Molecular recognition of G-quadruplex DNA by Pheophorbide a

2021 ◽  
Author(s):  
China Okamoto ◽  
Atsuya Momotake ◽  
Masami Kobayashi ◽  
Yasuhiko Yamamoto
Keyword(s):  
Molecular Recognition ◽  
Pheophorbide A ◽  
Quadruplex Dna ◽  
G Quadruplex

Molecular recognition of parallel quadruplex [d-(TTGGGGT)]4 by mitoxantrone: binding with 1 : 4 stoichiometry leads to telomerase inhibition

RSC Advances ◽  
2016 ◽  
Vol 6 (75) ◽  
pp. 71652-71661 ◽  
Author(s):  
Tarikere Palakshan Pradeep ◽  
Sweta Tripathi ◽  
Ritu Barthwal
Keyword(s):  
Molecular Recognition ◽  
Thermal Stabilization ◽  
Cancer Drug ◽  
Telomerase Inhibition ◽  
Quadruplex Dna ◽  
Anti Cancer ◽  
G Quadruplex ◽  
Cd Studies

NMR and CD studies show that anti-cancer drug mitoxantrone (MTX) binds to parallel G-quadruplex DNA [d-(TTGGGGT)4] as stacked dimer at grooves leading to increase in thermal stabilization of DNA by ~25 °C and inhibits telomerase with IC50 = 2 μM.

scholarly journals The Thermodynamic Effects of Ligand Structure on the Molecular Recognition of Mono- and Biruthenium Polypyridyl Complexes with G-Quadruplex DNA

2017 ◽  
Vol 2017 (33) ◽  
pp. 3953-3960 ◽  
Author(s):  
Clinton G. Mikek ◽  
Venkata R. Machha ◽  
Jake C. White ◽  
Logan R. Martin ◽  
Savannah J. West ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Polypyridyl Complexes ◽  
Quadruplex Dna ◽  
Ligand Structure ◽  
G Quadruplex ◽  
Thermodynamic Effects

scholarly journals Correction: A study on a telo21 G-quadruplex DNA specific binding ligand: enhancing the molecular recognition ability via the amino group interactions

RSC Advances ◽  
2018 ◽  
Vol 8 (41) ◽  
pp. 22931-22931
Author(s):  
Dongli Li ◽  
Jin-Qiang Hou ◽  
Wei Long ◽  
Yu-Jing Lu ◽  
Wing-Leung Wong ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Specific Binding ◽  
Amino Group ◽  
Group Interactions ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Recognition Ability

Correction for ‘A study on a telo21 G-quadruplex DNA specific binding ligand: enhancing the molecular recognition ability via the amino group interactions’ by Dongli Li et al., RSC Adv., 2018, 8, 20222–20227.

Targeting G-quadruplex DNA and B-DNA with a natural alkaloid: a comparative spectroscopic study

RSC Advances ◽  
2016 ◽  
Vol 6 (111) ◽  
pp. 109846-109856 ◽  
Author(s):  
Paulami Mandal ◽  
Maitree Bhattacharya ◽  
Joydeep Chowdhury
Keyword(s):  
Molecular Recognition ◽  
Spectroscopic Study ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Natural Alkaloid

Different modes of binding of natural alkaloid harmine with G-quadruplex DNA and B-DNA: key roles in molecular recognition.

Hybrid Imidazole-Pyridine Derivatives: An Approach to Novel Anticancer DNA Intercalators

2020 ◽  
Vol 27 (1) ◽  
pp. 154-169 ◽  
Author(s):  
Claudiu N. Lungu ◽  
Bogdan Ionel Bratanovici ◽  
Maria Mirabela Grigore ◽  
Vasilichia Antoci ◽  
Ionel I. Mangalagiu
Keyword(s):  
Experimental Data ◽  
Antimicrobial Properties ◽  
Qsar Model ◽  
Therapeutic Effectiveness ◽  
Computational Results ◽  
Pyridine Derivatives ◽  
Quadruplex Dna ◽  
Dna Intercalators ◽  
Structure Activity ◽  
G Quadruplex

Lack of specificity and subsequent therapeutic effectiveness of antimicrobial and antitumoral drugs is a common difficulty in therapy. The aim of this study is to investigate, both by experimental and computational methods, the antitumoral and antimicrobial properties of a series of synthesized imidazole-pyridine derivatives. Interaction with three targets was discussed: Dickerson-Drew dodecamer (PDB id 2ADU), G-quadruplex DNA string (PDB id 2F8U) and DNA strain in complex with dioxygenase (PDB id 3S5A). Docking energies were computed and represented graphically. On them, a QSAR model was developed in order to further investigate the structure-activity relationship. Results showed that synthesized compounds have antitumoral and antimicrobial properties. Computational results agreed with the experimental data.

Emerging Role of G-quadruplex DNA as Target in Anticancer Therapy

2017 ◽  
Vol 22 (44) ◽  
pp. 6612-6624 ◽  
Author(s):  
Graziella Cimino-Reale ◽  
Nadia Zaffaroni ◽  
Marco Folini
Keyword(s):  
Anticancer Therapy ◽  
Quadruplex Dna ◽  
G Quadruplex

scholarly journals The Functional Role of Loops and Flanking Sequences of G-Quadruplex Aptamer to the Hemagglutinin of Influenza a Virus

2021 ◽  
Vol 22 (5) ◽  
pp. 2409
Author(s):  
Anastasia A. Bizyaeva ◽  
Dmitry A. Bunin ◽  
Valeria L. Moiseenko ◽  
Alexandra S. Gambaryan ◽  
Sonja Balk ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Core Structure ◽  
Dna Aptamer ◽  
Tertiary Structures ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Flanking Sequences ◽  
Related Proteins

Nucleic acid aptamers are generally accepted as promising elements for the specific and high-affinity binding of various biomolecules. It has been shown for a number of aptamers that the complexes with several related proteins may possess a similar affinity. An outstanding example is the G-quadruplex DNA aptamer RHA0385, which binds to the hemagglutinins of various influenza A virus strains. These hemagglutinins have homologous tertiary structures but moderate-to-low amino acid sequence identities. Here, the experiment was inverted, targeting the same protein using a set of related, parallel G-quadruplexes. The 5′- and 3′-flanking sequences of RHA0385 were truncated to yield parallel G-quadruplex with three propeller loops that were 7, 1, and 1 nucleotides in length. Next, a set of minimal, parallel G-quadruplexes with three single-nucleotide loops was tested. These G-quadruplexes were characterized both structurally and functionally. All parallel G-quadruplexes had affinities for both recombinant hemagglutinin and influenza virions. In summary, the parallel G-quadruplex represents a minimal core structure with functional activity that binds influenza A hemagglutinin. The flanking sequences and loops represent additional features that can be used to modulate the affinity. Thus, the RHA0385–hemagglutinin complex serves as an excellent example of the hypothesis of a core structure that is decorated with additional recognizing elements capable of improving the binding properties of the aptamer.

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).

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