scholarly journals Insight into G-quadruplex-hemin DNAzyme/RNAzyme: adjacent adenine as the intramolecular species for remarkable enhancement of enzymatic activity

2016 ◽  
Vol 44 (15) ◽  
pp. 7373-7384 ◽  
Author(s):  
Wang Li ◽  
Yong Li ◽  
Zhuoliang Liu ◽  
Bin Lin ◽  
Haibo Yi ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
G Quadruplex ◽  
Insight Into

The effect of amino substituents on the interactions of quinazolone derivatives with c-KIT G-quadruplex: insight from molecular dynamics simulation study for rational design of ligands

RSC Advances ◽  
2015 ◽  
Vol 5 (93) ◽  
pp. 76642-76650 ◽  
Author(s):  
Kiana Gholamjani Moghaddam ◽  
Seyed Majid Hashemianzadeh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Rational Design ◽  
Ligand Design ◽  
Dynamics Simulation ◽  
Rational Ligand Design ◽  
G Quadruplex ◽  
Ligand Interactions ◽  
Insight Into

Our study provides insight into the effect of different substituents on the G-quadruplex–ligand interactions which helps us rational ligand design.

scholarly journals Impact of a Single Nucleotide Change or Non-Nucleoside Modifications in G-Rich Region on the Quadruplex–Duplex Hybrid Formation

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1236
Author(s):  
Dorota Gudanis ◽  
Karolina Zielińska ◽  
Daniel Baranowski ◽  
Ryszard Kierzek ◽  
Piotr Kozłowski ◽  
...  
Keyword(s):  
Target Sequence ◽  
Rich Region ◽  
Rna Sequences ◽  
Single Nucleotide ◽  
Alternative Structures ◽  
Single Nucleotide Change ◽  
G Quadruplex ◽  
Quadruplex Formation ◽  
Target Rna ◽  
Insight Into

In this paper, a method to discriminate between two target RNA sequences that differ by one nucleotide only is presented. The method relies on the formation of alternative structures, i.e., quadruplex–duplex hybrid (QDH) and duplex with dangling ends (Dss), after hybridization of DNA or RNA G-rich oligonucleotides with target sequences containing 5′–GGGCUGG–3′ or 5′–GGGCGGG–3′ fragments. Using biophysical methods, we studied the effect of oligonucleotide types (DNA, RNA), non-nucleotide modifications (aliphatic linkers or abasic), and covalently attached G4 ligand on the ability of G-rich oligonucleotides to assemble a G-quadruplex motif. We demonstrated that all examined non-nucleotide modifications could mimic the external loops in the G-quadruplex domain of QDH structures without affecting their stability. Additionally, some modifications, in particular the presence of two abasic residues in the G-rich oligonucleotide, can induce the formation of non-canonical QDH instead of the Dss structure upon hybridization to a target sequence containing the GGGCUGG motif. Our results offer new insight into the sequential requirements for the formation of G-quadruplexes and provide important data on the effects of non-nucleotide modifications on G-quadruplex formation.

scholarly journals How to split a G-quadruplex for DNA detection: new insight into the formation of DNA split G-quadruplex

2015 ◽  
Vol 6 (8) ◽  
pp. 4822-4827 ◽  
Author(s):  
Jinbo Zhu ◽  
Libing Zhang ◽  
Shaojun Dong ◽  
Erkang Wang
Keyword(s):  
Dna Detection ◽  
G Quadruplex ◽  
Insight Into

A magic “law of 4 : 8” to split the G-quadruplex for DNA detection has been found.

scholarly journals Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy

2020 ◽  
Vol 21 (8) ◽  
pp. 2673 ◽  
Author(s):  
Kwang-Im Oh ◽  
Jinwoo Kim ◽  
Chin-Ju Park ◽  
Joon-Hwa Lee
Keyword(s):  
Nmr Spectroscopy ◽  
Biological Function ◽  
Conformational Exchange ◽  
Biological Processes ◽  
Dynamic Characterization ◽  
Dynamic Features ◽  
Dna Structures ◽  
Left Handed ◽  
G Quadruplex ◽  
Insight Into

The non-canonical structures of nucleic acids are essential for their diverse functions during various biological processes. These non-canonical structures can undergo conformational exchange among multiple structural states. Data on their dynamics can illustrate conformational transitions that play important roles in folding, stability, and biological function. Here, we discuss several examples of the non-canonical structures of DNA focusing on their dynamic characterization by NMR spectroscopy: (1) G-quadruplex structures and their complexes with target proteins; (2) i-motif structures and their complexes with proteins; (3) triplex structures; (4) left-handed Z-DNAs and their complexes with various Z-DNA binding proteins. This review provides insight into how the dynamic features of non-canonical DNA structures contribute to essential biological processes.

scholarly journals G-Quadruplex loops regulate PARP-1 enzymatic activation

2020 ◽  
Author(s):  
Andrea D Edwards ◽  
John C Marecki ◽  
Alicia K Byrd ◽  
Jun Gao ◽  
Kevin D Raney
Keyword(s):  
Dna Repair ◽  
Enzymatic Activity ◽  
Regulation Of Transcription ◽  
Dna Structures ◽  
Repair Enzymes ◽  
G Quadruplex ◽  
Associated Proteins ◽  
Enzymatic Activation ◽  
Forming Characteristics ◽  
Parp 1

Abstract G-Quadruplexes are non-B form DNA structures present at regulatory regions in the genome, such as promoters of proto-oncogenes and telomeres. The prominence in such sites suggests G-quadruplexes serve an important regulatory role in the cell. Indeed, oxidized G-quadruplexes found at regulatory sites are regarded as epigenetic elements and are associated with an interlinking of DNA repair and transcription. PARP-1 binds damaged DNA and non-B form DNA, where it covalently modifies repair enzymes or chromatin-associated proteins respectively with poly(ADP-ribose) (PAR). PAR serves as a signal in regulation of transcription, chromatin remodeling, and DNA repair. PARP-1 is known to bind G-quadruplexes with stimulation of enzymatic activity. We show that PARP-1 binds several G-quadruplex structures with nanomolar affinities, but only a subset promote PARP-1 activity. The G-quadruplex forming sequence found in the proto-oncogene c-KIT promoter stimulates enzymatic activity of PARP-1. The loop-forming characteristics of the c-KIT G-quadruplex sequence regulate PARP-1 catalytic activity, whereas eliminating these loop features reduces PARP-1 activity. Oxidized G-quadruplexes that have been suggested to form unique, looped structures stimulate PARP-1 activity. Our results support a functional interaction between PARP-1 and G-quadruplexes. PARP-1 enzymatic activation by G-quadruplexes is dependent on the loop features and the presence of oxidative damage.

Molecular insight into the selective binding between human telomere G‐quadruplex and a negatively charged stabilizer

2020 ◽  
Vol 47 (5) ◽  
pp. 892-902 ◽  
Author(s):  
Zhiguo Wang ◽  
Jianfeng Li ◽  
Jun Liu ◽  
Lihui Wang ◽  
Yanhua Lu ◽  
...  
Keyword(s):  
Selective Binding ◽  
G Quadruplex ◽  
Human Telomere ◽  
Insight Into
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