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strand may be "positively supercoiled" or "negatively supercoiled" (more or less tightly wound). The amount of a strand's supercoiling affects a number of biological...

to, respectively, as positively or negatively supercoiled. DNA in vivo is typically negatively supercoiled, which facilitates the unwinding (melting) of...

(overwound helix) ahead of RNAP and negative supercoiling (underwound helix) behind it. The supercoiled structure of the DNA around the transcription...

become over-twisted (positively supercoiled) and the DNA behind RNAP would become under-twisted (negatively supercoiled). It has been found that a topological...

Sutthibutpong T, Chen M, et al. (October 2015). "Structural diversity of supercoiled DNA". Nature Communications. 6 (1) 8440. Bibcode:2015NatCo...6.8440I...

changes in the topological state of DNA, interconverting relaxed and supercoiled forms, linked (catenated) and unlinked species, and knotted and unknotted...

is a three-dimensional matrix formed of helical agarose molecules in supercoiled bundles that are aggregated into three-dimensional structures with channels...

Three topoisomers of a closed circular DNA molecule. Left: negatively supercoiled; center: relaxed; right: positively supercoiled...

ToNV, TpNV Absent Absent Nucleic acid Circular, supercoiled dsDNA of 80-180 kbp Circular, supercoiled dsDNA of 96-232 kbp Circular, dsDNA of 124 kbp (MdSGHV)...

positive supercoils can be introduced to DNA that is either negatively supercoiled or fully relaxed. Where DNA gyrase forms a tetramer and is capable of...

cells is negatively supercoiled and has the tendency to unwind. Hence the separation of strands is easier in negatively supercoiled DNA than in relaxed...

right-handed catenanes without acting on right-handed plectonemes in negatively supercoiled DNA molecules, based on geometrical specificity of juxtapositions. Topoisomerase...

is faced with significant stress, a negative supercoiled conformation is adopted. A negative supercoiled conformation is marked with fewer helical turns...

extension cord and then plugging it into itself. Supercoiled denatured DNA is similar to supercoiled DNA, but has unpaired regions that make it slightly...

Almirall) is a broad spectrum antibiotic that inhibits the uncoiling of supercoiled DNA in various bacteria by blocking the activity of DNA gyrase and topoisomerase...

mathematics. Strogatz completed his senior thesis, titled "The Mathematics of Supercoiled DNA: An Essay in Geometric Biology", under the supervision of Frederick...

vertebrates, Cdk1-mediated phosphorylation is essential for both the DNA supercoiling activity and chromosome assembly activity of condensin I. Experiments...

Prokaryotic chromosomes and plasmids are, like eukaryotic DNA, generally supercoiled. The DNA must first be released into its relaxed state for access for...

the prefix trans- and the word "infection." Genetic material (such as supercoiled plasmid DNA or siRNA constructs), may be transfected. Transfection of...

subunit of DNA gyrase that releases the positive binding stress on the supercoiled DNA. Hives, rash, intense itching, or fainting soon after a dose may...

writhe is referred to as DNA supercoiling and is quite commonplace, and in fact in most organisms DNA is negatively supercoiled. Any elastic rod, not just...

Jagadeesan, Rahul; Ribeiro, Andre S (2022-08-03). "Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli"...

interacting with positively supercoiled DNA and introduces (additional) negative supercoils when binding to relaxed or negatively supercoiled DNA. Netropsin's effect...

than supercoiled DNA, and the single-stranded form (which can sometimes appear depending on the preparation methods) may move ahead of the supercoiled DNA...

and centrifugation. Alkaline lysis takes advantage of the small and supercoiled physical composition of plasmid DNA compared to chromosomal DNA, along...

circle mechanism. This is the mechanism by which the double stranded supercoiled genome is nicked on the positive strand by a virus-encoded A protein...

functions. Prokaryotic topoisomerase I (topo IA) can only relax negative supercoiled DNA, whereas eukaryotic topoisomerase I (topo IB) can introduce positive...

DNA, minimizing interfering reactions. DMSO in a PCR is applicable for supercoiled plasmids (to relax before amplification) or DNA templates with high GC-content...

were also shown to be directly genotoxic by effectuating scissions in supercoiled ΦX174 DNA. Increased arsenic exposure is associated with an increased...

the growing RNA molecule, topoisomerases, which change the amount of supercoiling in DNA, helping it wind and unwind, as well as a large variety of transcription...

analytical band centrifugation, and contributed to the understanding of DNA supercoiling. Vinograd obtained his undergraduate degree in chemistry from the University...

transcription in vitro only when the DNA template is not already denatured or is supercoiled. The CAK subunits, CDK7 and cyclin H, are responsible for the phosphorylation...

study originated in response to questions that arise in the study of supercoiled double-stranded DNA rings. About the writhing number, mathematician W...

action of enzymes like topoisomerases, which alter the linking number and supercoiling of DNA, and to model processes such as recombination and replication...

regions. The N-terminal 214 amino acids are dispensable for relaxation of supercoiling activity in vitro and there are four nuclear localization signals and...

occurs even in absence of any origin binding proteins due to negative supercoiling forces, making it an energetically favourable action. DUEs are typically...

are lysed with detergent and high salt to form nucleoids containing supercoiled loops of DNA linked to the nuclear matrix. Electrophoresis at high pH...

topoisomerase (Grindley 2002). Wild type resolvase system absolutely requires a supercoiled substrate and that the recombination sites are oriented in a direct repeat...

PMID 16516151. Stillman BW, Gluzman Y (August 1985). "Replication and supercoiling of simian virus 40 DNA in cell extracts from human cells". Molecular...

van der Torre J, Dekker C (2022). "Condensin-driven loop extrusion on supercoiled DNA". Nat Struct Mol Biol. 29 (7): 719–727. doi:10.1038/s41594-022-00802-x...

reaction Endonucleolytic cleavage of supercoiled plasma DNA to linear DNA duplexes This enzyme has preference for supercoiled DNA. DasGupta U, Ghosh S (March...

damage or disturbance does not occur at that level. DNA is, however, supercoiled and wound around "packaging" proteins called histones (in eukaryotes)...

and affects the motility of S. Typhi. Fis buffers decrease of negative supercoiling in tyrT and rrnA expression. The upstream FIS binding site of rrnA is...

junctions. It is an endonuclease that makes single-strand breaks in supercoiled double-stranded DNA, and promotes the formation of CO recombinants. Double...

replication fork. It is the only known enzyme to actively contribute negative supercoiling to DNA, while it also is capable of relaxing positive supercoils. It...

basis for this genetic disease. Triple-stranded DNA has been observed in supercoiled Satellite DNA in regions where microsatellite copy numbers are highly...

released in chemical reactions or stress induced destabilisations in supercoiled biopolymer chains. Therefore, conformons can be defined as packets of...

of circular kDNA maxicircles and minicircles, most of which are not supercoiled. Exterior to the kDNA disk but directly adjacent are two complexes of...

larger plasmids transform less well than smaller plasmids. Forms of DNA – Supercoiled plasmid have a slightly better transformation efficiency than relaxed...

configuration, Dr. Manu designed a centrifuge using the toy's design and Supercoiling-mediated ultrafast spinning dynamics. The Paperfuge can be used to separate...

bacterium cannot divide. DNA gyrase, on the other hand, is responsible for supercoiling the DNA, so that it will fit in the newly formed cells. Both mechanisms...

including quantum mechanics, electromagnetism, and the study of DNA supercoiling. Any two closed curves in space, if allowed to pass through themselves...

(November 1991). "Trichosanthin, a potent HIV-1 inhibitor, can cleave supercoiled DNA in vitro". Nucleic Acids Res. 19 (22): 6309–12. doi:10.1093/nar/19...

smallest plasmids. Thermotoga petrophila RKU1 plasmid (pRKU1) is negatively supercoiled, contains 846 base pairs, and carries only the rep gene. Due to T. Petrophila...

activity neuropilin binding SH2 domain binding ephrin receptor binding supercoiled DNA binding sequence-specific double-stranded DNA binding Cellular component...

transcription coactivator activity chromatin binding protein binding supercoiled DNA binding RNA binding Cellular component cytosol nuclear periphery...

Upon binding, Chartreusin may inhibit the relaxation of negatively supercoiled DNA, or induce strand scission. Consequently, this compound has been...

(together referred to as a nucleosome) are responsible for the amount of supercoiling of DNA, and these complexes can be temporarily modified by processes...

histones with which these proteins are associated collaborate in its supercoiling. Hyperthermophiles have a great diversity in metabolism including chemolithoautotrophy...

alternating purine–pyrimidine sequence (especially poly(dGC)2), negative DNA supercoiling or high salt and some cations (all at physiological temperature, 37 °C...

topoisomerases, DNA gyrase and topoisomerase IV, which cut DNA to introduce supercoiling, while leaving nuclease activity unaffected. With the ligase activity...

with Nicholas Cozzarelli's group on the structure and properties of supercoiled DNA and DNA catenanes. Levene's group has made both experimental and...

high temperatures and helps to relax both positively and negatively supercoiled DNA . Topoisomerase V is a unique enzyme because it possesses both topoisomerase...

genomics Substantial equivalence Substitution Suicide gene Supercoil Supercoiling Supergene Superinfection Suppressor gene Suppressor mutation Svedberg...

and the agarose polymer chains form helical fibers that aggregate into supercoiled structure with a radius of 20-30 nanometer (nm). The fibers are quasi-rigid...

K (April 2010). "Conformational change of flagellin for polymorphic supercoiling of the flagellar filament". Nature Structural & Molecular Biology. 17...

bands, the speed of migration may depend on whether it is relaxed or supercoiled. Single-stranded DNA or RNA tends to fold up into molecules with complex...

production of positive supercoils in a closed circular DNA. Positive supercoiling is important to prevent the formation of open complexes. Reverse gyrases...

drug-DNA recognition: a molecular dynamics study Structural diversity of supercoiled DNA She won the Suffrage Science award in 2019. Ascona B-DNA Consortium...

interaction with Topoisomerase I. When Topoisomerase I, Topo I, reduces supercoiling caused by transcription when it is bound to DNA. When Topo I is not bound...

13% of the virus's weight and contains a single molecule of circular, supercoiled, double-stranded DNA of 10 kilobases in length. The genome has a g +...

shape of DNA to drive their motion along the DNA molecule and to detect supercoiling, whereas the α3β3 hexamer uses the conformational changes through the...

form chromatin as in eukaryotes but instead exists as a highly compact supercoiled structure, the precise nature of which remains unclear. Most bacterial...

structures can arise due to various factors, including DNA sequence, length, supercoiling, and environmental conditions. Non-B DNA structures can have important...

PMID 17360403. Marko, J.F.; Siggia, E.D. (1995). "Statistical mechanics of supercoiled DNA". Physical Review E. 52 (3): 2912–2938. Bibcode:1995PhRvE..52.2912M...

S2CID 1364720. Dorman, C. J.; Bhriain, N. N.; Higgins, C. F. (1990). "DNA supercoiling and environmental regulation of virulence gene expression in Shigella...

virions are enveloped rod shaped nucleocapsids containing circular, supercoiled, double stranded DNA. The NPV which enters the insect gut, lyses in the...

condensed, nonsegmented and consists of a single molecule of circular, supercoiled double-stranded DNA, 12 kilobase pairs in length. The genome has a rather...

as a model plasmid. For example, biophysical studies on its naturally supercoiled state have determined its radius of gyration to be 65.6 nm and its Stokes...

H1 into higher-order structures such as 30-nm fibers and ultimately supercoiled chromatids. Because the histone–DNA interaction limits access to the...

circular dsDNA enter the nucleus via the nuclear pore. The viral DNA forms supercoiled mini-chromosome structures upon entering the host nucleus, where it is...

springs to connect spheres described by the Lennard-Jones potential; DNA supercoiling has been investigated using 1–3 pseudo-atoms per basepair, and at even...

DNA; HU also binds to RNA and DNA-RNA hybrids with the same affinity as supercoiled DNA. Recent research has revealed that HU binds with high specificity...

at the end of the GFP gene. The plasmid is 5371 base pairs long. In supercoiled form, it runs on an agarose gel in the 4200–4500 range. The GFP gene...

to show that the covalent binding of platinum complexes changes the supercoiling of the DNA, "bending and unwinding" the double helix. Further experiments...

forming sequences of the c-MYC oncogene promoter were placed into a supercoiled plasmid, inducing super helicity of both structures. The conditions of...

the DNA strands as they are unwound and causes the strands to become supercoiled. This is a critical step in DNA replication in these cells which results...

32225-38 Assays for the preferential binding of human topoisomerase I to supercoiled DNA. Yang Z, Champoux JJ Methods in Molecular Biology. 2009 ; 582 : 49-57...

DNA; HU also binds to RNA and DNA-RNA hybrids with the same affinity as supercoiled DNA. Recent research has revealed that HU binds with high specificity...

"pan-kinetoplast DNA" and are distributed throughout the mitochondrion, and are supercoiled unlike most kinetoplast DNA. The fish parasite Trypanoplasma borreli...

topoisomerase I. The biological role of topoisomerase is to cleave and rejoin supercoiled DNA ends to facilitate replication. Vaccinia virus topoisomerase I specifically...

DNA of approximately 13 bp, referred to as the "transcription bubble". Supercoiling plays an important part in polymerase activity because of the unwinding...

rather than nucleosomes, whilst prokaryotes package their DNA through supercoiling. Maeshima, Kazuhiro; Hihara, Saera; Eltsov, Mikhail (2010-06-01). "Chromatin...

MLH1-MLH3 heterodimer is an endonuclease that makes single-strand breaks in supercoiled double-stranded DNA. MLH1-MLH3 binds specifically to Holliday junctions...

Zaenen I, Van Larebeke N, Teuchy H, Van Montagu M, Schell J. 1974. Supercoiled circular DNA in crown gall inducing Agrobacterium strains. J. Mol. Biol...

lasso), where one tail pierces the surface n times; the LSn class (the supercoiling lasso), where one tail pierces the surface n times, winding around the...

the supercoiling also stimulates enhancer promoter contacts and it is proposed that transcription of eRNA sends the first wave of supercoiling that can...

of extracellular signalling. Recent data suggest different degrees of supercoiling distinguish the permissive and inactive states. The bursting phenomenon...

the Met box contains a pyrimidine-purine step that becomes positively supercoiled forming a kink in the phosphodiester backbone. This is how the protein...

these single stranded "nicks" in the viral DNA are repaired, forming a supercoiled molecule that binds to histones. This DNA is transcribed into a full...

Varidnaviria is unclear since morphological features, such as the circular, supercoiled genome of bacteriophage PM2, seemingly prohibit translocation by the...

Zaenen I, Van Larebeke N, Van Montagu M, Schell J (June 1974). "Supercoiled circular DNA in crown-gall inducing Agrobacterium strains". Journal of...

conspicuous under a microscope during prophase due to systemic coiling and supercoiling of chromatic strands of DNA in preparation for cell division. chromosome...

hRAD54 has been shown to specifically exhibit DNA-dependent ATPase and supercoiling activities. hRAD54 transcripts are expressed primarily in the testis...

transcription if the DNA template is not already denatured or if it is supercoiled. Mediator then encases all the transcription factors and Pol II. It interacts...

Racko D, Benedetti F, Dorier J, Stasiak A (January 2019). "Are TADs supercoiled?". Nucleic Acids Research. 47 (2): 521–532. doi:10.1093/nar/gky1091....

handed polyproline II-type (PPII) helices assemble to form a right-handed supercoiled helical motif. Short synthetic peptides known as collagen mimetic peptides...

whereas tektin C forms homodimers. Tektin filaments are present in a supercoiled state. This structure of tektins suggests that they are evolutionarily...

to transcription or replication. ATP is used. Topoisomerases reduce supercoiling of DNA in the cell. ATP is used. RSC and SWI/SNF complexes remodel chromatin...

in the 2019 WHO Model List for Essential Medicines. TopI relaxes DNA supercoiling during replication and transcription. Under normal circumstances, TopI...

(similar size as Dps). For instance, Dps shows higher preference towards supercoiled DNA where two DNA strands are in closer vicinity. In Escherichia coli...

Molecules other than proteins can be separated by 2D electrophoresis. In supercoiling assays, coiled DNA is separated in the first dimension and denatured...

Bagga R, Emerson BM (1997). "An HMG I/Y-containing repressor complex and supercoiled DNA topology are critical for long-range enhancer-dependent transcription...

MLH1-MLH3 heterodimer is an endonuclease that makes single-strand breaks in supercoiled double-stranded DNA. MLH1-MLH3 binds specifically to Holliday junctions...

within their mitochondrion, have supercoiled minicircles as opposed to the open circle conformation (not supercoiled) observed in Dimastigella. D. trypaniformis...

hundreds of nm -1 per base plasmid DNA 0.5 - 10 kilo-basepairs DNA (double-stranded) ~650 Da per base hundreds of nm; depends on supercoiling -1 per base...

Drosophila ORC, like its budding yeast counterpart, bends DNA and negative supercoiling has been reported to enhance DNA binding of this complex, suggesting...

junctions. It is an endonuclease that makes single-strand breaks in supercoiled double-stranded DNA. The MLH1-MLH3 heterodimer promotes the formation...

extensively. DNA gyrase is an enzyme that binds to DNA and introduces negative supercoiling. This helps unwind the DNA for replication. If there is a mutation in...

DNA passing through the center. hDMC1 can conduct D-loop formation in supercoiled DNA. DMC1 has weak ATPase activity and is able to promote heteroduplex...

Hoogsteen base pairing, while a GAA repeat forms a triplex due to negative supercoiling. CAG, CTG, and CGG repeats form a hairpin. After the hairpin forms, the...

takes place in living cells that should involve transient uncoiling of supercoiled DNA fibers. Although DNA consists of relatively rigid, very large elongated...

deacetylase, which is in control of energy metabolism, chemotaxis, and DNA supercoiling in many bacteria.CobB does contain a sequence length of 235. It can be...

formation is a dynamic process, largely controlled by the amount of supercoiling. ZBP1 recognizes DNA in the cytoplasm as an antiviral mechanism. Viral...

unstable than double-stranded DNA. During elongation of transcription, supercoiling can occur behind an elongating RNA polymerase, leading to single-stranded...

chromatin complex of DNA is folded in a way that functionally mimics the supercoiled state characteristic of prokaryotic DNA, so although the enhancer DNA...

Allemand, J.-F.; Croquette, V.; Croquette, V. (April 1998). "Behavior of Supercoiled DNA". Biophysical Journal. 74 (4): 2016–2028. Bibcode:1998BpJ....74.2016S...

neutralization buffer to lower the pH to around 7, the large and less supercoiled chromosomal DNA and proteins form large complexes and precipitate; but...

point and loop in the shape of a cruciform, stabilized by negative DNA supercoiling. Two classes of cruciform DNA have been described; folded and unfolded...

negatively supercoiled, in contrast to plasmids from other hyperthermophilic archaea which are typically found in a relaxed to positively supercoiled state...

D, Bensimon A, Croquette V (March 1996). "The elasticity of a single supercoiled DNA molecule". Science. 271 (5257): 1835–7. Bibcode:1996Sci...271.1835S...

Emerson BM (March 1997). "An HMG I/Y-containing repressor complex and supercoiled DNA topology are critical for long-range enhancer-dependent transcription...

Expression by a Novel DNA Structural Transmission Mechanism That Requires Supercoiling-induced DNA Duplex Destabilization in an Upstream Activating Sequence"...

Kendall, D.; Booth, A. J.; Levy, M.S.; Lye, G. J. (2001). "Separation of supercoiled and open-circular plasmid DNA by liquid-liquid counter-current chromatography"...

1042/bst0160001. PMID 3277879. Lilley, D. M. (1983). "Structural perturbation in supercoiled DNA: Hypersensitivity to modification by a single-strand-selective chemical...

PMID 6156450. Drolet M, Bi X, Liu LF (January 1994). "Hypernegative supercoiling of the DNA template during transcription elongation in vitro". The Journal...

covalently closed circular dsDNA. During another aspect of SPLCV replication, supercoiled (ccc)dsDNA is converted into dsDNA and ssDNA by rolling-circle replication...

nucleosome) (1975) 4. Discovery that histones are responsible for the supercoiling of DNA in chromatin (1975)   5. Discovery of split genes in animal genomes...

in size from 10 to 200 kilodaltons.[citation needed] The genome is a supercoiled, circular double stranded DNA (dsDNA) molecule ranging in size from 120...

At 37 degrees Celsius, chromosomally encoded Ymo, which regulates DNA supercoiling around the virF gene, changes conformation, allowing for virF expression...

DNA binding damaged DNA binding protein binding DNA binding, bending supercoiled DNA binding DNA binding four-way junction DNA binding RAGE receptor binding...

PMID 1840671. Travers A, Schneider R, Muskhelishvili G (February 2001). "DNA supercoiling and transcription in Escherichia coli: the FIS connection". Biochimie...

novel mouse DNA topoisomerase III (Topo IIIbeta) possessing negatively supercoiled DNA relaxing activity, whose message is highly expressed in the testis"...

regulation by compacting replicated DNA prior to mitotic division via supercoiling of the DNA. SMC2 also functions in resolving Sister chromatids prior...

Alan C. (2002). "IHF redistributes bound initiator protein, DnaA, on supercoiled oriC of Escherichia coli". Molecular Microbiology. 35 (4): 835–844. doi:10...

deformed as a result of torsional stress (a phenomenon known as DNA supercoiling). The topological interpretation of helicity in terms of the Gauss linking...

pyrimidine DNA binding endodeoxyribonuclease activity protein kinase binding supercoiled DNA binding DNA binding Hsp90 protein binding microtubule binding protein...

chemoattractant activity double-stranded DNA binding DNA binding, bending supercoiled DNA binding RNA binding transcription coactivator activity Cellular component...

those nucleotides are annealed to form a strand. Two strands of DNA are supercoiled into double helix form and that is what people think of first when they...

circular DNA nanoparticles ("minimized vectors") that can be used to study supercoiling and the function of therapeutic topoisomerase inhibitors. The dynamic...

PMID 14527416. Drolet, M; Bi, X; Liu, LF (21 January 1994). "Hypernegative supercoiling of the DNA template during transcription elongation in vitro". The Journal...

of thread). Gyrase (a form of topoisomerase) relaxes and undoes the supercoiling caused by helicase. It does this by cutting the DNA strands, allowing...

simplifying freely jointed chain model and to demonstrate the key role of DNA supercoiling in transcription regulation, and for using tethered particle motion to...

and the plasmid PUC19. It was found that BE27 promoted the change of supercoiled PUC19 DNA to a more relaxed, linear form. In the three arbitrary stages...

binding to the B subunit of this enzyme and inhibit the ATP-dependent DNA supercoiling catalysed by gyrase. X-ray crystallography studies have confirmed binding...

mutants of DNA gyrase, he established a fundamental interplay between DNA supercoiling and transcription in E. coli. Mirkin conducted his postdoctoral studies...

unusual properties: they alternate from right-handed to left-handed supercoiling often interrupted by small globular domains, which owes to their appearance...

DNA gyrase is another thermal adaptation, it introduces positive DNA supercoiling to increase the heat stability of the genome, and is a protein unique...

S2CID 24833877. Vijayan V, Zuzow R, O'Shea EK (December 2009). "Oscillations in supercoiling drive circadian gene expression in cyanobacteria". Proceedings of the...

species of the nematode. fibers, macrofibers or bundles, produced by supercoiling of the filaments. A. suum MSP filaments frequently form rope-like structures...