dna cleavage

Summary

Summary: A reaction that severs one of the covalent sugar-phosphate linkages between NUCLEOTIDES that compose the sugar phosphate backbone of DNA. It is catalyzed enzymatically, chemically or by radiation. Cleavage may be exonucleolytic - removing the end nucleotide, or endonucleolytic - splitting the strand in two.

Top Publications

  1. de Laat W, Dekker J. 3C-based technologies to study the shape of the genome. Methods. 2012;58:189-91 pubmed publisher
  2. Zylicz Stachula A, Zolnierkiewicz O, Jasiecki J, Skowron P. A new genomic tool, ultra-frequently cleaving TaqII/sinefungin endonuclease with a combined 2.9-bp recognition site, applied to the construction of horse DNA libraries. BMC Genomics. 2013;14:370 pubmed publisher
    ..9-bp REase, with 70 shortened variants of the canonical recognition sequence detected. Because partial DNA cleavage is an inherent feature of the Thermus sp...
  3. Bazrafshan A, Ghaedi M, Hajati S, Naghiha R, Asfaram A. Synthesis of ZnO-nanorod-based materials for antibacterial, antifungal activities, DNA cleavage and efficient ultrasound-assisted dyes adsorption. Ecotoxicol Environ Saf. 2017;142:330-337 pubmed publisher
    ..Therefore, additional studies were performed which showed efficient antibacterial/antifungal activities and DNA cleavage of undoped and Au-doped ZnO nanorods as constituent of the adsorbent applied here.
  4. Sheng G, Gogakos T, Wang J, Zhao H, Serganov A, Juranek S, et al. Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes. Nucleic Acids Res. 2017;45:9149-9163 pubmed publisher
    ..These structural studies are complemented by cleavage assays that independently monitor the impact of bulges on TtAgo-mediated cleavage reaction. ..
  5. Adhikari A, Kumari N, Adhikari M, Kumar N, Tiwari A, Shukla A, et al. Zinc complex of tryptophan appended 1,4,7,10-tetraazacyclododecane as potential anticancer agent: Synthesis and evaluation. Bioorg Med Chem. 2017;25:3483-3490 pubmed publisher
    ..56GBq/µmol). Avid tumor/muscle ratio of >6 was depicted in biodistribution and SPECT imaging studies in U-87 MG xenograft model nude mice. ..
  6. Elghamry I, Youssef M, Al Omair M, Elsawy H. Synthesis, antimicrobial, DNA cleavage and antioxidant activities of tricyclic sultams derived from saccharin. Eur J Med Chem. 2017;139:107-113 pubmed publisher
    ..The MIC values of the tested compounds are in the of range 8-33 ?g/ml. In addition, their DNA cleavage ability, binding affinity and their anticancer activities against hepatic cancer cell were tested...
  7. Xu W, Xue X, Li T, Zeng H, Liu X. Ultrasensitive and selective colorimetric DNA detection by nicking endonuclease assisted nanoparticle amplification. Angew Chem Int Ed Engl. 2009;48:6849-52 pubmed publisher
  8. Alatrash N, Narh E, Yadav A, Kim M, Janaratne T, Gabriel J, et al. Synthesis, DNA Cleavage Activity, Cytotoxicity, Acetylcholinesterase Inhibition, and Acute Murine Toxicity of Redox-Active Ruthenium(II) Polypyridyl Complexes. ChemMedChem. 2017;12:1055-1069 pubmed publisher
    ..These, plus several structurally related but non-redox-active RPCs, were screened for DNA cleavage activity, cytotoxicity, acetylcholinesterase (AChE) inhibition, and acute mouse toxicity, and their activities ..
  9. Jensen K, Fløe L, Petersen T, Huang J, Xu F, Bolund L, et al. Chromatin accessibility and guide sequence secondary structure affect CRISPR-Cas9 gene editing efficiency. FEBS Lett. 2017;591:1892-1901 pubmed publisher
    ..This knowledge can aid in the further improvement of tools for gRNA design. ..

More Information

Publications36

  1. Wani T, Chakrabarty A, Shibata N, Yamazaki H, Guengerich F, Chowdhury G. The Dihydroxy Metabolite of the Teratogen Thalidomide Causes Oxidative DNA Damage. Chem Res Toxicol. 2017;30:1622-1628 pubmed publisher
    ..A mechanism of teratogenicity is proposed that not only explains the DNA-damaging property but also the metabolism, low concentration, and species-specificity requirements of thalidomide. ..
  2. Minniti E, Byl J, Riccardi L, Sissi C, Rosini M, De Vivo M, et al. Novel xanthone-polyamine conjugates as catalytic inhibitors of human topoisomerase IIα. Bioorg Med Chem Lett. 2017;27:4687-4693 pubmed publisher
    ..On the basis of activity, competition, and modeling studies, we propose that xanthones interact with the DNA cleavage/ligation active site of topoisomerase IIα and inhibit the catalytic activity of the enzyme by interfering with ..
  3. Skowron P, Anton B, Czajkowska E, Zebrowska J, Sulecka E, Krefft D, et al. The third restriction-modification system from Thermus aquaticus YT-1: solving the riddle of two TaqII specificities. Nucleic Acids Res. 2017;45:9005-9018 pubmed publisher
    ..Putative positions and aa that specify DNA recognition were identified and recognition motifs for 6 uncharacterized Thermus-family enzymes were predicted. ..
  4. Lee J, Kim M, Seo Y, Lee Y, Park H, Byun S, et al. The catalytic activity of a recombinant single chain variable fragment nucleic acid-hydrolysing antibody varies with fusion tag and expression host. Arch Biochem Biophys. 2017;633:110-117 pubmed publisher
    ..Thus, we demonstrate that the antigen-binding and catalytic activities of a catalytic antibody can be separately affected by the presence of additional residues at the N- and C-termini, and by the host cell type. ..
  5. Kumar S, Sukhvinder -, Kumar V, Gupta G, Beniwal V, Abdmouleh F, et al. Antibacterial, tyrosinase, and DNA photocleavage studies of some triazolylnucleosides. Nucleosides Nucleotides Nucleic Acids. 2017;36:543-551 pubmed publisher
    ..The compounds 8 and 12 exhibited excellent DNA photocleavage activity at a concentration of 10 ?g and may be used as template for antitumor drugs in the future. ..
  6. Barrangou R. RNA events. Cas9 targeting and the CRISPR revolution. Science. 2014;344:707-8 pubmed publisher
  7. Stella S, Alcón P, Montoya G. Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage. Nature. 2017;546:559-563 pubmed publisher
    ..by determining the structure of Francisella novicida Cpf1 with the triple-stranded R-loop generated after DNA cleavage. The structure reveals the machinery involved in DNA unwinding to form a CRISPR RNA (crRNA)-DNA hybrid and a ..
  8. Li P, Jiang H, Zhang W, Li Y, Zhao M, Zhou W, et al. Synthesis of carbazole derivatives containing chalcone analogs as non-intercalative topoisomerase II catalytic inhibitors and apoptosis inducers. Eur J Med Chem. 2018;145:498-510 pubmed publisher
    ..It was further confirmed by Annexin-V-FITC binding assay. Western blot analysis revealed that compound 3h induces apoptosis likely through the activation of caspase proteins. ..
  9. Tu M, Lin L, Cheng Y, He X, Sun H, Xie H, et al. A 'new lease of life': FnCpf1 possesses DNA cleavage activity for genome editing in human cells. Nucleic Acids Res. 2017;45:11295-11304 pubmed publisher
    ..Surprisingly, we found that FnCpf1 possesses DNA cleavage activity in human cells at multiple loci...
  10. Zarnegar M, Reinitz F, Newman A, Clarke M. Targeted chromatin ligation, a robust epigenetic profiling technique for small cell numbers. Nucleic Acids Res. 2017;45:e153 pubmed publisher
    ..Our technique eliminates loss of material and sensitivity due to multiple inefficient steps, while simplifying the workflow to enhance sensitivity and create the potential for novel applications...
  11. Yang Z, Price N, Johnson K, Wang Y, Gates K. Interstrand cross-links arising from strand breaks at true abasic sites in duplex DNA. Nucleic Acids Res. 2017;45:6275-6283 pubmed publisher
    ..LC-MS/MS methods developed herein provide powerful tools for studying the occurrence and properties of these cross-links in biochemical and biological systems. ..
  12. Jain S, Khan T, Patil Y, Pagariya D, Kishore N, Tapryal S, et al. Bio-affinity of copper(II) complexes with nitrogen and oxygen donor ligands: Synthesis, structural studies and in vitro DNA and HSA interaction of copper(II) complexes. J Photochem Photobiol B. 2017;174:35-43 pubmed publisher
    ..The DNA cleaving activity of all the three complexes was explored in the presence of reactive oxygen compound, H2O2. All the three complexes have primarily shown the DNA cleaving activity. ..
  13. Qayyum S, Oves M, Khan A. Obliteration of bacterial growth and biofilm through ROS generation by facilely synthesized green silver nanoparticles. PLoS ONE. 2017;12:e0181363 pubmed publisher
    ..AgNPs generated ROS on interaction with bacterial cells and this ROS production can be one of the possible reasons for their action. AgNPs exhibited no toxic effect on the cell viability of HeLa cell line. ..
  14. Gautam S, Chen J, Murray V. The DNA sequence specificity of bleomycin cleavage in a systematically altered DNA sequence. J Biol Inorg Chem. 2017;22:881-892 pubmed publisher
    ..A comparison with genome-wide results was also performed and while the core sequence was similar in both environments, the surrounding nucleotides were different. ..
  15. Ashley R, Blower T, Berger J, Osheroff N. Recognition of DNA Supercoil Geometry by Mycobacterium tuberculosis Gyrase. Biochemistry. 2017;56:5440-5448 pubmed publisher
    ..Canonical gyrase and topoisomerase IV distinguish supercoil handedness differently during the DNA cleavage reaction: while gyrase maintains lower levels of cleavage complexes on overwound DNA, topoisomerase IV ..
  16. Usman A, Ahmad M. Binding of Bisphenol-F, a bisphenol analogue, to calf thymus DNA by multi-spectroscopic and molecular docking studies. Chemosphere. 2017;181:536-543 pubmed publisher
    ..BPF induced DNA cleavage under in vitro conditions by plasmid nicking assay suggested it to be genotoxic.
  17. Sasnauskas G, Tamulaitiene G, Tamulaitis G, Calyševa J, Laime M, Rimseliene R, et al. UbaLAI is a monomeric Type IIE restriction enzyme. Nucleic Acids Res. 2017;45:9583-9594 pubmed publisher
    ..REases specific for a common recognition site often vary in their oligomeric structure, domain organization and DNA cleavage mechanisms...
  18. Oliva C, Sánchez Murcia P, Rico E, Bravo A, Menendez M, Gago F, et al. Structure-based domain assignment in Leishmania infantum EndoG: characterization of a pH-dependent regulatory switch and a C-terminal extension that largely dictates DNA substrate preferences. Nucleic Acids Res. 2017;45:9030-9045 pubmed publisher
  19. Gou Y, Li J, Fan B, Xu B, Zhou M, Yang F. Structure and biological properties of mixed-ligand Cu(II) Schiff base complexes as potential anticancer agents. Eur J Med Chem. 2017;134:207-217 pubmed publisher
  20. Kostiuk G, Dikic J, Schwarz F, Sasnauskas G, Seidel R, Siksnys V. The dynamics of the monomeric restriction endonuclease BcnI during its interaction with DNA. Nucleic Acids Res. 2017;45:5968-5979 pubmed publisher
    ..These results provide new insights into the intricate dynamics of BcnI-DNA interactions. ..
  21. Elsayed M, Su Y, Wang P, Sethi T, Agama K, Ravji A, et al. Design and Synthesis of Chlorinated and Fluorinated 7-Azaindenoisoquinolines as Potent Cytotoxic Anticancer Agents That Inhibit Topoisomerase I. J Med Chem. 2017;60:5364-5376 pubmed publisher
    ..630 ?M) range. Compounds 16b and 17b are the most potent in human cancer cell cultures with MGM GI50 values of 0.063 and 0.033 ?M, respectively. Possible binding modes to Top1 and TDP1were investigated by molecular modeling. ..
  22. Niyonzima N, Lambert A, Werther R, De Silva Feelixge H, Roychoudhury P, Greninger A, et al. Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analyses. Protein Eng Des Sel. 2017;30:503-522 pubmed publisher
    ..The structural basis for reprogrammed DNA cleavage specificity was further examined via high-resolution X-ray crystal structures of both enzymes...
  23. Toliusis P, Zaremba M, Silanskas A, Szczelkun M, Siksnys V. CgII cleaves DNA using a mechanism distinct from other ATP-dependent restriction endonucleases. Nucleic Acids Res. 2017;45:8435-8447 pubmed publisher
    ..Here, we report studies to evaluate the DNA cleavage mechanism of CglI...
  24. Shaytan A, Xiao H, Armeev G, Wu C, Landsman D, Panchenko A. Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning. Nucleic Acids Res. 2017;45:9229-9243 pubmed publisher
    ..Our model provides the basis for further understanding the cooperative engagement and interplay between Cse4p protein and the A-tracts important for centromere function...
  25. Suzuki T, Imada T, Komatsu Y, Kamiya H. Comparison of DNA fragments as donor DNAs upon sequence conversion of cleaved target DNA. Nucleosides Nucleotides Nucleic Acids. 2017;36:428-434 pubmed publisher
    ..single-stranded (ss) DNA fragment and a 5'-tailed duplex (TD) accomplished the desired sequence changes without DNA cleavage, and might serve as better donors for the cleaved target DNA than ODNs and plasmid DNAs...
  26. Wong T, Cheng C, Hsieh Z, Liang J. Effects of blue or violet light on the inactivation of Staphylococcus aureus by riboflavin-5'-phosphate photolysis. J Photochem Photobiol B. 2017;173:672-680 pubmed publisher
    ..FMN photolysis with blue or violet light irradiation enhanced the inactivation rates of S. aureus and MRSA. FMN photochemical treatment could be a supplemental technique in hygienic decontamination processes. ..
  27. Gaur R, Choubey D, Usman M, Ward B, Roy J, Mishra L. Synthesis, structures, nuclease activity, cytotoxicity, DFT and molecular docking studies of two nitrato bridged homodinuclear (Cu-Cu, Zn-Zn) complexes containing 2,2'-bipyridine and a chalcone derivative. J Photochem Photobiol B. 2017;173:650-660 pubmed publisher
    ..2±0. 044?? for complex 2. Complex 2 induces the cell apoptosis at a later-stage as compared to complex 1. The cell apoptosis and topoisomerase inhibition by complexes enable them to be potential candidates as future anticancer drugs. ..