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Topic: DNA topology

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Topological

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	Endogenous Fluctuations of DNA Topology in the Chloroplast of Chlamydomonas reinhardtii -- Salvador et al. 18 (12): ...
		Endogenous Fluctuations of DNA Topology in the Chloroplast of Chlamydomonas reinhardtii
		the Klenow fragment of DNA polymerase) and XhoI and subcloned
		of the endogenous fluctuations in DNA topology to the endogenous
	mcb.asm.org /cgi/content/full/18/12/7235 (5856 words)

	Biochemistry 201: DNA Topology
		Andersen, A. H., Svejstrup, J. and Westergaard, O. The DNA binding, cleavage, and religation reactions of eukaryotic topoisomerases I and II.
		Champoux, J. Mechanism of catalysis by eukaryotic DNA topoisomerase I. Adv Pharmacol, 29, 71-82.
		Cozzarelli, N. DNA gyrase and the supercoiling of DNA.
	cmgm.stanford.edu /biochem201/Handouts/DNAtopo.html (484 words)

	DNA Structure and Topology
		DNA is a double-stranded macromolecule in which each strand is a polymer of deoxyribonucleotide monomers.
		Topology is the branch of mathematics that studies properties of objects that are invariant to continuous deformations of the object.
		In the new ribbon model of DNA, a line drawn down the center of the ribbon represents the axis of the double helix and, when the ribbon is twisted around this line, the pseudodyad axes are always perpendicular to the surface of the ribbon at the double-helix axis of the ribbon.
	www.rpi.edu /~bellos/new_page_1.htm (5130 words)

	DNA-DNA hybridisation -- Facts, Info, and Encyclopedia article (Site not responding. Last check: 2007-10-21)
		When several species are compared that way, the similarity values allow the species to be arranged in a (additional info and facts about phylogenetic tree) phylogenetic tree; it is therefore one possible approach to carrying out (additional info and facts about molecular systematics) molecular systematics.
		The DNA double strand is then separated by heating into two single strands.
		The single-stranded DNA is now allowed to anneal with the DNA pieces of the other species.
	www.absoluteastronomy.com /encyclopedia/d/dn/dna-dna_hybridisation5.htm (369 words)

	Fifth Foresight Conference: DNA Nanotechnology
		DNA is an extremely favorable construction medium: The sticky-ended association of DNA molecules occurs with high specificity, and it results in the formation of B-DNA, whose structure is well known.
		DNA double crossover molecules (abbreviated DX) are analogs of intermediates in the process of genetic recombination [34].
		DNA nanotechnology is a promising avenue to achieve the goals of nanotechnology in general.
	www.foresight.org /Conferences/MNT05/Papers/Seeman (9193 words)

	DIMACS Workshop on DNA Sequence and Topology
		Topology Driven Transitions in DNA Structure: Their Mathematical Analysis and Roles in Biology Craig J. Benham, Mount Sinai School of Medicine This talk will briefly describe a formally exact mathematical method for analyzing the topologically driven destabilization of the DNA duplex.
		DNA Sequence-Structure Relationships Christopher A. Hunter, University of Sheffield The structural properties of double helical DNA are sensitive to the base sequence, and this plays an important role in determining the way in which this molecule can be manipulated.
		Antiparallel DNA Loop in the Gal Repressosome Victor B. Zhurkin, Natinal Cancer Institute, NIH Gal repressosome assembly and repression of the gal operon in E.
	dimacs.rutgers.edu /Workshops/TopologyIII/abstracts.html (3650 words)

	Amazon.ca: Books: DNA Topology (Site not responding. Last check: 2007-10-21)
		DNA as the genetic material is a topic of intense interest in the 21st century, with the genomes of many organisms having been sequenced.
		DNA Topology starts with a basic account of DNA structure before going on to cover DNA supercoiling, the definitions and physical meanings of linking number, twist, and writhe, and the free energy associated with supercoiling.
		The final chapters deal with the topoisomerases, the enzymes that control DNA topology, and, most importantly, with the biological significance of the topological aspects of DNA structure.
	www.amazon.ca /exec/obidos/ASIN/019856709X (366 words)

	DNA AND KNOT THEORY
		DNA packing can be visualized as two very long strands that have been intertwined millions of times, tied into knots, and subjected to successive coiling.
		The distance DNA fragments move on an electrophoretic gel is highly correlated with the average crossing number (see graph).
		In this case, the crossing points of the DNA or DNA of a particular knot type would be the substrate.
	www.tiem.utk.edu /~gross/bioed/webmodules/DNAknot.html (1424 words)

	In the Classroom
		This resilience mimics the natural tendency of DNA to adopt its lowest-energy conformation, the B-form double helix, in the absence of distorting forces.
		In circular DNA the double strands respond to excessive twist by supercoiling or writhing around each other, which allows the double strands to move back toward the natural amount of twist.
		For a closed circle of double-strand DNA (or for an open double strand restrained from rotation at the ends, such as a region looped out of a packed structure like a nucleosome), the number of twists plus writhes is a constant called L, the linking number, a term that originates in topology.
	www.usm.maine.edu /~rhodes/Goodies/text/DNADemo.html (2564 words)

	The nucleoid associated proteins: how they alter DNA topology and influence gene expression. (Site not responding. Last check: 2007-10-21)
		These proteins have the ability to alter the topology of the DNA by bending it and altering the levels of supercoiling.
		DNA is a dynamic molecule and the expression of many of the genes encoded within are sensitive to changes in the way that the DNA is twisted or bent.
		DNA supercoiling in a wild-type and hns mutant strain of Escherichia coli
	www.ifrn.bbsrc.ac.uk /safety/Molmicro/research_nucleoidproteins.html (234 words)

	DIMACS/PMMB/MBBC Workshop on DNA Topology II: Abstracts
		The DNA is stretched by moving the cover glass with respect to the trap using a piezo-driven stage, while the position of the bead is recorded at nanometer-scale resolution.
		It is important in molecular biology because, for example, the writhing of DNA is closely connected with the interlinking of the two strands of the double helix...an interlinking which must be overcome by the action of cut-and-paste enzymes during replication and reproduction.
		In addition, the coupling between diachronic and synchronic structures of DNA mediated by conformons not only provides rational mechanisms for linking evolution (which determines diachronic DNA) and function (which is determined by synchronic DNA) on the molecular level but also accounts for individual creativity of living cells within the constraint of their common genome.
	dimacs.rutgers.edu /Workshops/TopologyII/abstracts.html (6306 words)

	PHRI :: Karl Drlica, Ph.D.
		Mutation in the DNA gyrase A Gene of Escherichia coli that expands the quinolone resistance-determining region.
		In DNA Cleavers and Chemotherapy of Cancer or Viral Diseases, edited by B. Meunier, Kluwer Academic Publishers, Dordrecht, pp 91-106.
		Hsieh, L.-S., Burger, R.M., and Drlica, K. DNA topoisomerases and the bacterial chromosome.
	www.phri.org /research/res_pidrlica.asp (1509 words)

	THE TOPOLOGY OF DNA (Site not responding. Last check: 2007-10-21)
		Many important cellular processes (including segregation of daughter chromosomes, gene regulation, DNA repair, and generation of antibody diversity) are performed by enzymes which manipulate the geometry and topology of cellular DNA.
		In the topological approach to enzymology, circular DNA is incubated with an enzyme, producing an enzyme signature in the form of DNA knots and links.
		By observing the change in DNA geometry (supercoiling) and topology (knotting and linking) due to enzyme action, the enzyme mechanism can often be characterized.
	www.math.buffalo.edu /archive/myhill_lect_1997.html (227 words)

	Escherichia coli SeqA protein affects DNA topology and inhibits open complex formation at oriC -- Torheim and Skarstad ... (Site not responding. Last check: 2007-10-21)
		The DNA in the gels in (A) and (B) was taken from the same samples, but electrophoresed in the presence of 40 and 2 µg/ml chloroquine, respectively.
		The histone-like protein HU binds to DNA as a heterodimer, whereas the stoichiometric binding of SeqA to DNA is unknown.
		Gille, H. and Messer, W. Localized DNA melting and structural pertubations in the origin of replication, oriC, of Escherichia coli in vitro and in vivo.
	embojournal.npgjournals.com /cgi/content/full/18/17/4882 (4957 words)

	DNA topology, not DNA sequence, is a critical determinant for Drosophila ORC[ndash]DNA binding
		DNA topology, not DNA sequence, is a critical determinant for Drosophila ORC[ndash]DNA binding
		DNA topology, not DNA sequence, is a critical determinant for Drosophila ORC−DNA binding
		An ethidium-bromide-stained gel of the tested DNAs is shown on top of a graph depicting the ratios of bound supercoiled DNA to bound linear DNA as a function of
	www.nature.com /emboj/journal/v23/n4/fig_tab/7600077ft.html (724 words)

	Endogenous Fluctuations of DNA Topology in the Chloroplast of Chlamydomonas reinhardtii -- Salvador et al. 18 (12): ...
		Endogenous Fluctuations of DNA Topology in the Chloroplast of Chlamydomonas reinhardtii -- Salvador et al.
		DNA supercoiling in the chloroplast of the unicellular green alga Chlamydomonas reinhardtii was found to change with a diurnal
		in chloroplast DNA topology correlated tightly with the endogenous
	mcb.asm.org /cgi/content/abstract/18/12/7235 (399 words)

	BCH5425 Molecular Biology and Biotechnology (Site not responding. Last check: 2007-10-21)
		The enzymes that control DNA topology are critical to DNA replication and transcription.
		Thus, if no supercoiling is introduced, the DNA must adopt a conformation of 9.01 base pairs/twist of the helix within the region ahead of the replication fork.
		The 5' phosphate of the nicked strand is covalently attached to a tyrosine in the protein.
	www.sb.fsu.edu /~hongli/BCH5425/note3.html (1107 words)

	Knots Bibliography
		Although relatively old, this article is still a valid starting point to anybody interested in biological function of topoisomerases (enzymes which convert DNA rings from one topoisomer to another).
		An introduction to biochemical topology - from a biological standpoint.
		Use of site-specific recombination as a probe of DNA structure and metabolism in vivo.
	www.beloit.edu /~biology/Srebrenka/Knots.html (286 words)

	Home page for Alex Vologodskii (Site not responding. Last check: 2007-10-21)
		The study of the equilibrium fraction of catenanes formed between supercoiled DNA and linear molecules which are converting into circular form in the experiment, gives good example of the approach (click here to see a short description of this work).
		The approach should be especially efficient for enzymes that change DNA topology, such as type II DNA topoisomerases and site-specific recombinases.
		Typically, because of the flexibility of substrate DNA molecules, these enzymes form distributions of different topological forms rather than DNA molecules with a uniqe topology (click here to see an example).
	crab.nyu.edu:16080 /~alex (445 words)

	DWL Sumners
		I am interested in the applications of topology to molecular biology and polymer configuration, both in theory development and computational simulation. Another interest is the mathematical analysis of human brain functional data.
		Some enzymes maintain the proper geometry and topology by passing one strand of DNA through another via an enzyme-bridged transient break in the DNA; this enzyme action plays a crucial role in cell metabolism, including segregation of daughter chromosomes at the termination of replication and in maintaining proper in vivo (in the cell) DNA topology.
		The topological approach to enzymology is an indirect method in which the descriptive and analytical powers of topology and geometry are employed in an effort to infer the structure of active enzyme-DNA complexes in vitro (in a test tube) and in vivo.
	www.math.fsu.edu /~sumners (818 words)

	Long-Term Experimental Evolution in Escherichia coli. XII. DNA Topology as a Key Target of Selection -- Crozat et al. ...
		DNA Topology as a Key Target of Selection -- Crozat et al.
		DNA Topology as a Key Target of Selection
		DNA supercoiling increasing, usually in the first 2000 generations.
	www.genetics.org /cgi/content/abstract/169/2/523 (262 words)

	DNA Nanotechnology Bibliography from Ned Seeman's Laboratory. (Site not responding. Last check: 2007-10-21)
		Chen and N.C. Seeman, The Synthesis from DNA of a Molecule with the Connectivity of a Cube, Nature 350, 631-633 (1991).
		Zhang and N.C. Seeman, The Construction of a DNA Truncated Octahedron, Journal of the American Chemical Society 116, 1661-1669 (1994).
		N.C. Seeman, DNA Nanotechnology, In: WTEC Workshop Report on R and D Status and Trends in Nanoparticles, Nanostructured Materials, and Nanodevices in the United States, ed.
	seemanlab4.chem.nyu.edu /nanobib.html (2491 words)

	Untitled Document (Site not responding. Last check: 2007-10-21)
		Alpha-helical coiling of DNA strands is only the starting structural element, which we usually associate with DNA structure.
		Because supercoiling, knotting and linking are important in cellular processes, we should understand their geometry and topology.
		As a part of my special project in Mathematical Biology, I will attempt to present a few ideas of DNA topology and geometry, whose scientific, mathematical and aesthetic aspects will hopefully motivate further interest in this new and exciting field.
	www.beloit.edu /~biology/Srebrenka/indexsreb.html (158 words)

	BIMM 100 - 07.ProkChrom (Site not responding. Last check: 2007-10-21)
		A measure of the "superhelicity" of the DNA molecule
		All native DNA which is closed circular shows superhelical content...
		DNA structure, including Tertiary Structure, accounts for essentially all of the structure found in simple Replicons such as prokaryotic Plasmids.
	www-biology.ucsd.edu /classes/bimm100.FA00/07.ProkChrom.html (1449 words)

	[No title] (Site not responding. Last check: 2007-10-21)
		D.W. Sumners, Lifting the curtain: using topology to probe the hidden action of enzymes.
		Topology of Xer recombination on catenanes produced by lambda integrase.
		Roca, J., and Wang, J. DNA transport by a type II topoisomerase: evidence in favor of a two gate mechanism.
	www.ma.utexas.edu /~darcy/AMS/ref.html (364 words)

	DNA topology (Site not responding. Last check: 2007-10-21)
		Influence of sequence dependent bends: branching: influence of DNA bending (Laundon and Griffith)
		SV40 minichromosome preparation ---> topoisomerase --> extract DNA --> is sc.
		Biological relevance to linear DNA: topologically constrained regions.
	opbs.okstate.edu /~melcher/Lec.htmlfolder/232NAPS.html (240 words)

	DNA Topology in Ned Seeman's Laboratory. (Site not responding. Last check: 2007-10-21)
		The DNA polyhedra that we make in our DNA Nanotechnology program are catenanes of cyclic unknotted DNA molecules.
		The interconversion of knots and circles by topoisomerases makes this a good system to seek topoisomerase activity; we have used this interconversion to demonstrate that E. coli DNA topoisomerase III is an RNA topoisomerase.
		We have shown that there is a general way to design any knot from DNA, by equating a node in a projection of a knot with a half-turn of DNA.
	seemanlab4.chem.nyu.edu /topo.html (240 words)

	Joaquim Roca Bosch Home Page
		DNA replication, transcription, recombination and repair are linked to severe changes in the topological state of the double helix.
		Cells modulate the degree of supercoiling, knotting and catenation of DNA strands through the activity of DNA topoisomerases.
		Our work is complemented with mechanistic studies on DNA topoisomerases, and the development of topological methods to infer novel structural aspects of the genome.
	www.cid.csic.es /homes/roca (138 words)

	Cold Spring Harbor Laboratory
		It is the mission of the Office of Technology Transfer to protect and license intellectual property and to obtain industrial research funding in keeping with our educational mission.
		The Dolan DNA Learning Center is the world's first science museum and educational facility promoting DNA literacy.
		The meetings held at the Banbury Center are recognized internationally as being amongst the world's best discussion workshops for topics in molecular biology, molecular genetics and science policy.
	www.cshl.edu (219 words)

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