• supercoils
  • Addition of purified ZD domain to Top67 partially restored the relaxation activity, demonstrating that covalent linkage between the two domains is not necessary for removal of negative supercoils from DNA. (biomedcentral.com)
  • The A subunit carries out nicking of DNA, B subunit introduces negative supercoils, and then A subunit reseals the strands. (wikipedia.org)
  • The initial reaction requires binding of Hin and Fis to their respective DNA sequences and assemble into a higher-order nucleoprotein complex with branched plectonemic supercoils with the aid of the DNA bending protein HU. (wikipedia.org)
  • The twist is the number of helical turns in the DNA and the writhe is the number of times the double helix crosses over on itself (these are the supercoils). (wikipedia.org)
  • In eukaryotes, DNA supercoiling exists on many levels of both plectonemic and solenoidal supercoils, with the solenoidal supercoiling proving most effective in compacting the DNA. (wikipedia.org)
  • proteins
  • Cryptolepine induced DNA damage activated DNA damage response proteins as demonstrated by increased phosphorylation of ATM/ATR, BRCA1, Chk1/Chk2 and γH2AX. (aacrjournals.org)
  • Both protein families show structural similarity but limited amino acid identity.Moreover, the organization of the inverted repeat (IR) and the loop that shape the nic site differs in both proteins.The new Rep substrates provide new bioconjugation tools for the design of sophisticated DNA-protein nanostructures. (nih.gov)
  • Collaterally, the secondary structure that the permuted targets acquired within a supercoiled plasmid DNA resulted in poor conjugation frequencies underlying the importance of relaxase accessory proteins in conjugative DNA processing. (nih.gov)
  • Based on the properties of intercalating molecules i.e., fluorescing upon binding to DNA and unwinding of DNA base-pairs, recently a single-molecule technique has been introduced to directly visualize individual plectonemes along supercoiled DNA which would further allow to study the interactions of DNA processing proteins with supercoiled DNA. (wikipedia.org)
  • Fluoroquinolones
  • Limitations of use: Because fluoroquinolones have been associated with disabling and potentially irreversible serious adverse reactions (eg, tendinitis and tendon rupture, peripheral neuropathy, CNS effects), reserve gemifloxacin for use in patients who have no alternative treatment options for acute bacterial exacerbation of chronic bronchitis. (drugs.com)
  • strands
  • In a "relaxed" double-helical segment of B-DNA, the two strands twist around the helical axis once every 10.4-10.5 base pairs of sequence. (wikipedia.org)
  • metabolism
  • Supercoiling is important in a number of biological processes, such as compacting DNA, and by regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism and possibly gene expression. (wikipedia.org)
  • negative
  • Although it is known that the ZD domain can function as a DNA binding domain, its exact role in these individual steps of removal of a negative superhelical turn from DNA by E. coli topoisomerase I remains to be defined. (biomedcentral.com)
  • The A and B subunits together bind to DNA, hydrolyze ATP, and introduce negative supertwists. (wikipedia.org)
  • Cruciform DNA is a form of non-B DNA that requires at least a 6 nucleotide sequence of inverted repeats to form a structure consisting of a stem, branch point and loop in the shape of a cruciform, stabilized by negative DNA supercoiling. (wikipedia.org)
  • structures
  • The formation of cruciform structures in linear DNA is thermodynamically unfavorable due to the possibility of base unstacking at junction points and open regions at loops. (wikipedia.org)
  • Cruciform structures can increase genomic instability and are involved in the formation of various diseases, such as cancer Cruciform DNA structures are stabilized through supercoiling and their formation alleviates stress generated from DNA supercoiling. (wikipedia.org)
  • The ssDNA U-turn observed in Y2 relaxase domains TrwCR- and TraIR -DNA complex structures was also observed in the structure of Y1 relaxase NES [13- (nih.gov)
  • The conditions that trigger the formation of alternative DNA structures such as left-handed Z-DNA, inter- and intra-molecular triplexes, triple-stranded DNA, and linked catenanes and hemicatenanes are explained. (asmscience.org)
  • The related protein, gamma-delta resolvase shares high similarity to Hin, of which much structural work has been done, including structures bound to DNA and reaction intermediates. (wikipedia.org)
  • cleavage
  • The DNA cleavage event also requires the divalent metal cation magnesium. (wikipedia.org)
  • These drug concentrations were chosen so as to achieve comparable cleavage levels of the linear DNA substrate. (nih.gov)
  • Quinolones are known to stabilize DNA cleavage fragments that possess 3′ OH ends and hence co-migrate with chain termination DNA sequencing products (21,31). (nih.gov)
  • After cleavage induction with SDS and proteinase K, DNA was precipitated with ethanol. (nih.gov)
  • molecules
  • Bifunctional molecules having a DNA intercalator or DNA groove binder linked to ethylene diamine tetraacetic acid such as compounds having the formula: ##STR1## wherein R is methyl or ethyl. (google.com)
  • Also, the method of cleaving DNA by contact with one of the above-identified molecules in the presence of ferrous ion and oxygen. (google.com)
  • The process of preparing said molecules by the reaction of P-carboxy methidium halide, p-carboxy ethidium halide, or other DNA intercalator or DNA groove binder with 1-3-diaminopropane followed by condensation with ethylenediamine tetraacetic acid. (google.com)
  • In that study, Sytox Orange (an intercalating dye), has been used to induce supercoiling on surface tethered DNA molecules. (wikipedia.org)
  • molecular
  • This article links the original discoveries of superhelical structure and molecular topology to non-B form DNA structure and contemporary biochemical and biophysical techniques. (asmscience.org)
  • bacteria
  • Antibiotics such as doxorubicin and actinomycin D (dactinomycin), are not specific for bacteria and interfere with both bacterial and mammalian systems. (sigmaaldrich.com)
  • 1994
  • 1994. The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. (asmscience.org)
  • genetics
  • The discovery of the B-form structure of DNA by Watson and Crick led to an explosion of research on nucleic acids in the fields of biochemistry, biophysics, and genetics. (asmscience.org)
  • subunit
  • A large conformational change reveals a large hydrophobic interface that allows for subunit rotation which may be driven by superhelical torsion within the protein-DNA complex. (wikipedia.org)
  • vitro
  • We conducted in vitro DNA supercoiling assays, utilizing recombinant DNA gyrases, to elucidate the influence of the lineage-specific serine or threonine residue at position 95 of GyrA on fluoroquinolone resistance in Mycobacterium tuberculosis. (biomedsearch.com)
  • And methods are described for comparing in vivo and in vitro reactions to probe and understand the temporal pathways of DNA and chromosome chemistry that occur inside living cells. (asmscience.org)
  • damage
  • Relationship for ionizing radiation would result in drastic changes Although we do not know the precise mechanism by which ionizing radiation produces somatic and genetic effects, we understand that it involves damage to the DNA of the cell nucleus. (forex-live-news-today.com)
  • Many cancer chemotherapeutic drugs used in the clinics inhibit tumor growth by targeting topoisomerase functions resulting in DNA damage and cancer cell death. (aacrjournals.org)
  • Consequences of cryptolepine induced DNA damage were also associated with activation of p53 signaling cascade. (aacrjournals.org)
  • Inhibition of topoisomerase activity and activation of DNA damage response signaling culminated in significantly reduced cell viability and enhanced cell death of SCC-13 and A431 cells. (aacrjournals.org)
  • In A. thaliana, condensin II is essential for tolerance of excess boron stress, possibly by alleviating DNA damage. (wikipedia.org)
  • cleave
  • During bacterial conjugation and rolling circle replication, HUH endonucleases, respectively known as relaxases and replicases, form a covalent bond with ssDNA when they cleave their target sequence (nic site). (nih.gov)
  • covalent
  • Here we show that engineering a relaxase target by mimicking the replicase target, results in enhanced formation of protein-DNA covalent complexes. (nih.gov)
  • Streptococcus
  • Treatment of bacterial conjunctivitis caused by Staphylococcus aureus , Staphylococcus epidermidis , Streptococcus pneumoniae, Enterobacter cloacae , Haemophilus influenzae , Proteus mirabilis , and Pseudomonas aeruginosa . (drugs.com)
  • structural
  • Powerful techniques were developed to reveal a myriad of different structural conformations that change B-DNA as it is transcribed, replicated, and recombined and as sister chromosomes are moved into new daughter cell compartments during cell division. (asmscience.org)
  • The structural basis for substrate specificity in DNA topoisomerase IV. (ebi.ac.uk)
  • breakage
  • CL-stimulated DNA breakage exhibited a strong preference for guanine preceding the scission site (-1 position). (nih.gov)
  • mitosis
  • and to disentangle intertwined DNA during mitosis [ PMID: 12042765 , PMID: 11395412 ]. (ebi.ac.uk)
  • DNA packaging is greatly increased during nuclear division events such as mitosis or meiosis, where DNA must be compacted and segregated to daughter cells. (wikipedia.org)
  • specificity
  • This is a novel and unique molecule and superior in sequence specificity to the naturally occurring antitumor compound used in man, bleomycin which cleaves DNA at a two base pair recognition site. (google.com)
  • eukaryotes
  • Because the length of DNA can be thousands of times that of a cell, packaging this genetic material into the cell or nucleus (in eukaryotes) is a difficult feat. Supercoiling of DNA reduces the space and allows for DNA to be packaged. (wikipedia.org)
  • interactions
  • It is composed of a tandem array of helical repeats reminiscent of HEAT motifs, which are known to facilitate protein-protein interactions and have not yet been associated with DNA binding or catalytic activity. (wikipedia.org)