scholarly journals Structural revisions of small molecules reported to cross-link G-quadruplex DNA in vivo reveal a repetitive assignment error in the literature

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Paul E. Reyes-Gutiérrez ◽  
Tomáš Kapal ◽  
Blanka Klepetářová ◽  
David Šaman ◽  
Radek Pohl ◽  
...  
Keyword(s):  
Small Molecules ◽  
Cross Link ◽  
Quadruplex Dna ◽  
Mistaken Identity ◽  
G Quadruplex ◽  
Assignment Error

Abstract Two molecules of mistaken identity are addressed. Uncovering these assignment errors led us to formulate more general guidelines about additional misassignments in cases of published bis-imines derived from 1,2-phenylenediamine and hydroxybenzaldehydes having no substituent in ortho-positions. The main purpose of this article is to highlight this repetitive assignment error in the literature and thus increase the likelihood of correct assignments in future papers.

scholarly journals Erratum: Corrigendum: Structural revisions of small molecules reported to cross-link G-quadruplex DNA in vivo reveal a repetitive assignment error in the literature

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Paul E. Reyes-Gutiérrez ◽  
Tomáš Kapal ◽  
Blanka Klepetářová ◽  
David Šaman ◽  
Radek Pohl ◽  
...  
Keyword(s):  
Small Molecules ◽  
Cross Link ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Assignment Error

scholarly journals Erratum: Structural revisions of small molecules reported to cross-link G-quadruplex DNA in vivo reveal a repetitive assignment error in the literature

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Paul E. Reyes-Gutiérrez ◽  
Tomáš Kapal ◽  
Blanka Klepetářová ◽  
David Šaman ◽  
Radek Pohl ◽  
...  
Keyword(s):  
Small Molecules ◽  
Cross Link ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Assignment Error

scholarly journals G-quadruplex DNA drives genomic instability and represents a targetable molecular abnormality in ATRX-deficient malignant glioma

2018 ◽  
Author(s):  
Yuxiang Wang ◽  
Jie Yang ◽  
Wei Wu ◽  
Rachna Shah ◽  
Carla Danussi ◽  
...  
Keyword(s):  
Dna Damage ◽  
Malignant Glioma ◽  
Model Systems ◽  
Copy Number Alterations ◽  
Molecular Alteration ◽  
Quadruplex Dna ◽  
G4 Dna ◽  
G Quadruplex

AbstractMutational inactivation of ATRX (α-thalassemia mental retardation X-linked) represents a defining molecular alteration in large subsets of malignant glioma. Yet the pathogenic consequences of ATRX deficiency remain unclear, as do tractable mechanisms for its therapeutic targeting. Here we report that ATRX loss in isogenic glioma model systems induces replication stress and DNA damage by way of G-quadruplex (G4) DNA secondary structure. Moreover, these effects are associated with the acquisition of disease-relevant copy number alterations over time. We then demonstrate, both in vitro and in vivo, that ATRX deficiency selectively enhances DNA damage and cell death following chemical G4 stabilization. Finally, we show that G4 stabilization synergizes with other DNA-damaging therapies, including ionizing radiation, in the ATRX-deficient context. Our findings reveal novel pathogenic mechanisms driven by ATRX deficiency in glioma, while also pointing to tangible strategies for drug development.

scholarly journals N-methyl mesoporphyrin IX as a highly selective light-up probe for G-quadruplex DNA

2019 ◽  
Vol 23 (11n12) ◽  
pp. 1195-1215 ◽  
Author(s):  
Ariana Yett ◽  
Linda Yingqi Lin ◽  
Dana Beseiso ◽  
Joanne Miao ◽  
Liliya A. Yatsunyk
Keyword(s):  
Optical Properties ◽  
Small Molecules ◽  
Genomic Stability ◽  
Water Soluble ◽  
Biological Processes ◽  
Binding Properties ◽  
Quadruplex Dna ◽  
Dna Structures ◽  
G Quadruplex ◽  
High Fluorescence

[Formula: see text]-methyl mesoporphyrin IX (NMM) is a water-soluble, non-symmetric porphyrin with excellent optical properties and unparalleled selectivity for G-quadruplex (GQ) DNA. G-quadruplexes are non-canonical DNA structures formed by guanine-rich sequences. They are implicated in genomic stability, longevity, and cancer. The ability of NMM to selectively recognize GQ structures makes it a valuable scaffold for designing novel GQ binders. In this review, we survey the literature describing the GQ-binding properties of NMM as well as its wide utility in chemistry and biology. We start with the discovery of the GQ-binding properties of NMM and the development of NMM-binding aptamers. We then discuss the optical properties of NMM, focusing on the light-switch effect — high fluorescence of NMM induced upon its binding to GQ DNA. Additionally, we examine the affinity and selectivity of NMM for GQs, as well as its ability to stabilize GQ structures and favor parallel GQ conformations. Furthermore, a portion of the review is dedicated to the applications of NMM-GQ complexes as biosensors for heavy metals, small molecules ([Formula: see text] ATP and pesticides), DNA, and proteins. Finally and importantly, we discuss the utility of NMM as a probe to investigate the roles of GQs in biological processes.

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 Evaluation of small molecules that bind and stabilize G-Quadruplex DNA

2020 ◽  
Author(s):  
Jeremy McCallum
Keyword(s):  
Small Molecules ◽  
Quadruplex Dna ◽  
G Quadruplex

scholarly journals Enhanced sampling molecular dynamics simulations correctly predict the diverse activities of a series of stiff-stilbene G-quadruplex DNA ligands

2021 ◽  
Author(s):  
Michael P. O'Hagan ◽  
Susanta Haldar ◽  
Juan C. Morales ◽  
Adrian J. Mulholland ◽  
M. Carmen Galan
Keyword(s):  
Molecular Dynamics ◽  
Small Molecules ◽  
Molecular Dynamics Simulations ◽  
Solution Phase ◽  
Enhanced Sampling ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Dynamics Simulations

Enhanced sampling molecular dynamics simulations and solution-phase experiments come together to demonstrate the diverse effects of G4-interactive small molecules.

Recent advances in targeting the telomeric G-quadruplex DNA sequence with small molecules as a strategy for anticancer therapies

2016 ◽  
Vol 8 (11) ◽  
pp. 1259-1290 ◽  
Author(s):  
Mohammad K Islam ◽  
Paul JM Jackson ◽  
Khondaker M Rahman ◽  
David E Thurston
Keyword(s):  
Small Molecules ◽  
Dna Sequence ◽  
Quadruplex Dna ◽  
Recent Advances ◽  
G Quadruplex

scholarly journals G‐quadruplex‐binding small molecules ameliorate C9orf72 FTD / ALS pathology in vitro and in vivo

2017 ◽  
Vol 10 (1) ◽  
pp. 22-31 ◽  
Author(s):  
Roberto Simone ◽  
Rubika Balendra ◽  
Thomas G Moens ◽  
Elisavet Preza ◽  
Katherine M Wilson ◽  
...  
Keyword(s):  
Small Molecules ◽  
G Quadruplex
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