scholarly journals Synthesis of novel calix[4]arene p-benzazole derivatives and investigation of their DNA binding and cleavage activities with molecular docking and experimental studies

RSC Advances ◽  
2020 ◽  
Vol 10 (63) ◽  
pp. 38695-38708
Author(s):  
Seyda Cigdem Ozkan ◽  
Fatma Aksakal ◽  
Aydan Yilmaz
Keyword(s):  
Molecular Docking ◽  
Dna Binding ◽  
Dna Cleavage ◽  
Experimental Studies ◽  
Binding Properties ◽  
Dna Binding And Cleavage

In this study, p-benzazole-derived calix[4]arene compounds with aromatic structures are synthesized and their DNA cleavage/binding properties are investigated.

Syntheses, crystal structures, DNA binding, DNA cleavage, molecular docking and DFT study of Cu(ii) complexes involving N2O4 donor azo Schiff base ligands

2018 ◽  
Vol 42 (1) ◽  
pp. 246-259 ◽  
Author(s):  
Saikat Banerjee ◽  
Pravat Ghorai ◽  
Paula Brandão ◽  
Dipanjan Ghosh ◽  
Sutanwi Bhuiya ◽  
...  
Keyword(s):  
Schiff Base ◽  
Molecular Docking ◽  
Dna Binding ◽  
Crystal Structures ◽  
Dna Cleavage ◽  
Dft Study ◽  
Schiff Base Ligands ◽  
Dna Binding And Cleavage

DNA binding and cleavage properties of three novel copper(ii) complexes involving azo Schiff base ligands have been studied.

scholarly journals Synthesis, Characterization, DNA Binding, and Photocleavage Activity of Oxorhenium (V) Complexes withα-Diimine and Quinoxaline Ligands

2010 ◽  
Vol 2010 ◽  
pp. 1-9 ◽  
Author(s):  
Christiana A. Mitsopoulou ◽  
Constantinos Dagas
Keyword(s):  
Cyclic Voltammetry ◽  
Dna Binding ◽  
Dna Cleavage ◽  
2D Nmr ◽  
Base Pairs ◽  
Binding Properties ◽  
Supercoiled Form ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Dna Binding Properties

The complex [ReOCl3pq] (1) (where pq = 2-(2′pyridyl)quinoxaline) has been synthesized and fully characterized by UV-Vis, FTIR, 1 and 2D NMR, and cyclic voltammetry (CV). The DNA-binding properties of the complex1as well as of the compounds [ReOCl3bpy] (2), [ReOCl3phen] (3), and pq (4) were investigated by UV-spectrophotometric (melting curves), CV (cyclic voltammetry), and viscosity measurements. Experimental data suggest that complex1intercalates into the DNA base pairs. Upon irradiation, complex1was found to promote the cleavage of plasmid pBR 322 DNA from supercoiled form I to nicked form II. The mechanism of the DNA cleavage by complex1was also investigated.

Tris-chelated complexes of nickel(II) with bipyridine derivatives: DNA binding and cleavage, BSA binding, molecular docking, and cytotoxicity

2019 ◽  
Vol 37 (15) ◽  
pp. 3887-3904 ◽  
Author(s):  
Marzieh Anjomshoa ◽  
Masoud Torkzadeh-Mahani ◽  
Mehdi Sahihi ◽  
Corrado Rizzoli ◽  
Mehdi Ansari ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Dna Binding ◽  
Bsa Binding ◽  
Dna Binding And Cleavage

Half-sandwich iridiumIII complexes with pyrazole-substituted heterocyclic frameworks and their biological applications

2016 ◽  
Vol 40 (12) ◽  
pp. 9968-9980 ◽  
Author(s):  
Sanjay B. Gajera ◽  
Jugal V. Mehta ◽  
Parth Thakor ◽  
Vasudev R. Thakkar ◽  
Piyushkumar C. Chudasama ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Dna Binding ◽  
Metal Complexes ◽  
Antiproliferative Activity ◽  
Dna Cleavage ◽  
Biological Function ◽  
Biological Applications ◽  
Half Sandwich

Enhancement in the biological function, i.e., DNA binding, molecular docking, antiproliferative activity and DNA cleavage, of metal complexes as compared to free ligands is observed.

scholarly journals A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9

2017 ◽  
Author(s):  
Yavuz S. Dagdas ◽  
Janice S. Chen ◽  
Samuel H. Sternberg ◽  
Jennifer A. Doudna ◽  
Ahmet Yildiz
Keyword(s):  
Dna Binding ◽  
Single Molecule ◽  
Dna Cleavage ◽  
Genome Engineering ◽  
Divalent Cations ◽  
Guide Rna ◽  
Single Molecule Fret ◽  
Target Sites ◽  
Multiple Conformations ◽  
Dna Binding And Cleavage

AbstractThe Cas9 endonuclease is widely utilized for genome engineering applications by programming its single-guide RNA and ongoing work is aimed at improving the accuracy and efficiency of DNA targeting. DNA cleavage of Cas9 is controlled by the conformational state of the HNH nuclease domain, but the mechanism that governs HNH activation at on-target DNA while reducing cleavage activity at off-target sites remains poorly understood. Using single-molecule FRET, we identified an intermediate state of S. pyogenes Cas9, representing a conformational checkpoint between DNA binding and cleavage. Upon DNA binding, the HNH domain transitions between multiple conformations before docking into its active state. HNH docking requires divalent cations, but not strand scission, and this docked conformation persists following DNA cleavage. Sequence mismatches between the DNA target and guide RNA prevent transitions from the checkpoint intermediate to the active conformation, providing selective avoidance of DNA cleavage at stably bound off-target sites.

scholarly journals Binding of SPXK- and APXK-peptide motifs to AT-rich DNA. Experimental and theoretical studies.

1998 ◽  
Vol 45 (1) ◽  
pp. 221-231 ◽  
Author(s):  
J Brzeski ◽  
T Grycuk ◽  
A W Lipkowski ◽  
W Rudnicki ◽  
B Lesyng ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Dna Binding ◽  
Experimental Studies ◽  
Binding Mode ◽  
Binding Modes ◽  
Binding Properties ◽  
Peptide Motifs ◽  
Gel Shift Assay ◽  
Molecular Modeling Studies ◽  
Gel Shift

The binding properties of the SPXK- and APXK-type peptides to the AT-rich DNA fragments of different length were studied by measuring the competition of peptides with Hoechst 33258 dye for DNA binding and by the gel shift assay analysis. In parallel to the experimental studies, molecular modeling techniques were used to analyze possible binding modes of the SPXZ and APXK motifs to the AT-rich DNA. The results of the competition measurements and gel shift assays suggest that serine at the i-1 position (i is proline) can be replaced by alanine without affecting the binding properties of the motif. Thus, the presence of the conserved serine in this motif in many DNA-binding proteins is probably not dictated by structural requirements. Based on the results of molecular modeling studies we propose that the binding mode of the SPXK-type motifs to the AT-rich DNA resembles closely that between the N-terminal arm of the homeodomain and DNA. This model confirms that serine in the SPXK motifs is not essential for the DNA binding. The model also indicates that if X in the motif is glutamic acid, this residue is probably protonated in the complex with DNA.

scholarly journals Inhibition of CRISPR-Cas12a DNA Targeting by Nucleosomes and Chromatin

2020 ◽  
Author(s):  
Isabel Strohkendl ◽  
Fatema A. Saifuddin ◽  
Bryan A. Gibson ◽  
Michael K. Rosen ◽  
Rick Russell ◽  
...  
Keyword(s):  
Dna Binding ◽  
Histone Modifications ◽  
Dna Cleavage ◽  
Genome Engineering ◽  
Eukaryotic Cells ◽  
Loop Formation ◽  
Core Particle ◽  
Dna Targeting ◽  
Dna Binding And Cleavage ◽  
Nucleosome Arrays

AbstractGenome engineering nucleases, including CRISPR-Cas12a, must access chromatinized DNA. Here, we investigate how Acidaminococcus sp. Cas12a cleaves DNA within human nucleosomes and phase-condensed nucleosome arrays. Using quantitative kinetics approaches, we show that dynamic nucleosome unwrapping regulates DNA target accessibility to Cas12a. Nucleosome unwrapping determines the extent to which both steps of Cas12a binding–PAM recognition and R-loop formation–are inhibited by the nucleosome. Nucleosomes inhibit Cas12a binding even beyond the canonical core particle. Relaxing DNA wrapping within the nucleosome by reducing DNA bendability, adding histone modifications, or introducing a target-proximal nuclease-inactive Cas9 enhances DNA cleavage rates over 10-fold. Surprisingly, Cas12a readily cleaves DNA linking nucleosomes within chromatin-like phase separated nucleosome arrays—with DNA targeting reduced only ~4-fold. This work provides a mechanism for the observation that on-target cleavage within nucleosomes occurs less often than off-target cleavage within nucleosome-depleted regions of cells. We conclude that nucleosome wrapping restricts accessibility to CRISPR-Cas nucleases and anticipate that increasing nucleosome breathing dynamics will improve DNA binding and cleavage in eukaryotic cells.

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