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*  DNA supercoil
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 ...
*  SIDD
It is the melting of the DNA which is not induced by a promoter, but purely by the superhelical (also called topological) ... nature of the DNA. It is based on a statistical mechanics treatment of DNA made by Craig J. Benham and Richard M. Fye. This ... sites in superhelical DNA". Bioinformatics. 20 (9): 1477-1479. doi:10.1093/bioinformatics/bth304. PMID 15130924. [1]. ... "Activation of Gene Expression by a Novel DNA Structural Transmission Mechanism That Requires Supercoiling-induced DNA Duplex ...
*  DEK (gene)
The protein binds to cruciform and superhelical DNA and induces positive supercoils into closed circular DNA. It is also ... Waldmann T, Eckerich C, Baack M, Gruss C (2002). "The ubiquitous chromatin protein DEK alters the structure of DNA by ... "Entrez Gene: DEK DEK oncogene (DNA binding)". Campillos M, García MA, Valdivieso F, Vázquez J (Mar 2003). "Transcriptional ... "The protein encoded by the proto-oncogene DEK changes the topology of chromatin and reduces the efficiency of DNA replication ...
*  Polydnavirus
... superhelical DNA packaged in capsid proteins. They are around 2.0-31kb in length. Viral replication is nuclear. DNA-templated ... DNA, as contrasted with positive or negative-sense single-strand DNA or RNA, as found in some other viruses) with each segment ... "Polydnavirus DNA is integrated in the DNA of its parasitoid wasp host". Proceedings of the National Academy of Sciences. 88 (21 ... research.biology.arizona.edu/mosquito/willott/507/polydnaviruses.html Polydnavirus DNA is Integrated in the DNA of Its ...
*  Triple-stranded DNA
"Structures of homopurine-homopyrimidine tract in superhelical DNA". Biomol Struct Dyn. 3 (667-669). CS1 maint: Multiple names: ... There are two different types of intramolecular triplex DNA: H-DNA and H*-DNA. Formation of H-DNA is stabilized under acidic ... Triple-stranded DNA is a DNA structure in which three oligonucleotides wind around each other and form a triple helix. In this ... Triple-stranded DNA was a common hypothesis in the 1950s when scientists were struggling to discover DNA's true structural form ...
*  Bacterial circadian rhythm
Woelfle, M.A., Xu, Y., Qin, X., and Johnson, C.H. (2007). Circadian rhythms of superhelical status of DNA in cyanobacteria. ...
*  Difloxacin
... 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 ...
*  Ellipticine
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 ... Kohn, K W; Waring, M J; Glaubiger, D; Friedman, C A (1975). "Intercalative Binding of Ellipticine to DNA". Cancer Research. 35 ...
*  Transcription preinitiation complex
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 ...
*  General transcription factor
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 multiple- ... It attaches to the promoter of the DNA (e.i., TATA box) and helps position the RNA polymerase II to the gene transcription ...
*  DNA mismatch repair
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 ...
*  Condensin
Purified condensin I introduces positive superhelical tension into double-stranded DNA in an ATP-hydrolysis-dependent manner. ... It also displays a DNA-stimulated ATPase activity in vitro. An SMC2-SMC4 dimer has an ability to reanneal complementary single- ... In A. thaliana, condensin II is essential for tolerance of excess boron stress, possibly by alleviating DNA damage. It has been ... Uhlmann F (2016). "SMC complexes: from DNA to chromosomes". Nat. Rev. Mol. Cell Biol. 17: 399-412. doi:10.1038/nrm.2016.30. ...
*  Hin recombinase
... large hydrophobic interface that allows for subunit rotation which may be driven by superhelical torsion within the protein-DNA ... Hin belongs to the serine recombinase family of DNA invertases in which it relies on the active site serine to initiate DNA ... 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 ...
*  Nucleosome
The nucleosome core particle (shown in the figure) consists of about 146 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. ... The nucleosome core particle consists of approximately 146 base pairs (bp) of DNA wrapped in 1.67 left-handed superhelical ... Because DNA portions of nucleosome core particles are less accessible for DNAse than linking sections, DNA gets digested into ...
*  Satellite DNA
... pyrimidines shown to adopt a left-handed Z-DNA helical structure in equilibrium with a stem-loop structure under superhelical ... 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. Some types of satellite DNA ... The name "satellite DNA" refers to the phenomenon that repetitions of a short DNA sequence tend to produce a different ...
*  Cruciform DNA
Under negative superhelical stress p53 binds preferentially to cruciform forming targets due to the A/T rich environment which ... Cruciform DNA is found in both prokaryotes and eukaryotes and has a role in the transcription of DNA, double strand repair, DNA ... Cruciform DNA is a form of non-B DNA that requires at least a 6 nucleotide sequence of inverted repeats to form a structure ... DNA replication can then be inhibited by cruciform containing tertiary structures of DNA formed during recombination, which can ...
*  DNA gyrase
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 ... This process occurs in prokaryotes (in particular, in bacteria), whose single circular DNA is cut by DNA gyrase and the two ... a DNA polymerase. The ability of gyrase (and topoisomerase IV) to relax positive supercoils allows superhelical tension ahead ...
*  Histone
DNA)-like particle). Around 146 base pairs (bp) of DNA wrap around this core particle 1.65 times in a left-handed super-helical ... Marking sites of DNA damage is an important function for histone modifications. It also protects DNA from getting destroyed by ... The linker histone H1 binds the nucleosome at the entry and exit sites of the DNA, thus locking the DNA into place and allowing ... Bekker-Jensen S, Mailand N (Dec 2010). "Assembly and function of DNA double-strand break repair foci in mammalian cells". DNA ...
*  Histone octamer
Nucleosomes consist of a histone octamer surrounded by 147 base pairs of DNA wrapped in a superhelical manner. In addition to ... Once the DNA is bound the tails continue to interact with the DNA. The parts of the tail closest to the DNA hydrogen bond and ... This "wave" of DNA, spontaneously breaking and remaking the hydrogen bonds as it goes, then propagates down the nucleosomal DNA ... The N-terminal tails do not interact with a specific region of DNA but rather stabilize and guide the DNA wrapped around the ...
*  List of MeSH codes (D13)
... dna, kinetoplast MeSH D13.444.308.283.250 --- dna, superhelical MeSH D13.444.308.291 --- dna, concatenated MeSH D13.444.308.295 ... dna adducts MeSH D13.444.308.142 --- dna, a-form MeSH D13.444.308.148 --- dna, algal MeSH D13.444.308.150 --- dna, antisense ... dna, c-form MeSH D13.444.308.243 --- dna, catalytic MeSH D13.444.308.283 --- dna, circular MeSH D13.444.308.283.084 --- dna, ... dna, fungal MeSH D13.444.308.315 --- dna, helminth MeSH D13.444.308.324 --- dna, intergenic MeSH D13.444.308.324.230 --- dna, ...
*  Nucleic acid structure
Z-DNA is a relatively rare left-handed double-helix. Given the proper sequence and superhelical tension, it can be formed in ... A-DNA and Z-DNA. B-DNA is the most common form of DNA in vivo and is a more narrow, elongated helix than A-DNA. Its wide major ... A-DNA, is a form of the DNA duplex observed under dehydrating conditions. It is shorter and wider than B-DNA. RNA adopts this ... Molecular and cellular biology portal Biomolecular structure Crosslinking of DNA DNA nanotechnology DNA supercoil Gene ...
*  Type I topoisomerase
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 ...
*  Nucleic acid double helix
W = writhe - number of turns of the double stranded DNA helix around the superhelical axis L = T + W and ΔL = ΔT + ΔW Any ... Other conformations are possible; A-DNA, B-DNA, C-DNA, E-DNA, L-DNA (the enantiomeric form of D-DNA), P-DNA, S-DNA, Z-DNA, etc ... At least three DNA conformations are believed to be found in nature, A-DNA, B-DNA, and Z-DNA. The B form described by James ... A-DNA and Z-DNA differ significantly in their geometry and dimensions to B-DNA, although still form helical structures. It was ...
*  Joel Sussman
He subsequently determined the structures of 'bulge'-containing DNA fragments as models for insertion mutations. Sussman's ... A novel anchoring device for AChE involving superhelical assembly of its subunits around a polyproline-II helix; The specific ... "The three-dimensional structure of a DNA duplex containing looped out bases" Nature 334, 82-84 PMID 3386751 J.L. Sussman, M. ...
*  AlkD
... (Alkylpurine glycosylase D) is an enzyme belonging to a family of DNA glycosylases that are involved in DNA repair. It was ... These helical repeats are stacked into a superhelical solenoid in which helices B, C, E, G, I, K and M form a concave surface ... The enzyme specifically targets 7mG (methyl-guanine) in the DNA, and is, therefore, unique among DNA glycosylases. It can also ... It then induces flipping of the alkylated and opposing base accompanied by DNA stack compression. The exposed DNA portion can ...
*  Tetratricopeptide repeat protein 39B
The genomic DNA is 136,517 bases long, consists of 39 introns and 20 exons, and is on the minus strand. The mRNA has a length ... 40% of its structure matches with d1w3ba, the superhelical domain of o-linked GlcNAc transferase. O-GlcNAc couples metabolic ... Ubiquitination has been associated with protein degradation, DNA repair, cell cycle regulation, kinase modification, ...