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IUBMB CommentsThese enzymes bring about the conversion of one topological isomer of DNA into another, e.g., the relaxation of superhelical turns in DNA, the interconversion of simple and knotted rings of single-stranded DNA, and the intertwisting of single-stranded rings of complementary sequences, cf. EC 5.6.2.2 DNA topoisomerase (ATP-hydrolysing).
Synonyms
topoisomerase, topoisomerase i, topo i, dna topoisomerase i, topoisomerase iv, dna topoisomerase, topoisomerase 1, human topoisomerase i, reverse gyrase, topoisomerase-i,
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ATP-independent type I topoisomerase
bi-subunit topoisomerase I
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Bi-subunit topoisomerase IB
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Dam DNA topoisomerase III
Deoxiribonucleate topoisomerase
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Deoxiribonucleic topoisomerase
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DNA topoisomerase I alpha
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DNA topoisomerase I-B
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DNA topoisomerase III
belongs to the type IA family of DNA topoisomerases
DNA topoisomerase IIIalpha
DNA topoisomerase type I
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EC 5.99.1.2
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formerly
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human DNA topoisomerase I
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Isomerase, deoxiribonucleate topo-
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Nicking-closing enzyme
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Poxviridae topoisomerase IB
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topoisomerase I homolog
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topoisomerase IIIalpha
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type IA DNA topoisomerase
type IB topoisomerase
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type IB topoisomerase V
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Untwisting enzyme
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Vaccinia DNA topoisomerase I
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variola topoisomerase IB
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type IB
yeast DNA topoisomerase I
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ATP-independent type I topoisomerase
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ATP-independent type I topoisomerase
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bcTopo IIIbeta
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Dam DNA topoisomerase III
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Dam DNA topoisomerase III
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DNA topoisomerase
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DNA topoisomerase 1
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DNA topoisomerase I
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DNA topoisomerase I
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677937, 678207, 678377, 679159, 682092, 691221, 691728, 691729, 692660, 692707, 693400, 693401, 702077, 702620, 714330, 728560, 728639, 747263, 747646, 747693, 747698, 748187, 748337, 748369, 749223, 750368, 750702
DNA topoisomerase I
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DNA topoisomerase I
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DNA topoisomerase IB
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DNA topoisomerase IIIalpha
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DNA topoisomerase IIIalpha
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hTop1p
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hTopoI
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hTopoI
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htopoI readily and very efficiently forms double cleavage complexes after the relaxation of negatively supercoiled plasmid DNA both with recombinant enzyme and with purified htopoI. When topo I is isolated from HeLa S3 cells, a considerable fraction migrates to the same gel electrophoretic position as topo I bearing a covalently bound 13-mer oligonucleotide. This may suggest that double cleavage complexes also form under intracellular conditions
LdTopIIIbeta
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MttopoI
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Reverse gyrase
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Reverse gyrase
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is a DNA topoisomerase, specific to microorganisms living at high temperatures, which comprises a type IA topoisomerase fused to an SF2 helicase-like module and catalyzes ATP hydrolysis-dependent DNA positive supercoiling
Reverse gyrase
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is a DNA topoisomerase, specific to microorganisms living at high temperatures, which comprises a type IA topoisomerase fused to an SF2 helicase-like module and catalyzes ATP hydrolysis-dependent DNA positive supercoiling
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SiRe_1176
locus name
Top1
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Top1
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681292, 691221, 691619, 692707, 693113, 702176, 702620, 705842, 714760, 715867, 727204, 728098, 728293, 728558, 728560, 747263, 747474, 747693, 748187, 748337, 750702
TOP1alpha
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Top1p
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TopA
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TopIB
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Topo I
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Topo I
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678603, 681674, 690972, 691137, 691264, 691321, 691568, 691608, 691729, 692660, 702885, 703153, 714474, 714643, 714900, 726976, 727417, 747698, 750368
topoI
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topoisomerase 1
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Topoisomerase I
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Topoisomerase I
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677937, 678603, 679159, 681292, 681403, 681408, 681674, 682092, 682169, 682212, 691137, 691221, 691264, 691321, 691568, 691582, 691608, 692246, 692660, 693067, 693113, 693543, 702579, 702598, 702602, 702689, 702885, 703153, 705047, 705827, 705842, 705973, 714448, 714463, 714474, 714643, 714760, 714814, 714900, 714903, 715867, 716007, 716380, 726976, 727170, 727204, 727417, 728098, 728293, 728558, 728579, 728639, 728804
Topoisomerase I
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type IB topoisomerase
topoisomerase IB
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topoisomerase III
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topoisomerase IIIbeta
subfamily of prokaryotic type IA topoisomerases that are different from the prototypical ecTopo I and ecTopo III-like enzymes
topoisomerase IIIbeta
subfamily of prokaryotic type IA topoisomerases that are different from the prototypical ecTopo I and ecTopo III-like enzymes
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TopR1
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Type I DNA topoisomerase
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Type I DNA topoisomerase
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Type I DNA topoisomerase
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Type I DNA topoisomerase
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type IA DNA topoisomerase
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type IA DNA topoisomerase
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type IA topoisomerase
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type IA topoisomerase
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type IA topoisomerase
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vTopo
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vTopo
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closely related to the human type I topoisomerase (hTopo)
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ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
mechanism
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ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
acts by directing a nucleophilic attack from the hydroxyl group of an internal Tyr into a phosphodiester bond in the DNA backbone, resulting in nicking of one strand of the DNA double helix and formation of a covalent linkage between the 3'-phosphate and the Tyr hydroxyl group
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ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
alters the linking number in steps of one
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ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
alters the linking number in steps of one
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ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
enzyme closes its substrate DNA molecule after the removal of each superhelical turn, dissociation of the enzyme substrate complex may but does not necessarily occur after each cycle of the reaction
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ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
bcTopo IIIbeta does not act on partially relaxed DNA. In contrast to ecTopo III Escherichia coli topoisomerase bcTopo IIIbeta can not further relax this substrate. bcTopo IIIbeta and ecTopo III exhibit comparable single stranded DNA binding activities and cleavage site specificities. bcTopo IIIbeta does not possess decatenation activity. Unlike ecTopo III, bcTopo III beta is not capable of decatenating replication intermediates
ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
cleaves single-stranded DNA (ssDNA) via a 5' phosphotyrosine intermediate
ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
demonstrated that human Topo I specifically stimulates the origin binding activity of PV E1, apparently through a protein-protein interaction. Topo I stimulates the origin binding activity of papillomavirus protein E1. Topo I stimulation of E1 binding is highly specific, verified by enzyme-linked immunosorbent assays using a nonorigin DNA fragment, Topo I stimulation of E1 DNA binding activity is origin specific. E1 does not affect the DNA binding activity of Topo I. DNA modulates the interaction between E1 and Topo I (ELISA-based protein interaction assays). Topo I and E2 stimulate the origin binding of E1 independently(enzyme-linked immunosorbent assay)
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ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
Human topoisomerase I-mediated DNA relaxation reaction studied following modification of the enzyme at the active site tyrosine (position 723)
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ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
Identification of proteins that bind nicked DNA intermediates formed in the course of base excision repair (BER) in cell free extracts of Saccharomyces cerevisiae. Using a photocrosslinking technique with photoactivable dNTP analogues to trap proteins that interact with damaged DNA. Top1 has the potential to interfere with base excision repair in vivo
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ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
Vaccinia DNA topoisomerase (vTopo) catalyzes highly specific nucleophilic substitution at a single phosphodiester linkage in the pentapyrimidine recognition sequence 5'-(C/T)+5C4+C3+T+2T+1pN-1 using an active-site tyrosine nucleophile, thereby expelling a 5'hydroxyl leaving group of the DNA. Equilibrium binding and cleavage measurements. Cleavage reactions and modified substrates for vTopo, kinetic and thermodynamic parameters for variable length vTopo substrates with guanine base substitutions and deletions are shown
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ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
catalytic mechanism of DNA cleavage/religation and molecular basis for selectivity of a cytosine base at the -4 position. E9 acts as a general base in DNA cleavage, assisted by charge relay through D111 and H365
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ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
deprotonation of the 5' DNA end might be the limiting step in the topoisomerase religation mechanism
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ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
mechanism of DNA relaxation for type IA topoisomerases, overview
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ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
bcTopo IIIbeta does not act on partially relaxed DNA. In contrast to ecTopo III Escherichia coli topoisomerase bcTopo IIIbeta can not further relax this substrate. bcTopo IIIbeta and ecTopo III exhibit comparable single stranded DNA binding activities and cleavage site specificities. bcTopo IIIbeta does not possess decatenation activity. Unlike ecTopo III, bcTopo III beta is not capable of decatenating replication intermediates
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ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
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(TTA)35
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trinucleotide repeat (TTA)35 lying in the intergenic region of chromosome XIII of Saccharomyces cerevisiae, between the RPM2 (RNase P mitochondrial 2) and PRE8 genes. This sequence contains the structural elements suitable to be susceptible to DNA topoisomerase I site-specific activity and to assemble nucleosomes. DNA topoisomerase I strongly recognizes the TTA repeats. The (TTA)35 repeat is engaged in a positioned nucleosome in vivo. DNA topoisomerase I efficiently reacts with the TTA repeat, the (TTA)35 sequence, the longest and most stable among the simple repeated sequences in Saccharomyces cerevisiae, is organized in a positioned nucleosome and this can possibly account for its high stability, in fact each nucleosome stores one negative supercoil, thus preventing DNA denaturation and induction of conformational alterations responsible for genetic instability. DNA topoisomerase I in vivo cleaves the (TTA)35 sequence after nucleosome removal, the positioned nucleosome on the (TTA)35 sequence represents a hindrance to the DNA topoisomerase I activity. This last conclusion, based on the glucose/galactose experiments, represents the first formal evidence that DNA topoisomerase I cannot react with nucleosomal DNA
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117-base pair DNA oligonucleotide
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DNA
DNA
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so-called suicide substrate, contains a htopoI preferential binding sequence and is designed to trap the liberated 5'-OH end
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Holliday Junction Substrate H1-4
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close relationship between tyrosine recombinases and type IB topoisomerases, investigation of ability of human topoisomerase I to resolve the typical intermediate of recombinase catalysis, the Holliday junction, results consolidate the relationship between type IB topoisomerases and tyrosine recombinases
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negatively supercoiled DNA
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negatively supercoiled DNA
relaxed DNA
negatively supercoiled pBlueScript KSII(+) DNA
relaxed pBlueScript KSII(+) DNA
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negatively supercoiled pHC624 plasmid DNA
relaxed pHC624 plasmid DNA
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negatively supercoiled pHOTI plasmid DNA
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negatively supercoiled plasmid pXXZ06 DNA
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negatively supercoiled PUC18 DNA
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unable to relax positively supercoiled DNA
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Nicked circular DNA
Large catenated DNA networks
relaxed pBR322 DNA
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SF2/ASF protein + ATP
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kinase activity
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supercoiled DNA
relaxed closed circular DNA
supercoiled DNA
relaxed DNA
supercoiled pBAD/Thio plasmid DNA
relaxced pBAD/Thio plasmid DNA
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supercoiled pBR322 DNA
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supercoiled pBR322 plasmid DNA
relaxed pBR322 plasmid DNA
supercoiled plasmid DNA pBR322
relaxed plasmid DNA pBR322
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supercoiled plasmid DNA pGEM-5T
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relaxation
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supercoiled plasmid pBAD-GFPuv
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supercoiled plasmid pBR322 DNA
relaxed plasmid pBR322 DNA
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additional information
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DNA
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specific for single-stranded DNA, the enzyme drives extensive unwinding of closed circular DNA at high temperature. At 60-80°C it relaxes negatively but not positively supercoiled DNA. At 95°C, the enzyme unwinds both positively and negatively supercoiled substrates and produces extensively unwound form I* and I** DNA
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DNA
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specific for single-stranded DNA, the enzyme drives extensive unwinding of closed circular DNA at high temperature. At 60-80°C it relaxes negatively but not positively supercoiled DNA. At 95°C, the enzyme unwinds both positively and negatively supercoiled substrates and produces extensively unwound form I* and I** DNA
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DNA
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the enzyme exhibits a very high DNA relaxing activity. Strong preference for a cytosine at position -4 of the cleavage
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DNA
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the enzyme exhibits a very high DNA relaxing activity. Strong preference for a cytosine at position -4 of the cleavage
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negatively supercoiled DNA
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negatively supercoiled DNA
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negatively supercoiled DNA
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5.6.2.1 DNA topoisomerase
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