Characterization of the interaction between heme and a parallel G-quadruplex DNA formed from d(TTGAGG)

2017 ◽  
Vol 1861 (5) ◽  
pp. 1264-1270 ◽  
Author(s):  
Tomokazu Shibata ◽  
Yusaku Nakayama ◽  
Yuya Katahira ◽  
Hulin Tai ◽  
Yuki Moritaka ◽  
...  
Keyword(s):  
Quadruplex Dna ◽  
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 DNA G-quadruplexes for native mass spectrometry in potassium: a database of validated structures in electrospray-compatible conditions

2020 ◽  
Author(s):  
Anirban Ghosh ◽  
Eric Largy ◽  
Valérie Gabelica
Keyword(s):  
Mass Spectrometry ◽  
Drug Targets ◽  
Native Mass Spectrometry ◽  
Drug Binding ◽  
Quadruplex Dna ◽  
Link Type ◽  
Nmr Structures ◽  
G Quadruplex ◽  
Screening Assays

ABSTRACTG-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) K+, and report here their circular dichroism (CD), melting temperature (Tm), NMR spectra and electrospray mass spectra in 1 mM KCl/100 mM TMAA. 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).

Synthesis and characterization of chiral ruthenium(II) complexes Λ/Δ-[Ru(bpy)2(H2iip)](ClO4)2 as stabilizers of c-myc G-quadruplex DNA

2015 ◽  
Vol 68 (8) ◽  
pp. 1465-1475 ◽  
Author(s):  
Zhao Zhang ◽  
Wenjie Mei ◽  
Xiaohui Wu ◽  
Xicheng Wang ◽  
Baoguo Wang ◽  
...  
Keyword(s):  
Synthesis And Characterization ◽  
Quadruplex Dna ◽  
G Quadruplex

ChemInform Abstract: Characterization of the Interaction Between Heme and a Parallel G-Quadruplex DNA Formed from d(TTAGGGT)

ChemInform ◽  
2015 ◽  
Vol 46 (36) ◽  
pp. no-no
Author(s):  
Haruna Shimizu ◽  
Hulin Tai ◽  
Kaori Saito ◽  
Tomokazu Shibata ◽  
Masashi Kinoshita ◽  
...  
Keyword(s):  
Quadruplex Dna ◽  
Abstract Characterization ◽  
G Quadruplex

Characterization of Interaction of the MBP-Tagged MuRif1-C-Terminal Domain with G-Quadruplex DNA by SPR

2021 ◽  
Vol 86 (7) ◽  
pp. 898-905
Author(s):  
Hamed Ghadiri ◽  
Sana Alavi ◽  
Bahareh Dabirmanesh ◽  
Khosro Khajeh
Keyword(s):  
Quadruplex Dna ◽  
Terminal Domain ◽  
G Quadruplex
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