scholarly journals Direct Observation of Strand Passage by DNA-Topoisomerase and Its Limited Processivity

PLoS ONE ◽  
2012 ◽  
Vol 7 (4) ◽  
pp. e34920 ◽  
Author(s):  
Katsunori Yogo ◽  
Taisaku Ogawa ◽  
Masahito Hayashi ◽  
Yoshie Harada ◽  
Takayuki Nishizaka ◽  
...  
Keyword(s):  
Direct Observation ◽  
Dna Topoisomerase ◽  
Strand Passage

scholarly journals Chromosome disentanglement driven via optimal compaction of loop-extruded brush structures

2019 ◽  
Vol 116 (50) ◽  
pp. 24956-24965 ◽  
Author(s):  
Sumitabha Brahmachari ◽  
John F. Marko
Keyword(s):  
Expression Patterns ◽  
Polymer Brush ◽  
Mitotic Chromosomes ◽  
Mechanical Stiffness ◽  
Structural Reorganization ◽  
Metaphase Chromosomes ◽  
Dna Topoisomerase ◽  
Topo Ii ◽  
Strand Passage

Eukaryote cell division features a chromosome compaction–decompaction cycle that is synchronized with their physical and topological segregation. It has been proposed that lengthwise compaction of chromatin into mitotic chromosomes via loop extrusion underlies the compaction-segregation/resolution process. We analyze this disentanglement scheme via considering the chromosome to be a succession of DNA/chromatin loops—a polymer “brush”—where active extrusion of loops controls the brush structure. Given type-II DNA topoisomerase (Topo II)-catalyzed topology fluctuations, we find that interchromosome entanglements are minimized for a certain “optimal” loop that scales with the chromosome size. The optimal loop organization is in accord with experimental data across species, suggesting an important structural role of genomic loops in maintaining a less entangled genome. Application of the model to the interphase genome indicates that active loop extrusion can maintain a level of chromosome compaction with suppressed entanglements; the transition to the metaphase state requires higher lengthwise compaction and drives complete topological segregation. Optimized genomic loops may provide a means for evolutionary propagation of gene-expression patterns while simultaneously maintaining a disentangled genome. We also find that compact metaphase chromosomes have a densely packed core along their cylindrical axes that explains their observed mechanical stiffness. Our model connects chromosome structural reorganization to topological resolution through the cell cycle and highlights a mechanism of directing Topo II-mediated strand passage via loop extrusion-driven lengthwise compaction.

scholarly journals 3P-261 Direct Observation of DNA Unlinking Magic by a Type-II DNA Topoisomerase.(Bioimaging,Oral Presentations,The 47th Annual Meeting of the Biophysical Society of Japan)

2009 ◽  
Vol 49 (supplement) ◽  
pp. S194
Author(s):  
Katsunori Yogo ◽  
Taisaku Ogawa ◽  
Saki Obata ◽  
Gen Nakajima ◽  
Junpei Suzuki ◽  
...  
Keyword(s):  
Annual Meeting ◽  
Direct Observation ◽  
Type Ii ◽  
Dna Topoisomerase ◽  
Biophysical Society ◽  
Oral Presentations

scholarly journals TOP2B: The First Thirty Years

2018 ◽  
Vol 19 (9) ◽  
pp. 2765 ◽  
Author(s):  
Caroline Austin ◽  
Ka Lee ◽  
Rebecca Swan ◽  
Mushtaq Khazeem ◽  
Catriona Manville ◽  
...  
Keyword(s):  
Dependent Manner ◽  
Type Ii ◽  
Dna Duplex ◽  
Topoisomerase Iiα ◽  
Dna Topoisomerase ◽  
Dna Topoisomerases ◽  
Cellular Processes ◽  
Double Stranded Dna ◽  
Type Ii Dna Topoisomerases ◽  
Strand Passage

Type II DNA topoisomerases (EC 5.99.1.3) are enzymes that catalyse topological changes in DNA in an ATP dependent manner. Strand passage reactions involve passing one double stranded DNA duplex (transported helix) through a transient enzyme-bridged break in another (gated helix). This activity is required for a range of cellular processes including transcription. Vertebrates have two isoforms: topoisomerase IIα and β. Topoisomerase IIβ was first reported in 1987. Here we review the research on DNA topoisomerase IIβ over the 30 years since its discovery.

scholarly journals Topoisomerase VI is a chirally-selective, preferential DNA decatenase

2021 ◽  
Author(s):  
Shannon J. McKie ◽  
Parth Desai ◽  
Yeonee Seol ◽  
Anthony Maxwell ◽  
Keir Neuman
Keyword(s):  
Dna Binding ◽  
Atpase Activity ◽  
Single Molecule ◽  
Magnetic Tweezers ◽  
Dna Topoisomerase ◽  
Methanosarcina Mazei ◽  
Strand Passage ◽  
Robust Evidence

AbstractDNA topoisomerase VI (topo VI) is a type IIB DNA topoisomerase found predominantly in archaea and some bacteria, but also in plants and algae. Since its discovery, topo VI has been proposed to be a DNA decatenase, however robust evidence and a mechanism for its preferential decatenation activity was lacking. Using single-molecule magnetic tweezers measurements and supporting ensemble biochemistry, we demonstrate that Methanosarcina mazei topo VI preferentially unlinks, or decatenates, DNA crossings, in comparison to relaxing supercoils, through a preference for certain DNA crossing geometries. In addition, topo VI demonstrates a dramatic increase in ATPase activity, DNA binding and rate of strand passage, with increasing DNA writhe, providing further evidence that topo VI is a DNA crossing sensor. Our study strongly suggests that topo VI has evolved an intrinsic preference for the unknotting and decatenation of interlinked chromosomes by sensing and preferentially unlinking DNA crossings with geometries close to 90°.

scholarly journals 3TP3-02 Direct Observation of DNA Unlinking Magic by a Type-II DNA Topoisomerase.(The 47th Annual Meeting of the Biophysical Society of Japan)

2009 ◽  
Vol 49 (supplement) ◽  
pp. S61
Author(s):  
Katsunori Yogo ◽  
Taisaku Ogawa ◽  
Saki Obata ◽  
Gen Nakajima ◽  
Junpei Suzuki ◽  
...  
Keyword(s):  
Annual Meeting ◽  
Direct Observation ◽  
Type Ii ◽  
Dna Topoisomerase ◽  
Biophysical Society

scholarly journals Direct Monitoring of the Strand Passage Reaction of DNA Topoisomerase II Triggers Checkpoint Activation

PLoS Genetics ◽  
2013 ◽  
Vol 9 (10) ◽  
pp. e1003832 ◽  
Author(s):  
Katherine L. Furniss ◽  
Hung-Ji Tsai ◽  
Jo Ann W. Byl ◽  
Andrew B. Lane ◽  
Amit C. Vas ◽  
...  
Keyword(s):  
Topoisomerase Ii ◽  
Dna Topoisomerase Ii ◽  
Checkpoint Activation ◽  
Dna Topoisomerase ◽  
Strand Passage

scholarly journals Type II DNA Topoisomerases Cause Spontaneous Double-Strand Breaks in Genomic DNA

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 868 ◽  
Author(s):  
Morimoto ◽  
Tsuda ◽  
Bunch ◽  
Sasanuma ◽  
Austin ◽  
...  
Keyword(s):  
Double Strand Breaks ◽  
Nonhomologous End Joining ◽  
Type Ii ◽  
Dna Double Strand Breaks ◽  
End Joining ◽  
Dna Topoisomerase ◽  
Strand Breaks ◽  
Brca1 Brca2 ◽  
Type Ii Dna Topoisomerases ◽  
Strand Passage

Type II DNA topoisomerase enzymes (TOP2) catalyze topological changes by strand passage reactions. They involve passing one intact double stranded DNA duplex through a transient enzyme-bridged break in another (gated helix) followed by ligation of the break by TOP2. A TOP2 poison, etoposide blocks TOP2 catalysis at the ligation step of the enzyme-bridged break, increasing the number of stable TOP2 cleavage complexes (TOP2ccs). Remarkably, such pathological TOP2ccs are formed during the normal cell cycle as well as in postmitotic cells. Thus, this ‘abortive catalysis’ can be a major source of spontaneously arising DNA double-strand breaks (DSBs). TOP2-mediated DSBs are also formed upon stimulation with physiological concentrations of androgens and estrogens. The frequent occurrence of TOP2-mediated DSBs was previously not appreciated because they are efficiently repaired. This repair is performed in collaboration with BRCA1, BRCA2, MRE11 nuclease, and tyrosyl-DNA phosphodiesterase 2 (TDP2) with nonhomologous end joining (NHEJ) factors. This review first discusses spontaneously arising DSBs caused by the abortive catalysis of TOP2 and then summarizes proteins involved in repairing stalled TOP2ccs and discusses the genotoxicity of the sex hormones.

scholarly journals Direct Observation of DNA Untangling Magic by a Type-II DNA Topoisomerase

2009 ◽  
Vol 96 (3) ◽  
pp. 291a
Author(s):  
Katsunori Yogo ◽  
Taisaku Ogawa ◽  
Saki Obata ◽  
Gen Nakajima ◽  
Junpei Suzuki ◽  
...  
Keyword(s):  
Direct Observation ◽  
Type Ii ◽  
Dna Topoisomerase

Direct Observation of Heat Exchanger Deposits by Cross Sectioning

1967 ◽  
Vol 25 ◽  
pp. 364-365
Author(s):  
R. W. Anderson ◽  
D. L. Senecal
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Heat Exchanger ◽  
Direct Observation ◽  
Cross Sections ◽  
Preparation Method ◽  
Specimen Preparation ◽  
Flowing Water ◽  
Transmission Electron ◽  
Deposit Layer

A problem was presented to observe the packing densities of deposits of sub-micron corrosion product particles. The deposits were 5-100 mils thick and had formed on the inside surfaces of 3/8 inch diameter Zircaloy-2 heat exchanger tubes. The particles were iron oxides deposited from flowing water and consequently were only weakly bonded. Particular care was required during handling to preserve the original formations of the deposits. The specimen preparation method described below allowed direct observation of cross sections of the deposit layers by transmission electron microscopy.The specimens were short sections of the tubes (about 3 inches long) that were carefully cut from the systems. The insides of the tube sections were first coated with a thin layer of a fluid epoxy resin by dipping. This coating served to impregnate the deposit layer as well as to protect the layer if subsequent handling were required.

Application of a Simple Cold Stub to the Direct Observation of Frozen Hydrated Sand

1973 ◽  
Vol 31 ◽  
pp. 212-213
Author(s):  
John M. Wehrung ◽  
Richard J. Harniman
Keyword(s):  
United States ◽  
Surface Water ◽  
Direct Observation ◽  
Controlled Study ◽  
Clay Particles ◽  
Organic Debris ◽  
Rock Formations ◽  
Water Tables ◽  
Permeable Rock ◽  
Natural Means

Water tables in aquifer regions of the southwest United States are dropping off at a rate which is greater than can be replaced by natural means. It is estimated that by 1985 wells will run dry in this region unless adequate artificial recharging can be accomplished. Recharging with surface water is limited by the plugging of permeable rock formations underground by clay particles and organic debris.A controlled study was initiated in which sand grains were used as the rock formation and water with known clay concentrations as the recharge media. The plugging mechanism was investigated by direct observation in the SEM of frozen hydrated sand samples from selected depths.

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