• 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)
  • The degree of compaction results from the level of DNA-supercoiling and the presence of nucleoid-binding proteins. (frontiersin.org)
  • The relaxosome is a protein-DNA complex formed by several proteins and a DNA segment called the Origin of Transfer. (irbbarcelona.org)
  • Portal proteins or connectors are large multimeric proteins involved in DNA packaging into viral capsids. (irbbarcelona.org)
  • With the help of other proteins, they translocate the DNA through one vertex of the capsid. (irbbarcelona.org)
  • We are currently analysing various connectors and other related DNA packaging proteins, in collaboration with José L. Carrsacosa and José María Valpuesta (CNB-CSIC). (irbbarcelona.org)
  • We study several transcription factors and their complexes with other proteins and DNA promoter regions. (irbbarcelona.org)
  • 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)
  • strands
  • Cleavage of TOP and BOTTOM DNA strands by both drugs was markedly enhanced by the inclusion of ATP and required the presence of gyrase: no breakage was seen with CL alone consistent with the known poor reactivity of CL toward duplex DNA (Figure 3, Introduction section). (nih.gov)
  • CL-induced gyrase scission occurred either at single sites or more frequently in pairs on complementary strands showing the characteristic 4-bp stagger expected of double-stranded DNA breakage by gyrase (31). (nih.gov)
  • In molecular biology Type I topoisomerases are enzymes that cut one of the two strands of double-stranded DNA, relax the strand, and reanneal the strand. (wikipedia.org)
  • 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)
  • Genes
  • Bacterial diversity based on type II DNA topoisomerase genes. (ebi.ac.uk)
  • Hin functions to invert a 900 base pair (bp) DNA segment within the salmonella genome that contains a promoter for downstream flagellar genes, fljA and fljB. (wikipedia.org)
  • Inversion of the intervening DNA alternates the direction of the promoter and thereby alternates expression of the flagellar genes. (wikipedia.org)
  • The control of DNA-supercoiling in S. pneumoniae occurs mainly via the regulation of topoisomerase gene transcription: relaxation triggers the up-regulation of gyrase and the down-regulation of topoisomerases I and IV, while hypernegative supercoiling down-regulates the expression of topoisomerase I. Relaxation affects 13% of the genome, with the majority of the genes affected located in 15 domains. (frontiersin.org)
  • This paper published online his summer is a true mind-blower showing the irreducible organizational complexity (author's description) of DNA analog and digital information, that genes are not arbitrarily positioned on the chromosome etc. (heavenforum.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)
  • molecules
  • The number of superhelical turns introduced into an initially relaxed circular DNA has been calculated to be approximately equal to the number of ATP molecules hydrolyzed by gyrase. (wikipedia.org)
  • 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)
  • Direct visualization of supercoiled DNA molecules in solution. (asmscience.org)
  • In that study, Sytox Orange (an intercalating dye), has been used to induce supercoiling on surface tethered DNA molecules. (wikipedia.org)
  • chromosome
  • 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)
  • The bacterial chromosome is compacted in a manner optimal for DNA transactions to occur. (frontiersin.org)
  • The compaction of DNA by up to 1000-fold ( Holmes and Cozzarelli, 2000 ) in the bacterial chromosome, or nucleoid, achieves the optimal condition under which its essential functions - replication, segregation and gene expression (reviewed by Dorman, 2013 ) - can be reconciled. (frontiersin.org)
  • Second, the paper links local DNA structure, to domains, to the overall chromosome configuration as a dynamic system keying off the metabolic signals of the cell. (heavenforum.org)
  • subunit
  • Aminocoumarins work by competitive inhibition of energy transduction of DNA gyrase by binding to the ATPase active site located on the GyrB subunit. (wikipedia.org)
  • 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)
  • cleavage
  • The DNA cleavage event also requires the divalent metal cation magnesium. (wikipedia.org)
  • We establish by genetic means that CL targets DNA gyrase in the gram-positive bacterium Streptococcus pneumoniae, and promotes gyrase-dependent single- and double-stranded DNA cleavage in vitro. (nih.gov)
  • CL-promoted DNA cleavage mediated by gyrase occurs at specific sites and is stimulated by ATP. (nih.gov)
  • These drug concentrations were chosen so as to achieve comparable cleavage levels of the linear DNA substrate. (nih.gov)
  • The specificity of gyrase-mediated DNA breakage promoted by CL was examined using the 5′-end 33P-labelled S fragment from the S. pneumoniae parE gene and compared to that of gemifloxacin, an anti-pneumococcal quinolone whose induction of sequence-specific cleavage has been studied in detail for pneumococcal gyrase and topo IV (31). (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)
  • CL induces DNA modification and irreversible/reversible DNA breakage at gyrase cleavage sites. (nih.gov)
  • After cleavage induction with SDS and proteinase K, DNA was precipitated with ethanol. (nih.gov)
  • 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)
  • 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)
  • In the present study, we examined the therapeutic effect of cryptolepine on non-melanoma skin cancer cells (NMSCC), SCC-13 and A431 as an in vitro model, and underlying mechanism of action with special emphasis on topoisomerases and DNA damage check points. (aacrjournals.org)
  • 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)
  • 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)
  • Inhibition of topoisomerases expression and function by cryptolepine resulted in significant DNA damage and enhanced expression of DNA-PK expressions. (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)
  • Clerocidin selectively modifies the gyrase-DNA gate to induce irreversible and reversible DNA damage. (nih.gov)
  • In A. thaliana, condensin II is essential for tolerance of excess boron stress, possibly by alleviating DNA damage. (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)
  • DNA structure and drug-DNA interactions. (irbbarcelona.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)
  • sequence
  • The computational model itself calculates the probability profile of a given base-pair sequence of DNA to denature, as well as the energy profile of sequence. (wikipedia.org)
  • De.Fe(II) cleaves DNA contiguous to a five base pair A+T rich sequence. (google.com)
  • 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)
  • In short, the linear DNA sequence contains both types of information. (heavenforum.org)
  • As a class of protein, general transcription factors bind to promoters along the DNA sequence or form a large transcription preinitiation complex to activate transcription. (wikipedia.org)
  • 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)
  • breakage
  • CL-stimulated DNA breakage exhibited a strong preference for guanine preceding the scission site (-1 position). (nih.gov)
  • cell
  • It was based on the assumption that a bacterial cell is equivalent to a sexually reproducing multicellular organism. (wikipedia.org)
  • 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)