Environmentally Sensitive Fluorescent Nucleoside Analogues for Surveying Dynamic Interconversions of Nucleic Acid Structures

2018 ◽  
Vol 24 (52) ◽  
pp. 13850-13861 ◽  
Author(s):  
Marianna Sholokh ◽  
Rajhans Sharma ◽  
Natalia Grytsyk ◽  
Lyes Zaghzi ◽  
Viktoriia Y. Postupalenko ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Nucleoside Analogues ◽  
Environmentally Sensitive ◽  
Fluorescent Nucleoside ◽  
Nucleic Acid Structures

scholarly journals Novel nucleic acid origami structures and conventional molecular beacon–based platforms: a comparison in biosensing applications

2021 ◽  
Author(s):  
Noemi Bellassai ◽  
Roberta D’Agata ◽  
Giuseppe Spoto
Keyword(s):  
Nucleic Acid ◽  
Structural Properties ◽  
Molecular Beacon ◽  
Dna Origami ◽  
Molecular Beacons ◽  
Conformational Polymorphism ◽  
Functional Systems ◽  
Similarities And Differences ◽  
Nucleic Acid Structures ◽  
Nucleic Acid Sequences

AbstractNucleic acid nanotechnology designs and develops synthetic nucleic acid strands to fabricate nanosized functional systems. Structural properties and the conformational polymorphism of nucleic acid sequences are inherent characteristics that make nucleic acid nanostructures attractive systems in biosensing. This review critically discusses recent advances in biosensing derived from molecular beacon and DNA origami structures. Molecular beacons belong to a conventional class of nucleic acid structures used in biosensing, whereas DNA origami nanostructures are fabricated by fully exploiting possibilities offered by nucleic acid nanotechnology. We present nucleic acid scaffolds divided into conventional hairpin molecular beacons and DNA origami, and discuss some relevant examples by focusing on peculiar aspects exploited in biosensing applications. We also critically evaluate analytical uses of the synthetic nucleic acid structures in biosensing to point out similarities and differences between traditional hairpin nucleic acid sequences and DNA origami. Graphical abstract

scholarly journals Overlapping but distinct: a new model for G-quadruplex biochemical specificity

2021 ◽  
Author(s):  
Martin Volek ◽  
Sofia Kolesnikova ◽  
Katerina Svehlova ◽  
Pavel Srb ◽  
Ráchel Sgallová ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Drug Design ◽  
Solution Structure ◽  
Biochemical Data ◽  
Biological Regulation ◽  
New Model ◽  
G Quadruplex ◽  
Range Of Functions ◽  
Nucleic Acid Structures ◽  
Sequence Requirements

Abstract G-quadruplexes are noncanonical nucleic acid structures formed by stacked guanine tetrads. They are capable of a range of functions and thought to play widespread biological roles. This diversity raises an important question: what determines the biochemical specificity of G-quadruplex structures? The answer is particularly important from the perspective of biological regulation because genomes can contain hundreds of thousands of G-quadruplexes with a range of functions. Here we analyze the specificity of each sequence in a 496-member library of variants of a reference G-quadruplex with respect to five functions. Our analysis shows that the sequence requirements of G-quadruplexes with these functions are different from one another, with some mutations altering biochemical specificity by orders of magnitude. Mutations in tetrads have larger effects than mutations in loops, and changes in specificity are correlated with changes in multimeric state. To complement our biochemical data we determined the solution structure of a monomeric G-quadruplex from the library. The stacked and accessible tetrads rationalize why monomers tend to promote a model peroxidase reaction and generate fluorescence. Our experiments support a model in which the sequence requirements of G-quadruplexes with different functions are overlapping but distinct. This has implications for biological regulation, bioinformatics, and drug design.

ALKYLATION, INTERCALATION, AND CONFORMATIONAL PROPERTIES OF NUCLEIC ACID STRUCTURES

1981 ◽  
Vol 367 (1 Quantum Chemi) ◽  
pp. 295-325 ◽  
Author(s):  
D. Malhotra ◽  
R. Pearlstein ◽  
O. Kikuchi ◽  
S. N. Mohammad ◽  
Y. Nakata ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Conformational Properties ◽  
Nucleic Acid Structures

Four-Stranded Nucleic Acid Structures 25 Years Later: From Guanosine Gels to Telomer DNA

1990 ◽  
Vol 8 (3) ◽  
pp. 491-511 ◽  
Author(s):  
Wilhelm Guschlbauer ◽  
Jean-Francois Chantot ◽  
Danielle Thiele
Keyword(s):  
Nucleic Acid ◽  
Guanosine Gels ◽  
Nucleic Acid Structures

scholarly journals Development of Coarse-Grained Martini Model for Nucleic Acid Structures

2014 ◽  
Vol 106 (2) ◽  
pp. 704a
Author(s):  
Parisa Akhshi ◽  
Jaakko Uusitalo ◽  
Helgi Ingolfsson ◽  
Siewert-Jan Marrink ◽  
D. Peter Tieleman
Keyword(s):  
Nucleic Acid ◽  
Coarse Grained ◽  
Nucleic Acid Structures

scholarly journals Oxadiazole/Pyridine-Based Ligands: A Structural Tuning for Enhancing G-Quadruplex Binding

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2162 ◽  
Author(s):  
Filippo Doria ◽  
Valentina Pirota ◽  
Michele Petenzi ◽  
Marie-Paule Teulade-Fichou ◽  
Daniela Verga ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Structural Transition ◽  
Binding Mode ◽  
Telomeric Sequence ◽  
Recognition Element ◽  
New Family ◽  
G Quadruplex ◽  
Preferential Binding ◽  
High Cytotoxicity ◽  
Nucleic Acid Structures

Non-macrocyclic heteroaryls represent a valuable class of ligands for nucleic acid recognition. In this regard, non-macrocyclic pyridyl polyoxazoles and polyoxadiazoles were recently identified as selective G-quadruplex stabilizing compounds with high cytotoxicity and promising anticancer activity. Herein, we describe the synthesis of a new family of heteroaryls containing oxadiazole and pyridine moieties targeting DNA G-quadruplexes. To perform a structure–activity analysis identifying determinants of activity and selectivity, we followed a convergent synthetic pathway to modulate the nature and number of the heterocycles (1,3-oxazole vs. 1,2,4-oxadiazole and pyridine vs. benzene). Each ligand was evaluated towards secondary nucleic acid structures, which have been chosen as a prototype to mimic cancer-associated G-quadruplex structures (e.g., the human telomeric sequence, c-myc and c-kit promoters). Interestingly, heptapyridyl-oxadiazole compounds showed preferential binding towards the telomeric sequence (22AG) in competitive conditions vs. duplex DNA. In addition, G4-FID assays suggest a different binding mode from the classical stacking on the external G-quartet. Additionally, CD titrations in the presence of the two most promising compounds for affinity, TOxAzaPy and TOxAzaPhen, display a structural transition of 22AG in K-rich buffer. This investigation suggests that the pyridyl-oxadiazole motif is a promising recognition element for G-quadruplexes, combining seven heteroaryls in a single binding unit.

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