Insights into the Mechanism of DNA Cleavage by Dynemicin A as Revealed by DNA-Binding and -Cleavage Studies of Synthetic Analogs

1995 ◽  
Vol 117 (28) ◽  
pp. 7574-7575 ◽  
Author(s):  
Andrew G. Myers ◽  
Scott B. Cohen ◽  
Norma J. Tom ◽  
David J. Madar ◽  
Mark E. Fraley
Keyword(s):  
Dna Binding ◽  
Dna Cleavage ◽  
Synthetic Analogs ◽  
Dna Binding And Cleavage

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.

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.

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 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.

scholarly journals Synthesis, spectral characterization, DNA interaction studies, anthelmintic and antimicrobial activity of transition metal complexes with 3-(2- hydroxybenzylideneamino)-2-methylquinazolin-4(3H)-one and 1,10- phenanthroline

2011 ◽  
Vol 1 (4) ◽  
pp. 127-138 ◽  
Keyword(s):  
Antimicrobial Activity ◽  
Dna Binding ◽  
Dna Cleavage ◽  
Thermal Studies ◽  
Dna Interaction ◽  
Molar Conductance ◽  
H Nmr ◽  
Elemental Analyses ◽  
Dna Binding And Cleavage

Mixed ligand complexes of cobalt(II) (1), copper(II) (2) and oxovanadium(IV) (3) with 3- (2-hydroxy benzylideneamino)-2-methylquinazolin-4(3H)-one and 1,10-phenanthroline have been synthesized and characterized by elemental analyses, IR, electronic, 1 H-NMR, mass spectra, molar conductance and thermal studies. The synthesized compounds were screened for their in vitro antimicrobial activity. The results show a significant increase in antimicrobial activity of the complexes compared to ligand. Antihelmintic activity of the compounds has been tested on earthworms and the enhanced activity was observed upon complexation. In addition, DNA binding and DNA cleavage studies for the newly prepared compounds were also studied. These studies indicate that the DNA binding and cleavage efficacy were increased in the complexes relative to the parental ligand.

Dinuclear Cd(ii), Mn(ii) and Cu(ii) complexes derived from (anthraquinone-1-diyl) benzoate: DNA binding and cleavage studies

RSC Advances ◽  
2014 ◽  
Vol 4 (87) ◽  
pp. 46639-46645 ◽  
Author(s):  
Lin Liu ◽  
Gong-Ming Zhang ◽  
Ru-Gang Zhu ◽  
Yong-Hui Liu ◽  
Hui-Meng Yao ◽  
...  
Keyword(s):  
Dna Binding ◽  
Dna Cleavage ◽  
Dna Binding And Cleavage ◽  
Solvothermal Conditions

Three dinuclear Cd(ii), Mn(ii) and Cu(ii) complexes have been successfully synthesized under solvothermal conditions. Among them, only the Cu(ii) complex has the activity for DNA cleavage.

Synthesis, Structural, DNA Binding and Cleavage Studies of Cu(II) Complexes Containing Benzothiazole Cored Schiff Bases

2016 ◽  
Vol 26 (6) ◽  
pp. 2151-2163 ◽  
Author(s):  
Somapangu Tejaswi ◽  
Marri Pradeep Kumar ◽  
Aveli Rambabu ◽  
Narendrula Vamsikrishna ◽  
Shivaraj
Keyword(s):  
Dna Binding ◽  
Schiff Bases ◽  
Dna Binding And Cleavage

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.

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