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CyclizationBase SequenceMolecular Sequence DataAmino Acid SequenceNucleotidesCloning, MolecularSequence Homology, Nucleic AcidGenes, BacterialStereoisomerismGenesEscherichia coliDNA Restriction EnzymesSequence Analysis, DNARestriction MappingDNAMolecular StructureNucleic Acid ConformationPlasmidsDNA, BacterialPhylogenyCodonSequence Homology, Amino AcidOpen Reading FramesSequence AlignmentGenes, ViralTranscription, GeneticAlkenesBacterial ProteinsAdenine NucleotidesPolymorphism, Single NucleotideNucleic Acid HybridizationRNA, ViralCatalysisIntramolecular LyasesSpecies SpecificityAlkynesRNA, MessengerDNA, ViralMutationPolymerase Chain ReactionGuanine NucleotidesIon ChannelsPalladiumGenome, ViralRepetitive Sequences, Nucleic AcidAcetalsKineticsOperonBinding SitesModels, MolecularPurine NucleotidesKetonesPolyisoprenyl PhosphatesGenetic VariationDNA, ComplementaryDNA, RecombinantChemistry, OrganicPlant VirusesDNA PrimersMolecular WeightAlkadienesChromosome MappingBase CompositionNucleotides, CyclicViral ProteinsSubstrate SpecificityRNA, RibosomalProtein BiosynthesisBlotting, SouthernProtein ConformationPyransPeptides, CyclicPromoter Regions, GeneticIsomerasesOligoribonucleotidesRNABiological EvolutionMultigene FamilyStreptomycesLewis AcidsCycloparaffinsDNA Transposable ElementsPlantsMolecular ConformationRecombinant ProteinsRhodiumGenetic CodeOligonucleotide ProbesCell LineRibonuclease T1Combinatorial Chemistry TechniquesGenes, RegulatorGenotypeGuanine Nucleotide Exchange FactorsBacillusIminesOligonucleotidesIon Channel GatingIon TransportEvolution, Molecular
Nucleic acidReactionAtomsAlkenesEquivalentsIntermediateMoleculeEnzymeCommonlyCompoundsCarbocationArticleProteinProductChemicalMethodsVarietyCellsAnalysisLeaving groupEvolutionGenomeRearrangementAminoProtein sequencesConjugatePeptideFormationMoleculesSynthesisOligonucleotidesStructuralStructuresConsistsGeneExperimentsEnhancesExpressed sequRapidFormStructureMethodPresent
Nucleic acid4
  • Nucleic acid-based aptamers were first described in 1990, where the first aptamers were in vitro selected using a random library of single-stranded oligonucleotides sequences [ 1 ] by a selection procedure known as systematic evolution of ligands by exponential enrichment (SELEX). (encyclopedia.pub)
  • The present invention also relates to isolated trichodiene synthases and isolated nucleic acid sequences encoding the trichodiene synthases. (justia.com)
  • The invention also relates to nucleic acid constructs, vectors, and host cells comprising the nucleic acid sequences as well as methods for producing the trichodiene synthases. (justia.com)
  • vi)a nucleic acid sequence according to any of (i) and (ii) which is degenerate as a result of the genetic code. (allindianpatents.com)
Reaction5
  • However, the iminium ion (but not the imine itself) formed in situ during a reductive amination reaction is a stronger electrophile than the ketone starting material and will react with the hydride source at a synthetically useful rate. (wikipedia.org)
  • Importantly, the reaction is conducted under mildly acidic conditions that protonate the imine intermediate to a significant extent, forming the iminium ion, while not being strongly acidic enough to protonate the ketone, which would form the even more electrophilic oxocarbenium ion. (wikipedia.org)
  • Examples of methods utilizing such non-radioactive detection methods include DNA sequencing, oligonucleotide probe methods, detection of polymerase-chain-reaction products, immunoassays, and the like. (justia.com)
  • 1985). The product of the cyclization reaction in vitro was shown to be divinylPchlide (2,4-divinylpheoporphyrin a5) (Chereskin et al. (docksci.com)
  • Initial reaction of the nucleophilic double bond with H + gives a carbocation intermediate, which then reacts with halide ion. (openstax.org)
Atoms2
  • An oxocarbenium ion (or oxacarbenium ion) is a chemical species characterized by a central sp2-hybridized carbon, an oxygen substituent, and an overall positive charge that is delocalized between the central carbon and oxygen atoms. (wikipedia.org)
  • The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds. (lookformedical.com)
Alkenes1
  • Bromine and chlorine add to alkenes via three-membered-ring bromonium ion or chloronium ion intermediates to give addition products having anti stereochemistry . (openstax.org)
Equivalents2
  • It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (lookformedical.com)
  • The pentose phosphate pathway is a process of glucose turnover that produces NADPH as reducing equivalents and pentoses as essential parts of nucleotides. (easyomics.org)
Intermediate2
  • In organic reactions, ketones are commonly activated by the coordination of a Lewis acid or Brønsted acid to the oxygen to generate an oxocarbenium ion as an intermediate. (wikipedia.org)
  • Depending on the polyketide synthase activity, chalcone synthase (CHS, EC 2.3.1.74) or stilbene synthase (STS, EC 2.3.1.95), subsequent folding and cyclization of the generated tetraketide intermediate results either in the production of a chalcone or stilbene ring structure. (biomedcentral.com)
Molecule1
  • An alternative to elimination is direct deprotonation of the molecule to form the ion, however, this can be difficult and require strong bases to achieve. (wikipedia.org)
Enzyme1
  • Trichothecenes are produced by a sequence of oxygenations, isomerizations, cyclizations, and esterifications leading from trichodiene, which is produced from the cyclization of trans, trans-farnesyl pyrophosphate by the enzyme trichodiene synthase (Desjardins, Hohn, and McCormick, 1993, Microbiological Reviews 57: 595-604). (justia.com)
Commonly1
Compounds4
  • Compared to neutral carbonyl compounds like ketones or esters, the carbenium ion form is a larger contributor to the structure. (wikipedia.org)
  • Optimization of precursor conversion and cyclization of the bulky ferulic acid precursor by host metabolic engineering and protein engineering may afford the synthesis of even more structurally diverse stilbene compounds. (biomedcentral.com)
  • In an additional aspect, the invention includes methods utilizing such dye compounds and reagents including dideoxy polynucleotide sequencing and fragment analysis methods. (justia.com)
  • Based mostly on the truth that Girard's reagent T (GRT), as derivatization reagent, was each handy and environment friendly by way of the enhancement within the ionization effectivity and the manufacturing of diagnostic product ions associated to the steroid moiety, the latter was ideally chosen between methoxamine and hydroxylamine upon the mannequin compounds of androsterone glucuronide and androsterone sulfate. (n-egt.com)
Carbocation1
  • Compared to a ketone, the polarization of an oxocarbenium ion is accentuated: they more strongly resemble a "true" carbocation, and they are more reactive toward nucleophiles. (wikipedia.org)
Article1
  • The remainder of this article will focus on alkyl oxocarbenium ions, however, where the atom added to the oxygen is a carbon. (wikipedia.org)
Protein1
Product2
  • Intact part II steroid metabolites have poor product ion mass spectra beneath collision induced dissociation (CID) situations. (n-egt.com)
  • Product ion spectra embrace in all instances excessive variety of product ions that in some instances are attribute for sure constructions of the steroid spine. (n-egt.com)
Chemical3
  • These ions have since been proposed as reactive intermediates in a wide range of chemical transformations, and have been utilized in the total synthesis of several natural products. (wikipedia.org)
  • Modified aptamers may show improved chemical diversity relative to aptamers composed entirely of natural DNA or RNA nucleotides and expand their applications in diagnostics, therapeutics, and nanotechnology [ 1 ] . (encyclopedia.pub)
  • SELEX starts by chemical synthesis of a library of random sequences of double-stranded DNA (dsDNA). (encyclopedia.pub)
Methods2
  • In many applications the independent detection of multiple spatially overlapping analytes in a mixture is required, e.g., single-tube multiplex DNA probe assays, immuno assays, multicolor DNA sequencing methods, and the like. (justia.com)
  • In the case of automated DNA sequencing, multicolor labeling allows for the analysis of all four bases in a single lane thereby increasing throughput over single-color methods and eliminating uncertainties associated with inter-lane electrophoretic mobility variations. (justia.com)
Variety1
  • Aptamers are short single-stranded RNA or DNA oligonucleotides capable of folding into complex 3D structures, enabling them to bind to a large variety of targets ranging from small ions to an entire organism. (encyclopedia.pub)
Cells2
  • Targets on which aptamer selection is conducted against are diverse, ranging from ions to whole living cells. (encyclopedia.pub)
  • They perform many functions, including biochemical support of endothelial cells that form the blood-brain barrier , provision of nutrients to the nervous tissue, maintenance of extracellular ion balance, and a role in the repair and scarring process of the brain and spinal cord following traumatic injuries. (cureffi.org)
Analysis1
  • Lung tissues from HPH rats and normal rats underwent high-throughput sequencing and transcriptomic analysis. (bvsalud.org)
Leaving group1
  • One way that this sort of ion will form is the elimination of a leaving group. (wikipedia.org)
Evolution1
  • Leigh Brown (1992), Convergent and divergent sequence evolution in the surface envelope glycoprotein of HIV-1 within a single infected patient, Proc. (forexinfolink.com)
Genome5
  • Analysis of the RNA synthesis initiation site using the 3'-end 83 nucleotides of the JEV genome as a minimal RNA template revealed that the NS5 protein specifically initiates RNA synthesis from an internal site, U 81 , at the two nucleotides upstream of the 3'-end of the template. (biomedcentral.com)
  • The RNA genome of JEV consists of 98-nucleotide (nt) long 5' untranslated region (UTR) with the type-1 cap structure at its 5' terminus, a single open reading frame (ORF), and a 585-nt long 3'-UTR with no poly(A) tail at its 3' terminus [ 4 ]. (biomedcentral.com)
  • The sequencing and analysis of expressed sequence tags (ESTs) has been a primary tool for the discovery of novel genes in plants, especially in non-model plants for which full genome sequences are not currently available [ 1 ]. (biomedcentral.com)
  • In the past ten years, a number of genome sequencing projects have promoted application of computational approaches for the discovery of components involved in innate immunity of a given species. (biomedcentral.com)
  • All involve an initial directed incision of a circular DNA duplex, generally in the form of a recombinant bacterial plasmid, enzymatic removal of nucleotides from the ends of the incised molecules or addition of DNA to the ends, followed by ligation and cloning of the constructed mutant genome. (nih.gov)
Rearrangement1
  • Terpenoid synthases are responsible for the cyclization and/or rearrangement of linear isoprenoid diphosphates into cyclic terpenoids [ 12 , 13 ]. (biomedcentral.com)
Amino5
  • or conjugate, complex, or fusion protein or fusion polypeptide including the same disclosed amino acid sequence derived from bacterium (e.g., mycoplasma, anaplasma, etc. (patentsencyclopedia.com)
  • A multiple sequences alignment and phylogenetic tree demonstrate that Ct CHI1 shares 92% amino acid identity and close relationship with CHI to Saussurea medusa . (biomedcentral.com)
  • Analysis of the amino acid sequence of NS5 led to the prediction that it carries both methyltransferase and RNA-dependent RNA polymerase (RdRp) activities. (biomedcentral.com)
  • Most AMPs are cationic polypeptides, usually smaller than 100 amino acids in length, with enormous sequence diversity. (biomedcentral.com)
  • The cDNA display proteolysis method is fast, accurate and uniquely scalable, and promises to reveal the quantitative rules for how amino acid sequences encode folding stability. (nature.com)
Protein sequences3
  • Advances in DNA sequencing and machine learning are providing insights into protein sequences and structures on an enormous scale 1 . (nature.com)
  • Protein sequences vary by more than ten orders of magnitude in thermodynamic folding stability 2 (the ratio of unfolded to folded molecules at equilibrium). (nature.com)
  • First, the pocket, conservation, structural and energy profiles, and physicochemical properties of (non)covalently bound cysteines were collected from both protein sequences and 3D structures of protein-ligand complexes. (uni-freiburg.de)
Conjugate1
  • Amide ion (NH 2 − ), for example, the conjugate base of ammonia (p K a = 35), is often used to deprotonate terminal alkynes. (openstax.org)
Peptide6
  • Using the haloduracin b synthetase (HalM2) as a model LanM system, mass spectrometry-based kinetic studies show that conformational changes and enzyme:peptide interactions influence the kinetics and sequence of biosynthetic events. (ncsu.edu)
  • Hydrogen-deuterium exchange mass spectrometry (HDX-MS) studies show that HalM2 is a dynamic enzyme that undergoes local structural rearrangements and long-range allosteric signalling upon peptide or nucleotide binding. (ncsu.edu)
  • Mutations to previously overlooked, dynamic HalM2 structural elements impact the catalytic activities (dehydration and cyclization) of HalM2, providing evidence that conformational changes and enzyme-peptide interactions contribute to function. (ncsu.edu)
  • Finally, native mass spectrometry coupled to ion mobility shows that HalM2 exists in multiple three-dimensional conformations, and that this conformational landscape is influenced by HalA2 precursor peptide binding and by post-translational modification of the HalA2 core peptide. (ncsu.edu)
  • the PNA part (peptide nucleic acids) ensures sequence specific hybridization with the target and the quinone methide (highlighted in yellow) as a potent electrophile reversibly alkylates nucleophilic sites within the RNA (RNA nucleotides shown in black, PNA nucleotides in magenta). (uni-frankfurt.de)
  • The cyclization with a single non-peptide bond can lead them to be incorrectly called DEPSIPEPTIDES, but the echinocandins lack ester links. (lookformedical.com)
Formation3
  • Formation of oxocarbenium ions can proceed through several different pathways. (wikipedia.org)
  • Such compounds formed host-guest complexes and accelerated phosphoryl transfer reactions when conducted in DMF to promote ion pair formation. (uni-frankfurt.de)
  • goals for -aid are a Intermolecular OP inihstuy defined on Formation sequence &, sulphuric chemistry dyes of the Precipitate itself. (windhamny.com)
Molecules1
  • Many years ago, we investigated anion receptor molecules composed of guanidinium ions. (uni-frankfurt.de)
Synthesis2
  • These ions have since been proposed as reactive intermediates in a wide range of chemical transformations, and have been utilized in the total synthesis of several natural products. (wikipedia.org)
  • Assaying one library (up to 900,000 sequences in our experiments) requires one week and reagents costing about US$2,000, excluding the cost of DNA synthesis and sequencing. (nature.com)
Oligonucleotides2
  • Many of the advances made in protein MS have been adapted to make the technique appliable to the study of oligonucleotides, where attributes such as sequence, modification, and quantitation are critical. (biopharminternational.com)
  • This observation finally led us to the development of phosphoramidite 1 ( A ). Compound 1 can be attached in high yield to the 5' end of DNA or LNA oligonucleotides ( B ). Panel C depicts a duplex formed by such DNA-catalyst conjugates and dye-labeled RNA substrates (deoxy-nucleotides in blue and ribonucleotides in black letters). (uni-frankfurt.de)
Structural1
  • Compared to traditional ML models with only sequenced-based features or only 3D structural features, HyperCys is more accurate at predicting hyper-reactive druggable cysteines. (uni-freiburg.de)
Structures1
  • An oxocarbenium ion is represented by two limiting resonance structures, one in the form of a carbenium ion with the positive charge on carbon and the other in the form of an oxonium species with the formal charge on oxygen. (wikipedia.org)
Consists1
Gene2
  • The assembled sequences were annotated with gene names and Gene Ontology (GO) terms. (biomedcentral.com)
  • METHODS THAT GENERATE DELETIONS OR INSERTIONS In the initial stages of a mutational analysis of DNA function it is often desirable to delete segments of DNA from a given region of a cloned gene or gene cluster or to insert a defined sequence in the region of interest. (nih.gov)
Experiments2
  • In 2012, Taucher and Breuker (8) were amongst the first to report sequence coverage of full-length transfer RNA (tRNA) using Fourier transform ion cycloctron resonance (FT-ICR), combining data from electron detachment dissociation (EDD) and collision-activated dissociation (CAD) experiments. (biopharminternational.com)
  • MATERIALS AND METHODS: The study was based on network pharmacology, using a combination of RNA-sequencing, "quantity-effect" weighting coefficients, and pharmacodynamic experiments. (bvsalud.org)
Enhances1
Expressed sequ1
  • The goals of this study were to identify expressed sequence tags (EST) in Citrus sinensis (L.) Osbeck corresponding to genes involved in general phenylpropanoid biosynthesis and the key genes involved in the main flavonoids pathways (flavanones, flavones, flavonols, leucoanthocyanidins, anthocyanins and isoflavonoids). (scielo.br)
Rapid1
  • EST sequencing represents a rapid and cost-effective method for analyzing the transcribed regions of genomes. (biomedcentral.com)
Form1
  • One way that this sort of ion will form is the elimination of a leaving group. (wikipedia.org)
Structure2
  • The best Lewis structure for an oxocarbenium ion contains an oxygen-carbon double bond, with the oxygen atom attached to an additional group and consequently taking on a formal positive charge. (wikipedia.org)
  • HyperCys: A Structure- and Sequence-Based Predictor of Hyper-Reactive Druggable Cysteines. (uni-freiburg.de)
Method1
  • This method combines the strengths of cell-free molecular biology and next-generation sequencing and requires no on-site equipment larger than a quantitative PCR (qPCR) instrument. (nature.com)
Present1
  • A RISC complex charged with a specific miRNA (symbolized here by red color) would bind to the complementary "red" RNA sequence, not present in the mRNA example shown above. (uni-frankfurt.de)