (12) ◽  
pp. e0144510 ◽  
Author(s):  
Emmanuel O. Ariyo ◽  
Evan P. Booy ◽  
Trushar R. Patel ◽  
Edis Dzananovic ◽  
Ewan K. McRae ◽  
...  
Keyword(s):  
Biophysical Characterization ◽  
G Quadruplex ◽  
Specificity Domain

State-of-the-Art Methodologies for the Discovery and Characterization of DNA G-Quadruplex Binders

2012 ◽  
Vol 18 (14) ◽  
pp. 1880-1899 ◽  
Author(s):  
Bruno Pagano ◽  
Sandro Cosconati ◽  
Valerie Gabelica ◽  
Luigi Petraccone ◽  
Stefano De Tito ◽  
...  
Keyword(s):  
State Of The Art ◽  
G Quadruplex
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