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Topic: Topoisomers

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Catenane

Topoisomerase

DNA topology

Isomer

Rotaxane

Knot theory

Topological

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	Separation of polymeric topoisomers in a microchannel device: a Monte Carlo study (via CobWeb/3.1 ... (Site not responding. Last check: 2007-10-22)
		Separation of polymeric topoisomers in a microchannel device: a Monte Carlo study (via CobWeb/3.1 planetlab2.cs.unc.edu)
		[D40.105] Separation of polymeric topoisomers in a microchannel device: a Monte Carlo study
		However, in the wake of the current trend towards lab-on-a-chip technologies, we present simulation results for the separation of topoisomers in an entropic trap array, a microdevice etched on a silicon wafer recently used to separate DNA by size(J. Han, S. Turner and H. Craighead, Phys.
	flux.aps.org.cob-web.org:8888 /meetings/YR01/MAR01/abs/S1560105.html (196 words)

	RedOrbit - Science - Bulge Defects Do Not Destabilize Negatively Supercoiled DNA
		Distinct topoisomer populations of covalently closed, bulge- containing plasmids were prepared by ligation in the presence of different concentrations of ethidium.
		The signature for such structural transitions is a discontinuity in the are of topoisomer bands, commonly seen in plasmids containing sequences that undergo transitions to the Z- form or cruciform structures (6).
		There are well-defined, arc-shaped patterns of topoisomers in all cases, indicating the absence of sharp, supercoiling-dependent secondary- structure transitions.
	www.redorbit.com /news/science/316852/bulge_defects_do_not_destabilize_negatively_supercoiled_dna/index.html?source=r_science (1535 words)

	Effect of Varying the Supercoiling of DNA on Transcription and Its Regulation (Site not responding. Last check: 2007-10-22)
		We generated a series of topoisomers of the plasmid that harbors these promoters and studied the effect of DNA topology on in vitro transcription from these promoters in the absence and presence of their cognate regulatory proteins.
		In vitro transcriptions were performed using the topoisomers as DNA templates to analyze supercoiling dependency of the different promoters in pSA850 in the absence and presence of regulatory proteins.
		The topoisomers were separated by agarose gel electrophoresis in the presence of 0.5 mg/mL (upper gel) and 2.5 mg/mL (lower gel) of chloroquine.
	pubs.acs.org /cgi-bin/sample.cgi/bichaw/2003/42/i36/html/bi030110t.html (5512 words)

	Role of Histone N-Terminal Tails and Their Acetylation in Nucleosome Dynamics -- Morales and Richard-Foy 20 (19): 7230 ...
		The electrophoretic migration was performed in the presence of 125 µM chloroquine to resolve DNA topoisomer 0 from open circles.
		3A, lanes 2, 4, 6, and 8), the topoisomer equilibrium
		The migration position of the different naked DNA topoisomers is indicated on the left, and labeling is the same as in Fig.
	mcb.asm.org /cgi/content/full/20/19/7230 (5803 words)

	The dynamic response of upstream DNA to transcription-generated torsional stress - Nature Structural & Molecular ...
		Different topoisomers of pFLIP-FUSE were treated with potassium permanganate to selectively oxidize unpaired thymines in the absence (left) or presence (right) of 1.5 mM Mg The FUSE-containing fragment was cleaved at the modified residues with piperidine, followed by visualization of strand breaks on sequencing gels.
		A discontinuity in the two-dimensional topoisomer pattern indicates the number of helical turns locally unwound within the non-B-segment, and defines the superhelical stress driving the transition to the alternate structure.
		Topoisomers of circular or linear pFLIP-FUSE DNA (left), or linear DNA under conditions with (+) and without (-) transcription (right), were briefly treated with potassium permanganate.
	www.nature.com /nsmb/journal/v11/n11/full/nsmb848.html (6970 words)

	Gene 1998
		In both plasmids the topoisomer at the peak of the discontinuity, topoisomer -15, migrated in the first (vertical) direction as far as topoisomer -9.
		This means that close to six turns have become unwound in topoisomer -15 and beyond, and that is true for the bulk of the plasmid.
		Some topoisomer numbers are indicated; lin - linearized DNA (the faint linear band is positioned at the foot of letter l).
	www.weizmann.ac.il /~lcyagil/genepap.html (6062 words)

	Mapping of Abutilon Mosaic Geminivirus Minichromosomes -- Pilartz and Jeske 77 (20): 10808 -- The Journal of Virology
		Topoisomer distributions of AbMV covalently closed circular DNA obtained by two-dimensional (a to c) or one-dimensional gel(d) electrophoresis with chloroquine as the intercalator.
		Note the remarkably well preserved spacing of the topoisomers derived from different sources and runs on separate gels in independent experiments (a to c) and the predominant band representing viral DNA with 12 superhelical turns.
		Given the ruler for topoisomers obtained from this comparative analysis, it was now possible to determine the linking numbers in covalently closed circular DNA by counting back from topoisomers of higher values (a to c).
	jvi.asm.org /cgi/content/full/77/20/10808 (6340 words)

	DNA Unwinding Kit 1025
		Specifically, the influence of a compound on the distribution of topoisomers (generated by relaxation of closed circular DNA with topo I) will reveal the presence of a DNA intercalator.
		Upon terminating the reaction with SDS, digesting with proteinase and extracting the DNA with organic solvents, protein and drug are removed and any alteration in the population distribition of topoisomers is revealed by running an agarose gel.
		The gels are run to high resolution to display topoisomers; thus, gels are generally run without ethidium bromide at a low voltage for 12 hrs.
	www.topogen.com /html/dna_unwinding_kit.htm (667 words)

	IMM Reports No. 30
		Accomplishing the actual conversion of one topoisomer to the other is done via addition of a "fuel" strand, a technique used earlier by Bernard Yurke and colleagues to power their DNA actuator design (see Update 42).
		Although the two topoisomers have similar molecular masses, their different shapes enable separation by a bulk separation technique known as non-denaturing gel electrophoresis.
		Further, the mass of the marker that is rotated is comparable to the mass of the topoisomer that produces the rotation.
	www.imm.org /Reports/Rep030.html (2353 words)

	Protein A gene expression is regulated by DNA supercoiling which is modified by the ArlS-ArlR two-component system of ...
		(c) Scan analysis of topoisomer distribution in the plasmids separated in the gel shown in (b).
		(b) Scan analysis of topoisomer distribution in the plasmids separated in the gel shown in (a).
		Scan analyses of topoisomer distribution in the plasmids separated in the gel are presented on the right.
	mic.sgmjournals.org /cgi/content/full/150/11/3807 (5275 words)

	Early melting of supercoiled DNA topoisomers observed by TGGE -- Víglasky et al. 28 (11): e51 -- Nucleic Acids ...
		Early melting of supercoiled DNA topoisomers observed by TGGE -- Víglasky et al.
		However, the topoisomers were run at constant temperature (20°C) without a temperature gradient at 4 V/cm for 14 h, then the temperature gradient was switched on at 6 V/cm for 9 h.
		topoisomers by TGGE is a good distribution of supercoiled plasmids.
	nar.oxfordjournals.org /cgi/content/full/28/11/e51 (2598 words)

	Methods designed for the identification and characterization of in vitro and in vivo chromatin assembly mutants in ...
		Following the reaction, the intermediate DNA topoisomers (int.) were resolved, together with the open, relaxed (O, R) and supercoiled (sup.) species, through a 0.8% agarose gel.
		An extract is deemed to be defective if an accumulation of intermediate topoisomers is observed.
		One extract, H1G4, was found to be unable to fully supercoil the input plasmid (compare the accumulation of intermediate topoisomers to completely supercoiled bands).
	www.biologicalprocedures.com /bpo/arts/1/58/m58f1lg.htm (232 words)

	SIR2 modifies histone H4-K16 acetylation and affects superhelicity in the ARS region of plasmid chromatin in ... (Site not responding. Last check: 2007-10-22)
		Negatively and positively supercoiled topoisomers are found in the left and right parts of the arc, respectively.
		The cells were grown and the plasmids purified and analyzed as in Figure 1.
		Ind values reported at the bottom of each topoisomer distribution indicate the increased distribution of negative supercoils as evaluated by densitometric analysis.
	nar.oxfordjournals.org.cob-web.org:8888 /cgi/content/full/34/19/5426 (7044 words)

	The Elastic Rod Model for DNA and Its Application to the Tertiary Structure of DNA Minicircles in Mononucleosomes -- ...
		Equilibrium distributions of topoisomers are discussed in the final section of the paper.
		= 33) + 1.5 kcal/mol, and hence the topoisomer with
		present in an equilibrium mixture of topoisomers obtained by relaxation of DNA minicircles in mononucleosomes.
	www.biophysj.org /cgi/content/full/74/5/2515 (4733 words)

	The Switch in the Helical Handedness of the Histone (H3-H4)2 Tetramer within a Nucleoprotein Particle Requires a ...
		Topoisomer linking difference relative to its most probable configuration is given by the equation,
		DNA was eluted and purified, and the topoisomer distribution was
		DNA topoisomers +1 was assembled on histone tetramers untreated (lane 2) or treated with DTNB (lane 3).
	www.jbc.org /cgi/content/full/273/15/9261 (5754 words)

	Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble ...
		Relaxation, which results in a shift in the distribution of topoisomers and the appearance of new bands, is first detected in lane 5.
		the substrate sufficiently to resolve the topoisomers (lane 1).
		The positions of nicked DNA (N), relaxed topoisomers (R), and (+) supercoiled DNA (SC) are indicated.
	www.genesdev.org /cgi/content/full/14/22/2881 (7492 words)

	OUP Companion web site: Chapter 02
		We consider how supercoiling in circular DNA has been analysed by 1-D and 2-D gel electrophoresis and describe the effects of solution conditions, temperature and DNA-binding molecules on the conformation of supercoiled DNA.
		Different approaches to the thermodynamics of supercoiling are then described, including ethidium bromide binding, analysis of the equilibrium Gaussian distribution of topoisomers, and the effects of solution conditions and DNA length on the free energy of supercoiling.
		This then leads directly into consideration of the physical deformations underlying supercoiling (bending and twisting of the DNA helix) and the theoretical methods, including Monte Carlo simulations, that have been used to analyse the conformation of circular DNA.
	www.oup.com /uk/booksites/content/0198506554/resources/figs/chapter02 (283 words)

	Stability of a Human SWI-SNF Remodeled Nucleosomal Array -- Guyon et al. 21 (4): 1132 -- Molecular and Cellular Biology
		The topoisomers reflecting the different remodeled species were quantitated using a Molecular Dynamics PhosphorImager.
		Reversion is quantitated by measuring the total proportion of highly supercoiled DNA (indicated with brackets and "Sc DNA") versus that of all the topoisomers present on the gel.
		Normalization was done by determining the fractional signal representative for the topoisomer being quantitated relative to those of all the topoisomers and adjusting to a maximum relative value of 1.
	mcb.asm.org /cgi/content/full/21/4/1132 (6958 words)

	Topoisomer - Wikipedia, the free encyclopedia
		Topoisomers or topological isomers are molecules with the same chemical formula but different topologies.
		Examples of molecules for which there exist topoisomers include DNA, which can form knots, and catenanes.
		DNA topoisomers can be interchanged by enzymes called topoisomerases
	en.wikipedia.org /wiki/Topoisomer (101 words)

	Positive Torsional Strain Causes the Formation of a Four-way Junction at Replication Forks -- Postow et al. 276 (4): ...
		Negative topoisomers are resolved in the first dimension.
		The middle topoisomer of the distribution takes up just enough chloroquine to be relaxed in the second dimension.
		Lk than the relaxed topoisomer become (+) supercoiled in the second dimension, forming the top part of the arc.
	www.jbc.org /cgi/content/full/276/4/2790 (5502 words)

	Analysis of a DNase I hypersensitive site located -20.9 kb upstream of the CFTR gene -- Nuthall et al. 266 (2): 431 -- ... (Site not responding. Last check: 2007-10-22)
		The linking number difference of each topoisomer is determined by counting the number of forms from the relaxed form ‘0’.
		The magnitude of relaxation due to the structural transition is given by the relative linking number difference between two plasmid topoisomers, the topoisomer preceding the transition and the topoisomer with the same mobility in the first dimension as the topoisomer after the transition.
		Summary of the superhelical transitions that occur during two-dimensional agarose-gel electrophoresis of plasmid topoisomer distributions.
	content.febsjournal.org /cgi/content/full/266/2/431 (7366 words)

	Temperature, template topology, and factor requirements of archaeal transcription -- Bell et al. 95 (26): 15218 -- ...
		Positively supercoiled topoisomers were resolved by electrophoresis in the first dimension in TAE buffer (40 mM Tris·acetate/1
		Transcription reactions were incubated at 75°C (lanes 1 and 2) or 48°C (lanes 3 and 4) and RNA detected by primer extension.
		Generation of topoisomer pools for use in the reconstituted archaeal transcription system.
	www.pnas.org /cgi/content/full/95/26/15218 (3862 words)

	Long-Term Experimental Evolution in Escherichia coli. XII. DNA Topology as a Key Target of Selection -- Crozat et al. ...
		the topoisomer distribution of plasmid DNA from the ancestor
		of plasmid topoisomers between each clone and the ancestor.
		Plasmid DNA was isolated from ancestral and evolved cells carrying reporter plasmid pUC18 and analyzed by electrophoresis on gels that allow visualization of the topoisomer distribution, with more tightly supercoiled topoisomers migrating faster (H
	www.genetics.org /cgi/content/full/169/2/523 (5663 words)

	Osmotic regulation of the Streptomyces lividans thiostrepton-inducible promoter, ptipA -- Ali et al. 148 (2): 381 -- ...
		Topoisomers were resolved by electrophoresis in 1% agarose gels containing 5 µg chloroquine ml
		Topoisomer distribution of plasmid DNA isolated from 1326 and TK64 strains, respectively, when grown in complete medium containing: lanes 1 and 4, no added osmolyte; lanes 2 and 5, 0·7 M sucrose; lanes 3 and 6, 0·5 M NaCl.
		may contribute to the observed atypical distribution of topoisomers.
	mic.sgmjournals.org /cgi/content/full/148/2/381 (4614 words)

	Plasmid DNA Supercoiling and Gyrase Activity in Escherichia coli Wild-Type and rpoS Stationary-Phase Cells -- ...
		Plasmid DNA topoisomers were isolated and separated through 1% agarose gels containing chloroquine at 12 µg/ml as described in the text.
		RpoS influences the level of relaxation of plasmids isolated from stationary-phase cells and the capacity of these cells to supercoil plasmids after dilution into fresh medium.
		Plasmids were isolated, and topoisomers were separated as described for Fig.
	jb.asm.org /cgi/content/full/185/3/1097 (2697 words)

	Hypoxia Blocks In Vivo Initiation of Simian Virus 40 Replication at a Stage Preceding Origin Unwinding -- Riedinger et ...
		Isolation of SV40 topoisomers, Bal 31 digestion, and chloroquine gradient gel-electrophoresis.
		Migration pattern of distinct SV40 topoisomers in chloroquine (Chq) gradient gel electrophoresis.
		Lanes: 1, control, 4-min reoxygenated; 2, control, 7-min reoxygenated; 3: control, 16-min reoxygenated; 4 to 6, as lanes 1 to 3, with aphidicolin; 7, aphidicolin removed 6 min after reoxygenation, incubated for a further 2 min; 8, aphidicolin removed 6 min after reoxygenation, incubated for a further 6 min.
	jvi.asm.org /cgi/content/full/73/3/2243 (6763 words)

	Plasmid pGS5 from the Hyperthermophilic Archaeon Archaeoglobus profundus Is Negatively Supercoiled -- ...
		topoisomers are negatively supercoiled, since they remain on the
		Resolution of pGS5 topoisomers by one-dimensional gel electrophoresis in the presence of 2 µg of chloroquine per ml.
		Samples correspond to negatively supercoiled pTZ18 (2,880 bp) (lane 1), pGS5 extracted from cells allowed to cool slowly (lane 2) or immediately chilled (lane 3), and pTZ18 relaxed at 25°C that, under these conditions, migrates as a single band of positively supercoiled topoisomers (lane 4).
	jb.asm.org /cgi/content/full/182/17/4998 (1691 words)

	Bulge Defects Do Not Destabilize Negatively Supercoiled DNA -- You and Levene 89 (5): L43 -- Biophysical Journal
		of some topoisomers in the first dimension are reversed in the
		is a discontinuity in the arc of topoisomer bands, commonly
		There are well-defined, arc-shaped patterns of topoisomers in all cases, indicating the absence of sharp, supercoiling-dependent secondary-structure transitions.
	www.biophysj.org /cgi/content/full/89/5/L43 (1261 words)

	Nanoscience and Molecular Materials Research Group
		We have recently reported on the first synthesis of fused subphthalocyanine dimers, as a mixture of two topoisomers that have been separated and characterized.[61,55]
		The UV-vis spectra of the dimers revealed the presence of a Q band at 690 nm strongly shifted to the red (120 nm) with regard to a typical SubPc, whose intensity is comparable to that of Pcs.
		Syn and Anti Topoisomers of Subphthalocyanine Fused Dimers [61]
	www.uam.es /gruposinv/ftalo/Dimers.htm (199 words)

	Caltech Authors - The stability of Seeman JX DNA topoisomers of paranemic crossover (PX) molecules as a function of ... (Site not responding. Last check: 2007-10-22)
		Caltech Authors - The stability of Seeman JX DNA topoisomers of paranemic crossover (PX) molecules as a function of crossover number (via CobWeb/3.1 planetlab2.cs.unc.edu)
		Maiti, Prabal K. and Pascal, Tod A. and Vaidehi, Nagarajan and Goddard, William A., III (2004) The stability of Seeman JX DNA topoisomers of paranemic crossover (PX) molecules as a function of crossover number.
		You are granted permission for individual, educational, research and non-commercial reproduction, distribution, display and performance of this work in any format.
	resolver.caltech.edu.cob-web.org:8888 /CaltechAUTHORS:MAInar04 (604 words)

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