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  • 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)
  • 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)
  • enzymes
  • They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their C-terminal catalytic domain and the overall reaction mechanism with tyrosine recombinases [ PMID: 21087076 , PMID: 9488644 ]. (ebi.ac.uk)
  • This is the first designed synthetic molecule that approximates the double strand sequence specific cleavage of DNA(4-6 bp recognition level) by the natural substance restriction enzymes, tools which make possible recombinant DNA manipulations. (google.com)
  • Many topoisomerase enzymes sense supercoiling and either generate or dissipate it as they change DNA topology. (wikipedia.org)
  • 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)
  • structures
  • 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)
  • Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. (ebi.ac.uk)
  • 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 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)
  • covalent
  • 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)
  • Here we show that engineering a relaxase target by mimicking the replicase target, results in enhanced formation of protein-DNA covalent complexes. (nih.gov)
  • Activation of the 4 catalytic serine residues within the Hin tetramer make a 2-bp double stranded DNA break and forms a covalent reaction intermediate. (wikipedia.org)
  • 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)
  • Inhibition
  • 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)
  • Protein
  • A fluoroquinolone resistance protein from Mycobacterium tuberculosis that mimics DNA. (nih.gov)
  • The new Rep substrates provide new bioconjugation tools for the design of sophisticated DNA-protein nanostructures. (nih.gov)
  • 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)
  • 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)
  • 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)
  • 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)
  • Serine
  • 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)
  • structure
  • Its three-dimensional structure reveals a fold, which we have named the right-handed quadrilateral beta helix, that exhibits size, shape, and electrostatic similarity to B-form DNA. (nih.gov)
  • Human DNA topoisomerase IB: structure and functions. (ebi.ac.uk)
  • 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)
  • nuclear
  • 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)
  • mitosis
  • and to disentangle intertwined DNA during mitosis [ PMID: 12042765 , PMID: 11395412 ]. (ebi.ac.uk)
  • 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)
  • cell
  • It was based on the assumption that a bacterial cell is equivalent to a sexually reproducing multicellular organism. (wikipedia.org)
  • 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)