• proteins
  • First, Top1 may directly interact with many host cell proteins, including DNA repair factors, transcription factors, RNA splicing factors, cell cycle regulators, apoptosis-related proteins, and viral proteins, 6 suggesting the involvement of Top1 in a variety of physiologic processes mediated by those factors. (aacrjournals.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)
  • 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)
  • Genomes are circular and segmented, composed of multiple segments of double-stranded, superhelical DNA packaged in capsid proteins. (wikipedia.org)
  • Histone proteins H1, H2A, H2B, H3, and H4 are small and positively charged molecules involved in DNA compaction. (frontiersin.org)
  • Pioneering structural studies in the 1980s by Aaron Klug's group provided the first evidence that an octamer of histone proteins wraps DNA around itself in about 1.7 turns of a left-handed superhelix. (wikipedia.org)
  • The nucleosome core particle is composed of DNA and histone proteins. (wikipedia.org)
  • In biology, histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. (wikipedia.org)
  • histones
  • The binding of ethidium is measured fluorometrically, and using this probe we find that the DNA of nucleoids containing all the core histones behaves as if it were supercoiled slightly positively. (biologists.org)
  • This transition, which is reversible in the presence of the arginine-rich histones, occurs without dissociation of these histones from the DNA and so must reflect a conformational change in the complex. (biologists.org)
  • Approximately 147 bps of superhelical DNA is wrapped around dimers of histones H2A, H2B, H3, and H4 composing the nucleosome core particle ( 2 ). (frontiersin.org)
  • Without histones, the unwound DNA in chromosomes would be very long (a length to width ratio of more than 10 million to 1 in human DNA). (wikipedia.org)
  • The 4 'core' histones (H2A, H2B, H3 and H4) are relatively similar in structure and are highly conserved through evolution, all featuring a 'helix turn helix turn helix' motif (DNA-binding protein motif that recognize specific DNA sequence). (wikipedia.org)
  • As a result of the rotation, two ends of histones involved in DNA binding of the crescent shape H3-H4 are equivalent, yet they organize different stretches of DNA. (wikipedia.org)
  • covalent
  • Top1-mediated DNA cleavage-religation proceeds by the formation and resealing of covalent enzyme-DNA intermediates, which are referred to as the cleavage complexes (Top1cc). (aacrjournals.org)
  • Here we show that engineering a relaxase target by mimicking the replicase target, results in enhanced formation of protein-DNA covalent complexes. (nih.gov)
  • Consistent with product DNA resulting from covalent integration of protospacer DNA into the plasmid, the relaxed and linear forms of pCRISPR became radiolabeled in reactions containing 32P-labeled protospacer DNA (Fig. 1d and Extended Data Fig. 2). (nih.gov)
  • Camptothecin acts as an interfacial inhibitor interacting with both the enzyme and DNA stabilising the covalent enzyme-DNA complex, and slowing down the religation of the broken DNA strands brings cells to death. (els.net)
  • b) 3D structure of topoisomerase in covalent complex with a linear DNA double strand. (els.net)
  • Further DNA damage results from the formation of covalent DNA adducts following enzymatic activation of ellipticine by with cytochromes P450 and peroxidases, meaning that ellipticine is classified as a prodrug. (wikipedia.org)
  • 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)
  • strands
  • Intramolecular triplex DNA is formed from a duplex with homopurine and homopyrimidine strands with mirror repeat symmetry. (wikipedia.org)
  • Using nucleic acid segments that bind to the DNA duplexes to form triple strands as a way of regulating gene expression is under separate investigation by biotechnology companies and Yale University. (wikipedia.org)
  • The A subunit carries out nicking of DNA, B subunit introduces negative supercoils, and then A subunit reseals the strands. (wikipedia.org)
  • Sequences
  • Three widely different relaxases, which belong to MOBF, MOBQ and MOBP families, can properly cleave DNA sequences with permuted target sequences. (nih.gov)
  • Craig Benham has also developed an online applet that calculates the SIDD profile of input DNA sequences. (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)
  • Several RU sequences were cloned and sequenced to reveal conserved regions of conventional DNA sequences interspersed with five "divergent domains" within each copy of RU. (wikipedia.org)
  • The palindromic sequence CGCACGTGCG:CGCACGTGCG, flanked by extended palindromic Z-DNA sequences over a 35 bp domain, adopted a Z-DNA structure with a symmetrical arrangement in equilibrium with a stem-loop structure centered on the palindrome containing the CGCAC:GTGCG motif. (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)
  • 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)
  • 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)
  • It is suspected that, in eukaryotes, newly synthesized lagging-strand DNA transiently contains nicks (before being sealed by DNA ligase) and provides a signal that directs mismatch proofreading systems to the appropriate strand. (wikipedia.org)
  • A nucleosome is a basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight histone protein cores. (wikipedia.org)
  • The nucleosome core particle is the most basic form of DNA compaction in eukaryotes. (wikipedia.org)
  • Plasmids
  • This stress induced unwinding was shown to coincide with DNA promoter regions of bacterial plasmids, and may direct the global response of cells to changes in their external environments by affecting which genes are transcribed. (wikipedia.org)
  • enzyme
  • Human topoisomerase IB cuts a single DNA strand forming a transient enzyme-DNA cleavage complex. (els.net)
  • Camptothecin can trap the enzyme-DNA cleavage complex bringing cells to death. (els.net)
  • Camptothecin and its derivatives act as interfacial inhibitors interacting with both the enzyme and the DNA. (els.net)
  • Scheme of the DNA cleavage reaction from topoisomerase IB highlighting the formation of the DNA-enzyme cleavage complex. (els.net)
  • Scheme of the catalytic cycle of the Topo I enzyme, showing the different steps required to relax a supercoiled DNA substrate. (els.net)
  • Ellipticine is an alkaloid first extracted from trees of the species Ochrosia elliptica and Rauvolfia sandwicensis, which inhibits the enzyme topoisomerase II via intercalative binding to DNA. (wikipedia.org)
  • circular
  • If a DNA segment under twist strain were closed into a circle by joining its two ends and then allowed to move freely, the circular DNA would contort into a new shape, such as a simple figure-eight. (wikipedia.org)
  • The simple figure eight is the simplest supercoil, and is the shape a circular DNA assumes to accommodate one too many or one too few helical twists. (wikipedia.org)
  • Lobal contortions of a circular DNA, such as the rotation of the figure-eight lobes above, are referred to as writhe. (wikipedia.org)
  • WT or sir2Δ cells, transformed with the specified plasmid (indicated in each square) were grown to exponential phase and circular DNA purified. (nih.gov)
  • dimers
  • The resulting four distinct dimers then come together to form one octameric nucleosome core, approximately 63 Angstroms in diameter (a solenoid (DNA)-like particle). (wikipedia.org)
  • Then two H2A-H2B dimers are connected to the DNA- H32-H42 complex to form a nucleosome. (wikipedia.org)
  • genomic
  • The name "satellite DNA" refers to the phenomenon that repetitions of a short DNA sequence tend to produce a different frequency of the bases adenine, cytosine, guanine and thymine, and thus have a different density from bulk DNA - such that they form a second or 'satellite' band when genomic DNA is separated on a density gradient. (wikipedia.org)
  • Sequence
  • Our results demonstrate the Cas1-Cas2 complex to be the minimal machinery that catalyses spacer DNA acquisition and explain the significance of CRISPR repeats in providing sequence and structural specificity for Cas1-Cas2-mediated adaptive immunity. (nih.gov)
  • Product formation required Cas1, Cas2 and the protospacer DNA (Extended Data Fig. 1b-d), and was consistent with previous divalent metal ion-dependent and sequence-nonspecific in vitro activity requirements of Cas117-19 and Cas220-22. (nih.gov)
  • 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)
  • Once, the c-myc gene was extensively mutated to examine the role that triplex DNA structure, versus linear sequence, plays in gene regulation. (wikipedia.org)
  • A c-myc promoter element, termed the nuclease-sensitive element or NSE, can form tandem intramolecular triplexes of the H-DNA type and has a repeating sequence motif (ACCCTCCCC)4. (wikipedia.org)
  • topoisomerase
  • DNA topoisomerase I (Top1) is biologically and pharmacologically important for at least two reasons related to what might be considered its classic activity, enzymatic DNA nicking-closing. (aacrjournals.org)
  • Many topoisomerase enzymes sense supercoiling and either generate or dissipate it as they change DNA topology. (wikipedia.org)
  • 2003) Differential induction of topoisomerase I‐DNA cleavage complexes by the indenoisoquinoline MJ‐III‐65 (NSC 706744) and camptothecin. (els.net)
  • 2005) Effect on DNA relaxation of the single Thr718Ala mutation in human topoisomerase I: a functional and molecular dynamics study. (els.net)
  • negative
  • In this case also, the distribution of DNA topoisomers from sir2Δ cells was more biased towards negative supercoiling than in WT cells, as shown in Figure 1B. (nih.gov)
  • The A and B subunits together bind to DNA, hydrolyze ATP, and introduce negative supertwists. (wikipedia.org)
  • strand
  • Such cleavage complexes are particularly damaging when they produce collisions with replication forks, thereby introducing DNA double-strand breaks that can be detected as histone γ-H2AX foci ( 10 ). (aacrjournals.org)
  • DNA supercoiling refers to the over- or under-winding of a DNA strand, and is an expression of the strain on that strand. (wikipedia.org)
  • Intermolecular triplex refers to triplex formation between a duplex and a different strand of DNA. (wikipedia.org)
  • During DNA synthesis the newly synthesised (daughter) strand will commonly include errors. (wikipedia.org)
  • Upon activation by the MutS-DNA complex, MutH nicks the daughter strand near the hemimethylated site. (wikipedia.org)
  • The entire MutSHL complex then slides along the DNA in the direction of the mismatch, liberating the strand to be excised as it goes. (wikipedia.org)
  • DNA methylase then rapidly methylates the daughter strand. (wikipedia.org)
  • topology
  • Besides regulating DNA topology, Top1 has been proposed to serve other important functions that might be considered as independent of its classic DNA cleavage-religation activity. (aacrjournals.org)
  • The noun form "supercoil" is often used in the context of DNA topology. (wikipedia.org)
  • promoter
  • The latter facilitates DNA untwisting and thus increases the initiation rate of an upstream promoter (for review see Lilley, 1997 ). (embopress.org)
  • It attaches to the promoter of the DNA (e.i. (wikipedia.org)
  • 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)
  • Conformation
  • After this 180° rotation, Hin returns to its native conformation and re-ligates the cleaved DNA, without the aid of high energy cofactors and without the loss of any DNA. (wikipedia.org)
  • helical
  • 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)
  • increases
  • The cytotoxic activity of camptothecin increases in the presence of other compounds inhibiting enzymes involved in DNA repair. (els.net)
  • cleavage complex
  • The natural alkaloid camptothecin and its therapeutic derivatives, topotecan and the active metabolite of irinotecan, selectively trap Top1cc by binding at the interface of the Top1-DNA cleavage complex ( 3 , 5 ). (aacrjournals.org)
  • structure
  • Triple-stranded DNA is a DNA structure in which three oligonucleotides wind around each other and form a triple helix. (wikipedia.org)
  • 3D structure of the ternary Topo I-DNA-topotecan complex. (els.net)
  • Bowater RP (2015) Supercoiled DNA: structure. (els.net)
  • Any mutational event that disrupts the superhelical structure of DNA carries with it the potential to compromise the genetic stability of a cell. (wikipedia.org)
  • The human alpha-satellite palindromic DNA critical to achieving the 1997 nucleosome crystal structure was developed by the Bunick group at Oak Ridge National Laboratory in Tennessee. (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)
  • acidic
  • Formation of H-DNA is stabilized under acidic conditions and in the presence of divalent cations such as Mg2+. (wikipedia.org)
  • negatively charged
  • High content of positively charged amino acids allow them to closely associate with negatively charged DNA. (wikipedia.org)
  • The positive charges allow them to closely associate with the negatively charged DNA through electrostatic interactions. (wikipedia.org)
  • genes
  • Triple-stranded DNA is implicated in the regulation of several genes. (wikipedia.org)
  • By using highly specific DNA segments to target TFO regions, expression of genes can be controlled. (wikipedia.org)
  • substrates
  • Design of Novel Relaxase Substrates Based on Rolling Circle Replicases for Bioconjugation to DNA Nanostructures. (nih.gov)
  • Here we show that the purified Cas1-Cas2 complex integrates oligonucleotide DNA substrates into acceptor DNA to yield products similar to those generated by retroviral integrases and transposases. (nih.gov)
  • electrophoresis
  • After electrophoresis, DNA samples were transferred to a nitrocellulose filter and hybridized with the probes specified. (nih.gov)
  • Hence a very characteristic pattern similar to a ladder is visible during gel electrophoresis of that DNA. (wikipedia.org)
  • enzymes
  • Topoisomerases are crucial enzymes essential in the relaxation of supercoiled DNA. (els.net)
  • Quinolones bind to these enzymes and prevent them from decatenating replicating DNA. (wikipedia.org)
  • interactions
  • Both of these key components interact with DNA in their own way through a series of weak interactions, including hydrogen bonds and salt bridges. (wikipedia.org)