DNA and RNA in Anhydrous Media: Duplex, Triplex, and G-Quadruplex Secondary Structures in a Deep Eutectic Solvent

2010 ◽  
Vol 49 (36) ◽  
pp. 6310-6314 ◽  
Author(s):  
Irena Mamajanov ◽  
Aaron E. Engelhart ◽  
Heather D. Bean ◽  
Nicholas V. Hud
Keyword(s):  
Deep Eutectic Solvent ◽  
Secondary Structures ◽  
Dna And Rna ◽  
G Quadruplex

DNA and RNA in Anhydrous Media: Duplex, Triplex, and G-Quadruplex Secondary Structures in a Deep Eutectic Solvent

2010 ◽  
Vol 122 (36) ◽  
pp. 6454-6458 ◽  
Author(s):  
Irena Mamajanov ◽  
Aaron E. Engelhart ◽  
Heather D. Bean ◽  
Nicholas V. Hud
Keyword(s):  
Deep Eutectic Solvent ◽  
Secondary Structures ◽  
Dna And Rna ◽  
G Quadruplex

Chemical-biology approaches to probe DNA and RNA G-quadruplex structures in the genome

2020 ◽  
Vol 56 (9) ◽  
pp. 1317-1324 ◽  
Author(s):  
Federica Raguseo ◽  
Souroprobho Chowdhury ◽  
Aisling Minard ◽  
Marco Di Antonio
Keyword(s):  
Nucleic Acids ◽  
Chemical Biology ◽  
Secondary Structures ◽  
Biological Functions ◽  
Physiological Conditions ◽  
Dna And Rna ◽  
G Quadruplex

G-quadruplexes are nucleic-acids secondary structures that can be formed under physiological conditions. In this review, we critically present the most relevant chemical-biology methods to probe the biological functions of G-quadruplex structures.

scholarly journals Pif1 is essential for efficient replisome progression through lagging strand G-quadruplex DNA secondary structures

2018 ◽  
Vol 46 (22) ◽  
pp. 11847-11857 ◽  
Author(s):  
Danielle Dahan ◽  
Ioannis Tsirkas ◽  
Daniel Dovrat ◽  
Melanie A Sparks ◽  
Saurabh P Singh ◽  
...  
Keyword(s):  
Secondary Structures ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Dna Secondary Structures ◽  
Lagging Strand

scholarly journals G-Quadruplex-Based Drug Delivery Systems for Cancer Therapy

2021 ◽  
Vol 14 (7) ◽  
pp. 671
Author(s):  
Jéssica Lopes-Nunes ◽  
Paula Oliveira ◽  
Carla Cruz
Keyword(s):  
Drug Delivery ◽  
Small Molecules ◽  
Drug Delivery Systems ◽  
Delivery Systems ◽  
Nano Particles ◽  
Future Research ◽  
High Affinity ◽  
Dna And Rna ◽  
G Quadruplex ◽  
Gold Nano Particles

G-quadruplexes (G4s) are a class of nucleic acids (DNA and RNA) with single-stranded G-rich sequences. Owing to the selectivity of some G4s, they are emerging as targeting agents to overtake side effects of several potential anticancer drugs, and delivery systems of small molecules to malignant cells, through their high affinity or complementarity to specific targets. Moreover, different systems are being used to improve their potential, such as gold nano-particles or liposomes. Thus, the present review provides relevant data about the different studies with G4s as drug delivery systems and the challenges that must be overcome in the future research.

scholarly journals EXO1 resection at G-quadruplex structures facilitates resolution and replication

2020 ◽  
Vol 48 (9) ◽  
pp. 4960-4975 ◽  
Author(s):  
Susanna Stroik ◽  
Kevin Kurtz ◽  
Kevin Lin ◽  
Sergey Karachenets ◽  
Chad L Myers ◽  
...  
Keyword(s):  
Dna Replication ◽  
Genomic Instability ◽  
Secondary Structures ◽  
Replication Forks ◽  
End Joining ◽  
G Quadruplex ◽  
Exonuclease 1 ◽  
Telomere Loss

Abstract G-quadruplexes represent unique roadblocks to DNA replication, which tends to stall at these secondary structures. Although G-quadruplexes can be found throughout the genome, telomeres, due to their G-richness, are particularly predisposed to forming these structures and thus represent difficult-to-replicate regions. Here, we demonstrate that exonuclease 1 (EXO1) plays a key role in the resolution of, and replication through, telomeric G-quadruplexes. When replication forks encounter G-quadruplexes, EXO1 resects the nascent DNA proximal to these structures to facilitate fork progression and faithful replication. In the absence of EXO1, forks accumulate at stabilized G-quadruplexes and ultimately collapse. These collapsed forks are preferentially repaired via error-prone end joining as depletion of EXO1 diverts repair away from error-free homology-dependent repair. Such aberrant repair leads to increased genomic instability, which is exacerbated at chromosome termini in the form of dysfunction and telomere loss.

scholarly journals G-Quadruplexes in the Archaea Domain

Biomolecules ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1349
Author(s):  
Václav Brázda ◽  
Yu Luo ◽  
Martin Bartas ◽  
Patrik Kaura ◽  
Otilia Porubiaková ◽  
...  
Keyword(s):  
Random Distribution ◽  
Dna Structures ◽  
Cellular Processes ◽  
Dna And Rna ◽  
Non Coding Rna ◽  
Archaeal Species ◽  
G Quadruplex ◽  
Potential Part ◽  
Functional Relevance ◽  
Eukaryotic Genomes

The importance of unusual DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes (G4s) have gained in popularity during the last decade, and their presence and functional relevance at the DNA and RNA level has been demonstrated in a number of viral, bacterial, and eukaryotic genomes, including humans. Here, we performed the first systematic search of G4-forming sequences in all archaeal genomes available in the NCBI database. In this article, we investigate the presence and locations of G-quadruplex forming sequences using the G4Hunter algorithm. G-quadruplex-prone sequences were identified in all archaeal species, with highly significant differences in frequency, from 0.037 to 15.31 potential quadruplex sequences per kb. While G4 forming sequences were extremely abundant in Hadesarchaea archeon (strikingly, more than 50% of the Hadesarchaea archaeon isolate WYZ-LMO6 genome is a potential part of a G4-motif), they were very rare in the Parvarchaeota phylum. The presence of G-quadruplex forming sequences does not follow a random distribution with an over-representation in non-coding RNA, suggesting possible roles for ncRNA regulation. These data illustrate the unique and non-random localization of G-quadruplexes in Archaea.

Light-Induced Formation of G-Quadruplex DNA Secondary Structures

ChemBioChem ◽  
2005 ◽  
Vol 6 (11) ◽  
pp. 1966-1970 ◽  
Author(s):  
Günter Mayer ◽  
Lenz Kröck ◽  
Vera Mikat ◽  
Marianne Engeser ◽  
Alexander Heckel
Keyword(s):  
Secondary Structures ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Dna Secondary Structures

scholarly journals Perspectives for Applying G-Quadruplex Structures in Neurobiology and Neuropharmacology

2019 ◽  
Vol 20 (12) ◽  
pp. 2884 ◽  
Author(s):  
Sefan Asamitsu ◽  
Masayuki Takeuchi ◽  
Susumu Ikenoshita ◽  
Yoshiki Imai ◽  
Hirohito Kashiwagi ◽  
...  
Keyword(s):  
Neurological Disorders ◽  
Neurological Diseases ◽  
Secondary Structures ◽  
Neuronal Function ◽  
Double Stranded Rna ◽  
Quadruplex Dna ◽  
Functional Roles ◽  
G Quadruplex ◽  
Dna Secondary Structures

The most common form of DNA is a right-handed helix or the B-form DNA. DNA can also adopt a variety of alternative conformations, non-B-form DNA secondary structures, including the DNA G-quadruplex (DNA-G4). Furthermore, besides stem-loops that yield A-form double-stranded RNA, non-canonical RNA G-quadruplex (RNA-G4) secondary structures are also observed. Recent bioinformatics analysis of the whole-genome and transcriptome obtained using G-quadruplex–specific antibodies and ligands, revealed genomic positions of G-quadruplexes. In addition, accumulating evidence pointed to the existence of these structures under physiologically- and pathologically-relevant conditions, with functional roles in vivo. In this review, we focused on DNA-G4 and RNA-G4, which may have important roles in neuronal function, and reveal mechanisms underlying neurological disorders related to synaptic dysfunction. In addition, we mention the potential of G-quadruplexes as therapeutic targets for neurological diseases.

scholarly journals Reactive OFF-ON type alkylating agents for higher-ordered structures of nucleic acids

2019 ◽  
Vol 47 (13) ◽  
pp. 6578-6589 ◽  
Author(s):  
Kazumitsu Onizuka ◽  
Madoka E Hazemi ◽  
Norihiro Sato ◽  
Gen-ichiro Tsuji ◽  
Shunya Ishikawa ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Alkylating Agents ◽  
Side Reactions ◽  
Ordered Structures ◽  
Dna And Rna ◽  
G Quadruplex ◽  
Significant Research ◽  
Order Structures ◽  
Ap Site ◽  
Double Strand Dna

Abstract Higher-ordered structure motifs of nucleic acids, such as the G-quadruplex (G-4), mismatched and bulge structures, are significant research targets because these structures are involved in genetic control and diseases. Selective alkylation of these higher-order structures is challenging due to the chemical instability of the alkylating agent and side-reactions with the single- or double-strand DNA and RNA. We now report the reactive OFF-ON type alkylating agents, vinyl-quinazolinone (VQ) precursors with a sulfoxide, thiophenyl or thiomethyl group for the OFF-ON control of the vinyl reactivity. The stable VQ precursors conjugated with aminoacridine, which bind to the G-4 DNA, selectively reacted with a T base on the G-4 DNA in contrast to the single- and double-strand DNA. Additionally, the VQ precursor reacted with the T or U base in the AP-site, G-4 RNA and T-T mismatch structures. These VQ precursors would be a new candidate for the T or U specific alkylation in the higher-ordered structures of nucleic acids.

scholarly journals A short peptide that preferentially binds c-MYC G-quadruplex DNA

2020 ◽  
Vol 56 (63) ◽  
pp. 8940-8943 ◽  
Author(s):  
Aisling Minard ◽  
Danielle Morgan ◽  
Federica Raguseo ◽  
Anna Di Porzio ◽  
Denise Liano ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Human Genome ◽  
Promoter Region ◽  
Secondary Structures ◽  
Quadruplex Dna ◽  
Short Peptide ◽  
G Quadruplex

G-quadruplexes are nucleic-acids secondary structures that are highly abundant in the human genome. In this work,we identified a short-peptide that displays selectivity for the G-quadruplex formed in the promoter region of the oncogene c-MYC.

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