Characterization of Catalytic Activities and Heme Coordination Structures of Heme–DNA Complexes Composed of Some Chemically Modified Hemes and an All Parallel-Stranded Tetrameric G-Quadruplex DNA Formed from d(TTAGGG)

Biochemistry ◽  
2018 ◽  
Vol 57 (41) ◽  
pp. 5930-5937 ◽  
Author(s):  
Ryosuke Shinomiya ◽  
Yuya Katahira ◽  
Haruka Araki ◽  
Tomokazu Shibata ◽  
Atsuya Momotake ◽  
...  
Keyword(s):  
Dna Complexes ◽  
Quadruplex Dna ◽  
Catalytic Activities ◽  
Chemically Modified ◽  
G Quadruplex

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

Structural characterization of imidazole adducts of heme-DNA complexes

2014 ◽  
Vol 18 (08n09) ◽  
pp. 741-751 ◽  
Author(s):  
Yasuhito Suzuki ◽  
Hulin Tai ◽  
Kaori Saito ◽  
Tomokazu Shibata ◽  
Masashi Kinoshita ◽  
...  
Keyword(s):  
Repeat Sequence ◽  
Ternary Complexes ◽  
Dna Complexes ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Human Telomere ◽  
Optical Circular Dichroism ◽  
Dna Complex ◽  
Trifluoromethyl Groups

Ternary complexes composed of protoheme (heme( Fe 3+)) or 13,17-bis(2-carboxylatoethyl)-3,7-diethyl-12,18-trimethyl-2,8-ditrifluoromethylporphyrinatoiron(III) (2,8-DPF( Fe 3+)), a parallel G-quadruplex DNA formed from a single repeat sequence of the human telomere, d(TTAGGG), and imidazole (Im), in a ratio of 1:1:1, were prepared and their structures were characterized using optical, circular dichroism, and NMR spectroscopies. The study revealed that heme( Fe 3+) and 2,8-DPF( Fe 3+) stack onto the 3′-terminal G-quartet of the G-quadruplex DNA, ~0.4 nm apart, and that Im is coordinated to the Fe atom on the side of the heme opposite to the G-quartet in the complex. The stacking of the pseudo-C2 symmetric heme( Fe 3+) onto the C4 symmetric G-quartet in the complex resulted in the formation of two isomers with heme orientations differing by 180° about the pseudo-C2 axis, with respect to the DNA. The Im affinity of the 2,8-DPF( Fe 3+)-DNA complex was higher by a factor of ~2 than that of the heme( Fe 3+)-DNA one, which is possibly due to the stronger ligand-to-metal π donation in the 2,8-DPF( Fe 3+) as a result of a decrease in the electron density of the heme Fe atom caused by substitution of the two strongly electron-withdrawing trifluoromethyl groups.

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).

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

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
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