Vaccinia DNA topoisomerase catalyzes the cleavage and re-joining of DNA strands through a DNA-(3'-phosphotyrosyl)-enzyme intermediate formed at a specific target sequence, 5'-(C/T)CCTT downward arrow. The 314 aa protein consists of three protease-resistant structural domains demarcated by protease-sensitive interdomain segments referred to as the bridge and the hinge. The bridge is defined by t...

Background Sperm DNA fragmentation is known as an important cause of male infertility. The influence of sperm DNA damage on reproductive potential has been subject of many studies indicating various results and remaining the subject controversial. In this study, we investigated differences of the semen parameters and intracytoplasmic sperm injection (ICSI) outcome according to sperm DNA fragmen...

Iron promotes DNA damage by catalyzing hydroxyl radical formation. We examined the effect of chromatin structure on DNA susceptibility to oxidant damage. Oxygen radicals generated by H2O2, ascorbate and iron-ADP (1:2 ratio of Fe2+:ADP) extensively and randomly fragmented protein-free DNA, with double-strand breaks demonstrable even at 1 microM iron. In contrast, polynucleosomes from chicken ery...

DNA binding proteins find their cognate sequences within genomic DNA through recognition of specific chemical and structural features. Here we demonstrate that high-resolution DNase I cleavage profiles can provide detailed information about the shape and chemical modification status of genomic DNA. Analyzing millions of DNA backbone hydrolysis events on naked genomic DNA, we show that the intri...

Mn( ii ), Co( and Ni( ) morpholine 2,2′-bipyridine complexes gave potent DNA cleavage, antimicrobial antioxidant activity. Calculations support the results, with Co Ni showing better anticancer efficacy than cisplatin.

Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied characteristic of eukaryotic genome. As active regulatory DNA elements are generally ‘accessible’, genome-wide profiling chromatin accessibility can be used identify candidate genomic regions in tissue cell type. Multiple biochemical methods have been developed profile both bulk and at single-cell level. D...

DNA gyrase introduces negative supercoils into DNA in an ATP-dependent reaction. DNA supercoiling is catalyzed by a strand-passage mechanism, in which a T-segment of DNA is passed through the gap in a transiently cleaved G-segment. Strand passage requires the coordinated closing and opening of three protein interfaces in gyrase, the N-gate, DNA-gate, and C-gate. We show here that DNA binding to...

Continuous labelling of callus with H-thymidine results in intermittent peaks of H-DNA per chloroplast, showing synchrony of division. The increase in H-DNA could be due to several replication rounds, and the drop to successive plastid divisions without intervening DNA synthesis. The level of DNA-binding proteins in the chloroplast parallels the peaks of plastidal DNA synthesis; such pro...

We have designed and synthesized novel intercalating compounds that efficiently hydrolyze supercoiled plasmid DNA lacking depurine/depyrimidine sites. These intercalators consist of conjugates of diamine and thia-heterocyclic naphthalimide. Surprisingly, the initial hydrolyzed products comprised fragments with half the length of the original plasmid. We suggest a mechanochemical mechanism that ...