• 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)
  • 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)
  • 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)
  • 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)
  • cruciform
  • We present a rigorous mathematical procedure for extracting the cleavage pattern specific to supercoiled DNA and use this method to investigate the hydroxyl radical cleavage pattern in a cruciform DNA structure formed by a 60 bp inverted repeat sequence embedded in a negatively supercoiled plasmid. (utdallas.edu)
  • 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)
  • 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)
  • protein
  • The new Rep substrates provide new bioconjugation tools for the design of sophisticated DNA-protein nanostructures. (nih.gov)
  • Epigenetic modifications such as histone post-transcriptional modifications, DNA methylation, and non-protein-coding RNAs organize the DNA in the nucleus of eukaryotic cells and are critical for the spatio-temporal regulation of gene expression. (frontiersin.org)
  • H-NS forms a superhelical protein scaffold for DNA condensation. (ebi.ac.uk)
  • 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)
  • Furthermore, the details of protein-protein and protein-DNA interactions were fine-tuned by X-ray crystallography studies at 2.8 and 1.9 Å, respectively, in the 2000s. (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)
  • 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)
  • 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)
  • Chemical and enzymatic probing methods are powerful techniques for examining details of sequence-dependent structure in DNA and RNA. (utdallas.edu)
  • 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)
  • circular
  • WT or sir2Δ cells, transformed with the specified plasmid (indicated in each square) were grown to exponential phase and circular DNA purified. (nih.gov)
  • 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)
  • Moreover, we also show a decreased PSTVd accumulation and a reduced ratio of monomeric circular to total monomeric PSTVd forms in Nicotiana benthamiana Domin plants in which the endogenous DNA ligase 1 was silenced. (sebbm.es)
  • 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
  • In contrast to most eukaryotic cells, mature sperm cells largely use protamines to package their genomic DNA, most likely to achieve an even higher packaging ratio. (wikipedia.org)
  • 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)
  • 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)
  • eukaryotic
  • Using an electron paramagnetic resonance spin-labeling technique, British researchers measured the distances between the spools around which eukaryotic cells wind their DNA. (wikipedia.org)
  • 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)
  • Camptothecin can trap the enzyme-DNA cleavage complex bringing cells to death. (els.net)
  • 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)
  • The positive charges allow them to closely associate with the negatively charged DNA through electrostatic interactions. (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)
  • 1997
  • 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)
  • molecules
  • In that study, Sytox Orange (an intercalating dye), has been used to induce supercoiling on surface tethered DNA molecules. (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)
  • enzyme
  • Camptothecin and its derivatives act as interfacial inhibitors interacting with both the enzyme and the DNA. (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)
  • ligase
  • In this study we propose that PSTVd subverts host DNA ligase 1, converting it to an RNA ligase, for the final step. (sebbm.es)
  • To support this hypothesis, we show that the tomato (Solanum lycopersicum L.) DNA ligase 1 specifically and efficiently catalyzes circularization of the genuine PSTVd monomeric linear replication intermediate opened at position G95-G96 and containing 5′-phosphomonoester and 3′-hydroxyl terminal groups. (sebbm.es)
  • 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)
  • structure
  • 3D structure of the ternary Topo I-DNA-topotecan complex. (els.net)
  • Bowater RP (2015) Supercoiled DNA: structure. (els.net)
  • Triple-stranded DNA is a DNA structure in which three oligonucleotides wind around each other and form a triple helix. (wikipedia.org)
  • 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)
  • 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)