Synthesis, Spectroscopic, Antibacterial, Antioxidant, DNA Binding and Cleavage, Molecular Docking Studies of Ni(II) and Cu(II) Complexes of S and N Donor Schiff Base Ligands

Binary metal complexes of the ligands (L), H3FPT and H3FP4MT with Ni(II) and Cu(II) metal ions (M) were synthesized and characterized by different spectral and analytical techniques. Among these complexes, Ni(II)- H3FPT complex was found to be polymeric. The ligands and their complexes inhibited the growth of gram positive and gram negative bacterial strains to a moderate extent. The antioxidant nature of ligands and complexes was also established. Intercalative mode of binding of the complexes with calf thymus (CT) DNA was proposed from electronic absorption titrations, fluorescence quenching studies and viscosity measurements. The complexes showed hydrolytic cleavage of plasmid pBR322. Docking studies of metal complexes with DNA revealed that the complexes of H3FP4MT are more active than H3FPT.

Cas12a is a dynamic and precise RNA-guided nuclease without off-target activity on λ-DNA

Cas12a is an RNA-guided endonuclease that is emerging as a powerful genome-editing tool. Here we combined optical tweezers with fluorescence to monitor Cas12a binding onto λ-DNA, providing insight into its DNA binding and cleavage mechanisms. At low forces Cas12a binds DNA specifically with two off-target sites, while at higher forces numerous binding events appear driven by the mechanical distortion of the DNA and partial matches to the crRNA. Despite the multiple binding events, cleavage is only observed on the target site at low forces, when the DNA is flexible. Activity assays show that the preferential off-target sites are not cleaved, and the λ-DNA is severed at the target site. This precision is also observed in Cas12a variants where the specific dsDNA and the unspecific ssDNA cleavage are dissociated or nick the target DNA. We propose that Cas12a and its variants are precise endonucleases that efficiently scan the DNA for its target but only cleave the selected site in the λ-DNA.

Inhibition of CRISPR-Cas12a DNA Targeting by Nucleosomes and Chromatin

Genome 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.

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

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

Octahedral copper(ii)-diimine complexes of triethylenetetramine: effect of stereochemical fluxionality and ligand hydrophobicity on CuII/CuI redox, DNA binding and cleavage, cytotoxicity and apoptosis-inducing ability

Stereochemical fluxionality of octahedral [Cu(trien)(diimine)]2+ complexes determines the CuII/CuI redox potential, DNA binding affinity, ROS generation, cytotoxicity and apoptosis-inducing ability.