AnatomyOrganismsChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesInformation Science
DNA, SuperhelicalDNA, BacterialPeptide Nucleic AcidsNucleic Acid ConformationDNANucleic Acid HeteroduplexesDNA, CircularBase SequenceDNA Topoisomerases, Type INucleic Acid HybridizationEthidiumPlasmidsRNAThermodynamicsEscherichia coliOsmium TetroxideDNA, ViralToll-Like Receptor 9Simian virus 40Electrophoresis, Agar GelMolecular Sequence DataOligodeoxyribonucleotidesProtein BindingDeoxyribonucleasesColiphagesBinding SitesEndonucleasesCpG IslandsPolymerase Chain ReactionNovobiocinKineticsSingle-Strand Specific DNA and RNA EndonucleasesBacterial ProteinsDNA, Single-StrandedBacterial TranslocationNucleic Acid DenaturationCentrifugation, Density GradientDNA ReplicationCarbodiimidesHistonesDNA Topoisomerases, Type IIPolydeoxyribonucleotidesDeoxyribonucleoproteinsModels, MolecularOsmolar ConcentrationBacteriophagesBromosuccinimideDNA-Binding ProteinsBacteriaNucleosomesRNA, Ribosomal, 16SAmino Acid SequenceMicroscopy, ElectronDNA Restriction EnzymesTyrothricinDinucleoside PhosphatesNucleoproteinsAminocoumarinsCell LineProtein Structure, Tertiary
ProteinsStrandsGyrasePolymeraseSYNTHESISMoleculesSupercoilsTopoisomerase I enzymHelixEnzymesTaxonomicReplication bubbleNegatively supercoiledDifferential2019MitochondrialPromoterComplexesStructuresTOPOLOGYGeneticChromosomeBacteriaMechanismEukaryoticSubunitsStructuralStrand separationPhosphodiesterDistinctNucleotideSequencesHydrolysisSeparationEnzymeDomainsSitesDomainComplexFunctionsFoundFamilyFormStructure
Proteins13
  • The oriC site in E. coli has three AT rich 13 base pair regions (DUEs) followed by four 9 bp regions with the sequence TTAT(C or A)CA(C or A)A. Around 10 DnaA molecules bind to the 9 bp regions, which wrap around the proteins causing the DNA at the AT-rich region to unwind. (wikipedia.org)
  • Single-strand binding proteins (SSBs) stabilize the single DNA strands in order to maintain the replication bubble. (wikipedia.org)
  • DnaA is made up of four domains: the first is the N-terminal that associates with regulatory proteins, the second is a helical linker region, the third domain is a AAA+ region that binds to ATP, and the fourth domain is the C-terminal DNA binding region. (wikipedia.org)
  • Other proteins studied in the laboratory and whose structure we solved include single-strand binding protein mtSSB (or SSBP1, Piro-Mégy et al. (csic.es)
  • Overall, performed studies allowed us to postulate the hypothesis that KfrA type proteins have moonlighting activity - they not only act as transcriptional auto-regulators but form cytoskeletal structures, which might facilitate plasmid DNA delivery and its position in the cells. (edu.pl)
  • Adriana's BSc work entitled "Ancestral state reconstruction approach in investigating Rossmann fold evolution" focused on deciphering the evolution of regions responsible for the cofactor binding, whereas Kamil's MSc work entitled "Re-engineering cofactor specificity of the Rossmann fold proteins using graph neural networks" describes a new method for predicting the cofactor specificity in Rossmann enzymes. (edu.pl)
  • A method for determining the sequence specificity of DNA-binding proteins. (lookformedical.com)
  • A method for determining points of contact between interacting proteins or binding sites of proteins to nucleic acids. (lookformedical.com)
  • Proteins which bind to DNA. (lookformedical.com)
  • The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases. (lookformedical.com)
  • Crucially, the sequence of bases in DNA contains the information for making proteins. (rainis.pics)
  • TPR-containing proteins include the anaphase promoting complex (APC) subunits cdc16, cdc23 and cdc27, the NADPH oxidase subunit p67 phox, hsp90-binding immunophilins, transcription factors, the PKR protein kinase inhibitor, and peroxisomal and mitochondrial import proteins. (embl.de)
  • The compaction of mitochondrial DNA (mtDNA) is regulated by architectural HMG-box proteins whose limited cross-species similarity suggests diverse underlying mechanisms. (bvsalud.org)
Strands3
  • Removal of these positive supercoils is essential for replication fork progression and for the overall unlinking of the two duplex DNA strands, as well as for ongoing transcription. (york.ac.uk)
  • The double helix, made up of a pair of DNA strands, has bases in its core that are joined by hydrogen bonds to form base pairs: adenine always paired with thymine and guanine always paired with cytosine. (rainis.pics)
  • Two of these paired strands make up the DNA molecule, which then twists into a helix. (rainis.pics)
Gyrase10
  • Bacterial DNA gyrase introduces negative supercoils into chromosomal DNA and relaxes positive supercoils introduced by replication and transiently by transcription. (york.ac.uk)
  • We demonstrate that at least 300 gyrase molecules are stably bound to the chromosome at any time, with ~12 enzymes enriched near each replication fork. (york.ac.uk)
  • eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. (embl.de)
  • Like other fluoroquinolone anti-infectives, ciprofloxacin inhibits DNA synthesis in susceptible organisms via inhibition of the enzymatic activities of 2 members of the DNA topoisomerase class of enzymes, DNA gyrase and topoisomerase IV. (antiinfectivemeds.com)
  • DNA gyrase and topoisomerase IV have distinct essential roles in bacterial DNA replication. (antiinfectivemeds.com)
  • DNA gyrase is a tetramer composed of 2 GyrA and 2 GyrB subunits. (antiinfectivemeds.com)
  • DNA gyrase introduces negative superhelical twists in DNA, an activity important for initiation of DNA replication. (antiinfectivemeds.com)
  • DNA gyrase also facilitates DNA replication by removing positive super helical twists. (antiinfectivemeds.com)
  • Although all fluoroquinolones generally are active against both DNA gyrase and topoisomerase IV, the drugs differ in their relative activities against these enzymes. (antiinfectivemeds.com)
  • The mechanism by which ciprofloxacin's inhibition of DNA gyrase or topoisomerase IV results in death in susceptible organisms has not been fully determined. (antiinfectivemeds.com)
Polymerase3
  • DNA polymerase III is then able to start DNA replication. (wikipedia.org)
  • When DnaA binds to its own promoter it blocks RNA polymerase from binding the promoter and inhibits initiation of transcription. (wikipedia.org)
  • DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. (lookformedical.com)
SYNTHESIS5
  • A unique feature of mitochondria is that they possess their own genome, the mitochondrial DNA (mtDNA), which codes for subunits of the electron transport chain that eventually leads to the synthesis of the ATP molecule. (csic.es)
  • Their binding to DNA inhibits synthesis of nucleic acids. (lookformedical.com)
  • A cytotoxic polypeptide quinoxaline antibiotic isolated from Streptomyces echinatus that binds to DNA and inhibits RNA synthesis. (lookformedical.com)
  • The complementary structure immediately suggested to Watson and Crick how DNA could (and does) replicate, and further explains how information from DNA is transferred to RNA for protein synthesis. (rainis.pics)
  • Trading places: how do DNA polymerases switch during translesion DNA synthesis? (academicinfluence.com)
Molecules2
  • Nucleic acids, DNA and RNA, can be considered as the information molecules of the cell. (rainis.pics)
  • In this section, we examine the structures of DNA and RNA and how these structures relate to the functions of these molecules. (rainis.pics)
Supercoils2
  • High condensin concentrations restrain positive DNA supercoils. (bvsalud.org)
  • However, in experimental conditions of DNA loop extrusion, condensin restrains negative supercoils. (bvsalud.org)
Topoisomerase I enzym1
  • This entry represents the C-terminal region of DNA topoisomerase I enzymes from eukaryotes (type IB enzymes). (embl.de)
Helix5
  • DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). (lookformedical.com)
  • Today, every biology student knows about the double helix structure of DNA and how G pairs with C and A pairs with T. (rainis.pics)
  • In the more common B form, the DNA helix has a repeat of 10.5 base pairs per turn, with the sugar and phosphate forming the covalent phosphodiester "backbone" of the molecule, and the bases adenine, guanine, cytosine and thymine line up in the middle, where the base pairs we know today are, which look like the rungs of a ladder. (rainis.pics)
  • The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees within a single TPR and generates a right-handed superhelical shape. (embl.de)
  • Our crystallographic, biophysical, biochemical and computational analysis showed that Gcf1p forms dynamic protein/DNA multimers by a combined action of an N-terminal unstructured tail and a long helix. (bvsalud.org)
Enzymes1
  • Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. (embl.de)
Taxonomic2
  • We analyzed the bacterial and fungal taxonomic profiles and loads of 232 gut and respiratory samples and we measured the blood levels of Interleukin 6, IgG, and IgM in COVID-19 patients. (bvsalud.org)
  • During their ICU stay, the patients experienced increased bacterial and fungal loads, drastic decreased bacterial richness, and progressive changes in bacterial and fungal taxonomic profiles. (bvsalud.org)
Replication bubble1
  • Factor B2, who binds mtRNAP, creates the replication bubble. (csic.es)
Negatively supercoiled1
  • These findings indicate that during ATP binding, a short DNA domain delimited by condensin is pinched into a negatively supercoiled loop. (bvsalud.org)
Differential1
20191
  • 2019). In these studies we showed that TFAM/DNA complexes multimerize at higher concentrations. (csic.es)
Mitochondrial2
  • Structural basis of mitochondrial DNA transcription and compaction. (csic.es)
  • The mtDNA transcription initiation complex is formed by mitochondrial transcription factor A (TFAM) binding to one of the two mtDNA transcription promoters, HSP1 or LSP. (csic.es)
Promoter2
  • In addition to the DnaA protein, its concentration, binding to DnaA-boxes, and binding of ATP or ADP, we will cover the regulation of the DnaA gene, the unique characteristics of the DnaA gene expression, promoter strength, and translation efficiency. (wikipedia.org)
  • DnaA has the ability to bind its own promoter. (wikipedia.org)
Complexes2
  • The crystal structures of human topoisomerase I comprising the core and carboxyl-terminal domains in covalent and noncovalent complexes with 22-base pair DNA duplexes reveal an enzyme that 'clamps' around essentially B-form DNA. (embl.de)
  • these stabilized complexes block movement of the DNA replication fork and thereby inhibit DNA replication resulting in cell death. (antiinfectivemeds.com)
Structures1
  • Our biochemical analyses showed that TFAM binds to DNA structures, such as G-quadruplexes (Lyonnais et al. (csic.es)
TOPOLOGY3
  • This architectural protein thus uses its multiple domains to bridge co-aligned DNA segments without altering the DNA topology, revealing a new mechanism of mtDNA condensation. (bvsalud.org)
  • Here, we show how condensin activity alters the topology of the interacting DNA. (bvsalud.org)
  • These changes in DNA topology do not involve DNA unwinding, do not spread outside the condensin-DNA complex and can occur in the absence of the condensin subunit Ycg1. (bvsalud.org)
Genetic2
  • We start with DNA, the genetic information in every cell that is copied and passed from generation to generation. (rainis.pics)
  • DNA was discovered by Friedrich Miescher in 1869 and identified as genetic material in experiments conducted by Oswald Avery, Colin MacLeod, and Maclyn McCarty in the 1940s. (rainis.pics)
Chromosome1
  • Based on the Replicon Model, a positively active initiator molecule contacts with a particular spot on a circular chromosome called the replicator to start DNA replication. (wikipedia.org)
Bacteria1
Mechanism4
  • Molecular modeling and computational analyses suggests that the Sinorhizobium meliloti periplasmic regulator protein ExoR adopts a superhelical fold and is controlled by a unique mechanism of proteolysis. (cuny.edu)
  • 2017). This protein also bears two HMG-boxes but the mechanism of binding is from one side of the DNA, as a staple. (csic.es)
  • Condensin, an SMC (structural maintenance of chromosomes) protein complex, extrudes DNA loops using an ATP-dependent mechanism that remains to be elucidated. (bvsalud.org)
  • Such a "pinch and merge" mechanism implies that two DNA-binding sites produce the feeding loop, while a third site, plausibly involving Ycg1, might anchor the extruding loop. (bvsalud.org)
Eukaryotic1
  • Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. (lookformedical.com)
Subunits1
Structural1
  • The core domain and the first eight residues of the carboxyl-terminal domain of the enzyme, including the active-site nucleophile tyrosine-723, share significant structural similarity with the bacteriophage family of DNA integrases. (embl.de)
Strand separation1
  • Binding of DnaA leads to strand separation at the 13-mer repeats. (wikipedia.org)
Phosphodiester2
  • An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. (lookformedical.com)
  • A strand of DNA is a polymer of nucleoside monophosphates linked by phosphodiester bonds. (rainis.pics)
Distinct1
  • Two apparently homologous TFAM binding sites, DNA Site-X and Site-Y, similar to and downstream from LSP, unexpectedly show distinct DNA-structure features and TFAM binds to them in opposite directions, imposing again a U-turn (Cuppari el al. (csic.es)
Nucleotide2
  • Their activity is strictly dependent on the presence of a nucleotide-based cofactor bound to a conserved region called beta-alpha-beta core. (edu.pl)
  • The term nucleotide refers to the building blocks of DNA (deoxyribonucleoside triphosphate, dNTP) and RNA (ribonucleoside triphosphate, NTP). (rainis.pics)
Sequences1
Hydrolysis2
  • Although the active form of DnaA requires ATP, the formation of the oriC/DnaA complex and subsequent DNA unwinding does not require ATP hydrolysis. (wikipedia.org)
  • This ∆Lk increases to -0.8 during ATP binding and resets to -0.4 upon ATP hydrolysis. (bvsalud.org)
Separation1
  • Topoisomerase IV acts at the terminal states of DNA replication by allowing for separation of interlinked daughter chromosomes so that segregation into daughter cells can occur. (antiinfectivemeds.com)
Enzyme1
Domains2
  • This region covers both the catalytic core and the DNA-binding domains. (embl.de)
  • San A, Palmieri D, Saxena A, Singh S. In silico study predicts a key role of RNA-binding domains 3 and 4 in nucleolin-miRNA interactions. (cuny.edu)
Sites1
Domain2
  • DnaA contains two conserved regions: the first is located in the central part of the protein and corresponds to the ATP-binding domain, the second is located in the C-terminal half and is involved in DNA-binding. (wikipedia.org)
  • Furthermore, an HMG-box domain canonically binds the minor groove and dramatically bends the DNA while, unprecedentedly, a second HMG-box binds the major groove without imposing distortions. (bvsalud.org)
Complex1
  • Namely, following ATP-mediated loading onto DNA, each condensin complex constrains a DNA linking number difference (∆Lk) of -0.4. (bvsalud.org)
Functions1
  • There may be numerous gap-filling strategies to link OriC functions to bacterial lifestyles in nature, which may account for the wide variability of OriC DnaA recognition site patterns. (wikipedia.org)
Found2
  • Nucleotides that contain deoxyribose are called deoxyribonucleotides and are the forms found in DNA. (rainis.pics)
  • In the respiratory samples of the ICU-COV(+) patients, bacterial signatures including Pseudomonas and Streptococcus were found to be correlated with the length of ICU stay. (bvsalud.org)
Family1
Form1
  • by James Watson and Francis Crick to form a model of DNA with which we are familiar today. (rainis.pics)
Structure2
  • We solved the crystal structure of TFAM bound to LSP. (csic.es)
  • The race to unravel the structure of DNA was one of the greatest scientific stories of the 20th century. (rainis.pics)