Å of DNA length. Wr, called "writhe," is the number of superhelical twists. Since biological circular DNA is usually underwound ... DNA supercoiling is important for DNA packaging within all cells. Because the length of DNA can be thousands of times that of a ... Negative supercoiling is also thought to favour the transition between B-DNA and Z-DNA, and moderate the interactions of DNA ... Supercoiling is also required for DNA/RNA synthesis. Because DNA must be unwound for DNA/RNA polymerase action, supercoils will ...

"Preferential binding of IFI16 protein to cruciform structure and superhelical DNA". Biochemical and Biophysical Research ... Cruciform DNA is a form of non-B DNA, or an alternative DNA structure. The formation of cruciform DNA requires the presence of ... B-DNA can form transient structures of cruciform DNA that act as recognition signals near origins of replication in the DNA of ... Cruciform DNA is found in both prokaryotes and eukaryotes and has a role in DNA transcription and DNA replication, double ...

"Effect of the potential triplex DNA region on the in vitro expression of bacterial beta-lactamase gene in superhelical ... Triple-stranded DNA (also known as H-DNA or Triplex-DNA) is a DNA structure in which three oligonucleotides wind around each ... There are two different types of intramolecular triplex DNA: H-DNA and H*-DNA. Formation of H-DNA is stabilized under acidic ... Wang G, Vasquez KM (July 2014). "Impact of alternative DNA structures on DNA damage, DNA repair, and genetic instability". DNA ...

Woelfle MA, Xu Y, Qin X, Johnson CH (November 2007). "Circadian rhythms of superhelical status of DNA in cyanobacteria". ... in which the circadian clock orchestrates dramatic circadian changes in DNA topology, which causes a change in the ...

DNA supercoil (superhelical DNA) Knot theory Fuller, F. Brock (1971). "The writhing number of a space curve" (PDF). Proceedings ... In DNA this property does not change and can only be modified by specialized enzymes called topoisomerases. ... DNA Structure and Topology at Molecular Biochemistry II: The Bello Lectures. (Helices, Molecular biology, Molecular topology). ... This study originated in response to questions that arise in the study of supercoiled double-stranded DNA rings. About the ...

Chu, Y; Hsu, M T (1992). "Ellipticine increases the superhelical density of intracellular SV40 DNA by intercalation". Nucleic ... Further DNA damage results from the formation of covalent DNA adducts following enzymatic activation of ellipticine by with ... increasing the superhelical density of the DNA. Intercalated ellipticine binds directly to topoisomerase II, an enzyme involved ... DNA replication inhibitors, Prodrugs, Topoisomerase inhibitors, DNA intercalaters, Plant toxins). ...

It is the melting of the DNA which is not induced by a promoter, but purely by the superhelical (also called topological) ... sites in superhelical DNA". Bioinformatics. 20 (9): 1477-1479. doi:10.1093/bioinformatics/bth304. PMID 15130924. [1] v t e (All ... nature of the DNA. It is based on a statistical mechanics treatment of DNA made by Craig J. Benham and Richard M. Fye. This ... "Activation of Gene Expression by a Novel DNA Structural Transmission Mechanism That Requires Supercoiling-induced DNA Duplex ...

Negative superhelical tension causes approximately one turn of DNA to unwind and form the transcription bubble. The template ... Subunits within TFIIH that have ATPase and helicase activity create negative superhelical tension in the DNA. ... and DNA helicase activity (unwinds DNA at promoter). It also recruits nucleotide-excision repair proteins. ... Kim TK, Lagrange T, Wang YH, Griffith JD, Reinberg D, Ebright RH (November 1997). "Trajectory of DNA in the RNA polymerase II ...

This negative superhelical tension causes approximately one turn of DNA to unwind and form the transcription bubble. The ... Subunits within TFIIH that have ATPase and helicase activity create negative superhelical tension in the DNA. ... on DNA to activate transcription of genetic information from DNA to messenger RNA. GTFs, RNA polymerase, and the mediator (a ... It attaches to the promoter of the DNA (e.i., TATA box) and helps position the RNA polymerase II to the gene transcription ...

... superhelical DNA packaged in capsid proteins. They are around 2.0-31kb in length. Viral replication is nuclear. DNA-templated ... Fleming, J.-A. G. W. & Summers, M. D. (1991). "Polydnavirus DNA is integrated in the DNA of its parasitoid wasp host". ... DNA, as contrasted with positive- or negative-sense single-strand DNA or RNA, as found in some other viruses) with each segment ... "The Domestication of a Large DNA Virus by the Wasp Venturia canescens Involves Targeted Genome Reduction through ...

These circular sequences can withstand superhelical stresses, resulting in the formation of DNA supercoils. Whilst such ... To this end, minicircles of DNA (closed double-stranded DNA sequences) have been proposed as model systems. Harris developed ... Her publications include: Parmbsc1: a refined force field for DNA simulations Cooperativity in drug-DNA recognition: a ... Circular DNA sequences are present in bacterial, mitochondrial and cancer genomes, and offer promise for the design of gene ...

Kikuchi A, Asai K (21 June 1984). "Reverse gyrase--a topoisomerase which introduces positive superhelical turns into DNA". ... Where DNA gyrase forms a tetramer and is capable of cleaving a double-stranded region of DNA, reverse gyrase can only cleave ... how many times a strand of DNA is wrapped around the other strand) of the DNA strand as they are renatured. Following ATP ... initiates an unwinding of approximately 20 base pairs upon binding to a DNA structure. Upon initial binding to the DNA, the ...

Z-DNA is a relatively rare left-handed double-helix. Given the proper sequence and superhelical tension, it can be formed in ... B-DNA is the most common form of DNA in vivo and is a more narrow, elongated helix than A-DNA. Its wide major groove makes it ... A-DNA, is a form of the DNA duplex observed under dehydrating conditions. It is shorter and wider than B-DNA. RNA adopts this ... Biology portal Biomolecular structure Crosslinking of DNA DNA nanotechnology DNA supercoil Gene structure Non-helical models of ...

DNA polymerase III is then able to start DNA replication. DnaA is made up of four domains: the first is the N-terminal that ... When bound to ATP, but not to ADP, DnaA forms a super-helical structure with four monomers per turn. The structure of sphere I ... When DNA replication is about to commence, DnaA occupies all of the high and low affinity binding sites. The denatured AT-rich ... In contrary to dnaA mutants, the PC2 strain has a mutation in the dnaC gene, which codes for the loading factor for the DNA ...

Any mutational event that disrupts the superhelical structure of DNA carries with it the potential to compromise the genetic ... It nicks unmethylated DNA and the unmethylated strand of hemimethylated DNA but does not nick fully methylated DNA. Experiments ... DNA methylase then rapidly methylates the daughter strand. When bound, the MutS2 dimer bends the DNA helix and shields ... Sporadic cancers with a DNA repair deficiency only rarely have a mutation in a DNA repair gene, but they instead tend to have ...

H-NS has a specific topology that allows it to condense bacterial DNA into a superhelical structure based on evidence from X- ... H-NS is responsible for formation of nucleofilaments along the DNA and DNA-DNA bridges. H-NS is known as a passive DNA bridger ... The C-Terminal domain, also known as the DNA Binding Domain (DBD), shows high affinity for regions in DNA that are rich in ... Alpha helices 3 and 4 are then responsible for creating the superhelical structure of H-NS-DNA interactions by head to head ...

... large hydrophobic interface that allows for subunit rotation which may be driven by superhelical torsion within the protein-DNA ... of DNA invertases in which it relies on the active site serine to initiate DNA cleavage and recombination. The related protein ... including structures bound to DNA and reaction intermediates. Hin functions to invert a 900 base pair (bp) DNA segment within ... The DNA cleavage event also requires the divalent metal cation magnesium. A large conformational change reveals a ...

The number of superhelical turns introduced into an initially relaxed circular DNA has been calculated to be approximately ... Upon binding to DNA (the "Gyrase-DNA" state), there is a competition between DNA wrapping and dissociation, where increasing ... DNA cleavage and reunion is performed by a catalytic center located in DNA-gates build by all gyrase subunits. C-gates are ... This process occurs in bacteria, whose single circular DNA is cut by DNA gyrase and the two ends are then twisted around each ...

DNA)-like particle). Around 146 base pairs (bp) of DNA wrap around this core particle 1.65 times in a left-handed super-helical ... Without histones, unwound DNA in chromosomes would be very long. For example, each human cell has about 1.8 meters of DNA if ... Histones prevent DNA from becoming tangled and protect it from DNA damage. In addition, histones play important roles in gene ... Marking sites of DNA damage is an important function for histone modifications. Without a repair marker, DNA would get ...

I purified from Xenopus egg extracts is a DNA-stimulated ATPase and displays the ability to introduce positive superhelical ... Early single-DNA-molecule experiments also demonstrated in real time that condensin I is able to compact DNA in an ATP- ... It has been proposed that condensin I anchors DNA between Ycg1-Brn1 subunits and pulls DNA asymmetrically to form large loops. ... For eukaryotic complexes, it has been reported that HEAT repeat subunits contribute to part of DNA binding and to the assembly ...

... thereby generating superhelical torsion that facilitates melting of the adjacent AT-rich DUE. DNA strand separation is ... bends DNA and negative supercoiling has been reported to enhance DNA binding of this complex, suggesting that DNA shape and ... This can either involve the replication of DNA in living organisms such as prokaryotes and eukaryotes, or that of DNA or RNA in ... However, Orc1/Cdc6 severely underwinds and bends DNA, suggesting that it relies on a mix of both DNA sequence and context- ...

The nucleosome core particle consists of approximately 146 base pairs (bp) of DNA wrapped in 1.67 left-handed superhelical ... The DNA is non-uniformly bent and also contains twist defects. The twist of free B-form DNA in solution is 10.5 bp per turn. ... DNA twist defects are when the addition of one or a few base pairs from one DNA segment are transferred to the next segment ... Because DNA portions of nucleosome core particles are less accessible for DNAse than linking sections, DNA gets digested into ...

... negative super coiling during DNA replication Cell death can occur through the inability of bacteria to maintain the DNA super helical ... It exerts its antibacterial effect by interfering with the bacterial enzyme DNA gyrase, which is needed for the maintenance and ... Difloxacin inhibits DNA gyrase (also known as Topoisomerase II), an enzyme required for ... The primary mode of action of fluoroquinolones involves interaction with enzymes essential for major DNA functions such as ...

DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical ... separating the DNA of daughter chromosomes after DNA replication, and relax DNA. These enzymes have several functions: to ... DNA topoisomerases are divided into two classes: type I enzymes (EC; topoisomerases I, III and V) break single-strand DNA, and ... The topoisomerase also does not use ATP during uncoiling of the DNA; rather, the torque present in the DNA drives the uncoiling ...

Z-DNA, stem-loop, and other conformations under superhelical stress. Between the strand-biased microsatellite repeats and C:G ... Satellite DNA consists of very large arrays of tandemly repeating, non-coding DNA. Satellite DNA is the main component of ... Satellite DNA, together with minisatellite and microsatellite DNA, constitute the tandem repeats. The size of satellite DNA ... The name "satellite DNA" refers to the phenomenon that repetitions of a short DNA sequence tend to produce a different ...

It catalyses the relaxation of negatively or positively superhelical DNA and is employed in phage DNA replication during ... A strand of DNA, called the gate, or G-segment, is bound by a central DNA-binding gate (DNA-gate). A second strand of DNA, ... Roca J, Wang JC (May 1994). "DNA transport by a type II DNA topoisomerase: evidence in favor of a two-gate mechanism". Cell. 77 ... The structures formed a novel beta barrel, which bends DNA by wrapping the nucleic acid around itself. The bending of DNA by ...

... in the form of coiled ring structures that appear to correspond to multiply looped DNA configurations in which superhelical ... T7 DNA polymerase, assisted by E. coli thioredoxin, performs both leading and lagging-strand DNA synthesis. In phage T7, DNA ... PMID 10792729 Yu M, Masker W. T7 single strand DNA binding protein but not T7 helicase is required for DNA double strand break ... T7 polymerase uses E. coli's endogenous thioredoxin, a REDOX protein, as a sliding DNA clamp during phage DNA replication ( ...

DNA, superhelical MeSH D13.444.308.291 - DNA, concatenated MeSH D13.444.308.295 - DNA, cruciform MeSH D13.444.308.300 - DNA, ... DNA adducts MeSH D13.444.308.142 - DNA, a-form MeSH D13.444.308.148 - DNA, algal MeSH D13.444.308.150 - DNA, antisense MeSH ... DNA, bacterial MeSH D13.444.308.227 - DNA, c-form MeSH D13.444.308.243 - DNA, catalytic MeSH D13.444.308.283 - DNA, circular ... DNA, ribosomal spacer MeSH D13.444.308.425 - DNA, neoplasm MeSH D13.444.308.435 - DNA, plant MeSH D13.444.308.435.275 - DNA, ...

"Chemists slide a splitting catalyst over DNA for the first time". ""Alle data van de wereld op een draadje plastic", Trouw, ... Some of these formed super helical structures by a process in which information is transferred stepwise from the building ... More recently, he developed a synthetic catalyst that can move along a DNA chain and cleave it. He furthermore designed ... "A clamp-like biohybrid catalyst for DNA oxidation". Nature Chemistry. 5 (11): 945-51. Bibcode:2013NatCh...5..945V. doi:10.1038/ ...

DNA-dependent protein kinase) Fanconi anemia responsible protein FANCF (FANCF) Damaged DNA-binding protein AlkD (Alkylpurin DNA ... HEAT repeats form extended superhelical structures which are often involved in intracellular transport; they are structurally ... regulation Elongation factor eEF3 Initiation factor eIF4G Aminoacyl tRNA synthetase transfer protein Cex1p DNA repair DNA-PK ( ... "Crystal structure of DNA-PKcs reveals a large open-ring cradle comprised of HEAT repeats". Nature. 463 (7277): 118-121. doi: ...