Cation Coordination Alters the Conformation of a Thrombin-Binding G-Quadruplex DNA Aptamer That Affects Inhibition of Thrombin

2016 ◽  
Vol 26 (5) ◽  
pp. 299-308 ◽  
Author(s):  
Elena Zavyalova ◽  
Grigory Tagiltsev ◽  
Roman Reshetnikov ◽  
Alexander Arutyunyan ◽  
Alexey Kopylov
Keyword(s):  
Dna Aptamer ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Cation Coordination ◽  
Inhibition Of Thrombin

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 De novo post-SELEX optimization of a G-quadruplex DNA aptamer binding to marine toxin gonyautoxin 1/4

2020 ◽  
Vol 18 ◽  
pp. 3425-3433 ◽  
Author(s):  
Menghua Song ◽  
Gan Li ◽  
Qi Zhang ◽  
Jianping Liu ◽  
Qiang Huang
Keyword(s):  
De Novo ◽  
Dna Aptamer ◽  
Quadruplex Dna ◽  
Marine Toxin ◽  
G Quadruplex

scholarly journals Light-controlled thrombin catalysis and clot formation using a photoswitchable G-quadruplex DNA aptamer

2019 ◽  
Vol 55 (39) ◽  
pp. 5627-5630 ◽  
Author(s):  
Aysha Ali ◽  
Gemma A. Bullen ◽  
Benjamin Cross ◽  
Timothy R. Dafforn ◽  
Haydn A. Little ◽  
...  
Keyword(s):  
Dna Aptamer ◽  
Clot Formation ◽  
Quadruplex Dna ◽  
G Quadruplex

The application of light distorts the structure of an anthracene-functionalized DNA aptamer, preventing its inhibitive binding to the clotting enzyme thrombin, resulting in photoswitched catalysis.

scholarly journals Electrochemical Detection of Ultratrace Lead Ion through Attaching and Detaching DNA Aptamer from Electrochemically Reduced Graphene Oxide Electrode

Nanomaterials ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 817 ◽  
Author(s):  
Su Hwan Yu ◽  
Chang-Seuk Lee ◽  
Tae Hyun Kim
Keyword(s):  
Graphene Oxide ◽  
Reduced Graphene Oxide ◽  
Dna Aptamer ◽  
Lead Ion ◽  
Oxide Electrode ◽  
Quadruplex Dna ◽  
Simple Strategy ◽  
Reduced Graphene ◽  
Electrochemically Reduced Graphene Oxide ◽  
G Quadruplex

This paper describes a simple strategy for the ultratrace level detection of Pb2+ ion based on G-quadruplex DNA and an electrochemically reduced graphene oxide (ERGO) electrode. First, ERGO was formed on a glassy carbon electrode (GCE) by the reduction of graphene oxide (GO) using cyclic voltammetry. Subsequently, a methylene blue (MB)-tagged, guanine-rich DNA aptamer (Apt) was attached to the surface of ERGO via π-π interaction, leading to the Apt-modified ERGO electrode. The presence of Pb2+ could generate the folding of Apt to a G-quadruplex structure. The formation of G-quadruplex resulted in detaching the Apt from the ERGO/GCE, leading to a change in redox current of the MB tag. Electrochemical measurements showed the proposed sensor had an exceptional sensitivity for Pb2+ with a linear range from 10−15 to 10−9 M and a detection limit of 0.51 fM. The sensor also exhibited high selectivity for Pb2+, as well as many other advantages, such as stability, reproducibility, regeneration, as well as simple fabrication and operation processes.

Cell-SELEX-based selection and characterization of a G-quadruplex DNA aptamer against mouse dendritic cells

2016 ◽  
Vol 36 ◽  
pp. 324-332 ◽  
Author(s):  
M. Moghadam ◽  
M. Sankian ◽  
K. Abnous ◽  
A. Varasteh ◽  
S.M. Taghdisi ◽  
...  
Keyword(s):  
Dendritic Cells ◽  
Dna Aptamer ◽  
Quadruplex Dna ◽  
G Quadruplex

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 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).

Sign in / Sign up

Export Citation Format

Share Document