Base Pairing
Base Sequence
Skull Base
Schiff Bases
Skull Base Neoplasms
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Base Pair Mismatch
The presence of an uncomplimentary base in double-stranded DNA caused by spontaneous deamination of cytosine or adenine, mismatching during homologous recombination, or errors in DNA replication. Multiple, sequential base pair mismatches lead to formation of heteroduplex DNA; (NUCLEIC ACID HETERODUPLEXES).
Nucleic Acid Conformation
DNA
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. 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).
Denture Bases
Amino Acid Sequence
Knowledge Bases
Escherichia coli
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Mannich Bases
Oligodeoxyribonucleotides
Mutation
Cloning, Molecular
Models, Molecular
DNA Glycosylases
A family of DNA repair enzymes that recognize damaged nucleotide bases and remove them by hydrolyzing the N-glycosidic bond that attaches them to the sugar backbone of the DNA molecule. The process called BASE EXCISION REPAIR can be completed by a DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE which excises the remaining RIBOSE sugar from the DNA.
Oligonucleotides
DNA Repair
The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.
Hydrogen Bonding
Binding Sites
Transcription, Genetic
Plasmids
RNA
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Lewis Bases
Genes
Sequence Homology, Nucleic Acid
Nucleic Acid Hybridization
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
Substrate Specificity
Promoter Regions, Genetic
Restriction Mapping
DNA-(Apurinic or Apyrimidinic Site) Lyase
A DNA repair enzyme that catalyses the excision of ribose residues at apurinic and apyrimidinic DNA sites that can result from the action of DNA GLYCOSYLASES. The enzyme catalyzes a beta-elimination reaction in which the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. This enzyme was previously listed under EC 3.1.25.2.
N-Glycosyl Hydrolases
Nucleic Acid Heteroduplexes
Double-stranded nucleic acid molecules (DNA-DNA or DNA-RNA) which contain regions of nucleotide mismatches (non-complementary). In vivo, these heteroduplexes can result from mutation or genetic recombination; in vitro, they are formed by nucleic acid hybridization. Electron microscopic analysis of the resulting heteroduplexes facilitates the mapping of regions of base sequence homology of nucleic acids.
RNA, Messenger
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Sequence Analysis, DNA
Nucleotides
DNA Polymerase beta
Purines
Thermodynamics
A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)
Molecular Structure
Codon
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
Hydrogen-Ion Concentration
Anticodon
Magnetic Resonance Spectroscopy
Guanosine
Polymerase Chain Reaction
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
Repetitive Sequences, Nucleic Acid
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
DNA-Binding Proteins
DNA-Directed DNA Polymerase
DNA-dependent DNA polymerases found in bacteria, animal and plant cells. During the replication process, these enzymes catalyze the addition of deoxyribonucleotide residues to the end of a DNA strand in the presence of DNA as template-primer. They also possess exonuclease activity and therefore function in DNA repair.
DNA Primers
RNA, Transfer
The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.
Structure-Activity Relationship
Temperature
DNA-Formamidopyrimidine Glycosylase
Sequence Alignment
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Mutagenesis
Protein Binding
RNA, Bacterial
Crystallography, X-Ray
Introns
Deoxyribonuclease (Pyrimidine Dimer)
Templates, Genetic
Uracil-DNA Glycosidase
Catalysis
Mutagenesis, Site-Directed
Sequence Homology, Amino Acid
DNA Adducts
Oligonucleotide Probes
Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.
DNA, Single-Stranded
RNA, Ribosomal
The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)
Saccharomyces cerevisiae
Intercalating Agents
Protons
Point Mutation
Species Specificity
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Endodeoxyribonucleases
Protein Conformation
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
Single-Strand Specific DNA and RNA Endonucleases
Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA.
Models, Chemical
RNA, Catalytic
RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.
Acid-Base Equilibrium
Frameshift Mutation
A type of mutation in which a number of NUCLEOTIDES deleted from or inserted into a protein coding sequence is not divisible by three, thereby causing an alteration in the READING FRAMES of the entire coding sequence downstream of the mutation. These mutations may be induced by certain types of MUTAGENS or may occur spontaneously.
DNA, Recombinant
Protein Biosynthesis
Regulatory Sequences, Nucleic Acid
Models, Genetic
Bacteriorhodopsins
Operon
DNA, Complementary
Gene Expression Regulation
Nucleosides
Sphingolipids
A class of membrane lipids that have a polar head and two nonpolar tails. They are composed of one molecule of the long-chain amino alcohol sphingosine (4-sphingenine) or one of its derivatives, one molecule of a long-chain acid, a polar head alcohol and sometimes phosphoric acid in diester linkage at the polar head group. (Lehninger et al, Principles of Biochemistry, 2nd ed)
Chromosome Mapping
Ointment Bases
Transcription Factors
Spectrophotometry, Ultraviolet
Catalytic Domain
Nuclear Magnetic Resonance, Biomolecular
Cattle
Poly dA-dT
Alkylation
Deoxyribonucleotides
RNA Splicing
Water
Carbon-Oxygen Lyases
Deoxyribonuclease I
An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. The enzyme has a preference for double-stranded DNA.
Genetic Code
Osmium Tetroxide
Methylation
Nucleic Acids
Electrophoresis, Polyacrylamide Gel
Transfection
Hypoxanthine
Pentoxyl
Chemistry
Consensus Sequence
A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.
Cytidine
RNA, Transfer, Ala
HeLa Cells
DNA Polymerase I
A DNA-dependent DNA polymerase characterized in prokaryotes and may be present in higher organisms. It has both 3'-5' and 5'-3' exonuclease activity, but cannot use native double-stranded DNA as template-primer. It is not inhibited by sulfhydryl reagents and is active in both DNA synthesis and repair. EC 2.7.7.7.
Conserved Sequence
Chemical Phenomena
Deoxyribonucleases, Type II Site-Specific
Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC 3.1.21.4.
Deoxyadenosines
Sphingosine
Recombination, Genetic
DNA Probes
Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.
Ultraviolet Rays
That portion of the electromagnetic spectrum immediately below the visible range and extending into the x-ray frequencies. The longer wavelengths (near-UV or biotic or vital rays) are necessary for the endogenous synthesis of vitamin D and are also called antirachitic rays; the shorter, ionizing wavelengths (far-UV or abiotic or extravital rays) are viricidal, bactericidal, mutagenic, and carcinogenic and are used as disinfectants.
Software
Blotting, Southern
5-Methylcytosine
DNA Ligases
Circular Dichroism
Chromatography, High Pressure Liquid
Phenotype
Models, Biological
Gene Library
Genes, Regulator
Evolution, Molecular
DNA-Directed RNA Polymerases
Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).
Computer Simulation
Chordoma
Bacteriophage lambda
Echinomycin
Blotting, Northern
Biological Evolution
Pyrimidines
Algorithms
Cross-Linking Reagents
Reagents with two reactive groups, usually at opposite ends of the molecule, that are capable of reacting with and thereby forming bridges between side chains of amino acids in proteins; the locations of naturally reactive areas within proteins can thereby be identified; may also be used for other macromolecules, like glycoproteins, nucleic acids, or other.
DNA Breaks, Single-Stranded
Retinaldehyde
A carotenoid constituent of visual pigments. It is the oxidized form of retinol which functions as the active component of the visual cycle. It is bound to the protein opsin forming the complex rhodopsin. When stimulated by visible light, the retinal component of the rhodopsin complex undergoes isomerization at the 11-position of the double bond to the cis-form; this is reversed in "dark" reactions to return to the native trans-configuration.
Deoxyribonuclease IV (Phage T4-Induced)
DNA, Mitochondrial
Poly A
DNA Transposable Elements
Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
Stereoisomerism
Open Reading Frames
Alkylating Agents
Highly reactive chemicals that introduce alkyl radicals into biologically active molecules and thereby prevent their proper functioning. Many are used as antineoplastic agents, but most are very toxic, with carcinogenic, mutagenic, teratogenic, and immunosuppressant actions. They have also been used as components in poison gases.
DNA Repair Enzymes
Chloramphenicol O-Acetyltransferase
An enzyme that catalyzes the acetylation of chloramphenicol to yield chloramphenicol 3-acetate. Since chloramphenicol 3-acetate does not bind to bacterial ribosomes and is not an inhibitor of peptidyltransferase, the enzyme is responsible for the naturally occurring chloramphenicol resistance in bacteria. The enzyme, for which variants are known, is found in both gram-negative and gram-positive bacteria. EC 2.3.1.28.
Pyrimidine Nucleotides
Operator Regions, Genetic
A computational screen for methylation guide snoRNAs in yeast. (1/2613)
Small nucleolar RNAs (snoRNAs) are required for ribose 2'-O-methylation of eukaryotic ribosomal RNA. Many of the genes for this snoRNA family have remained unidentified in Saccharomyces cerevisiae, despite the availability of a complete genome sequence. Probabilistic modeling methods akin to those used in speech recognition and computational linguistics were used to computationally screen the yeast genome and identify 22 methylation guide snoRNAs, snR50 to snR71. Gene disruptions and other experimental characterization confirmed their methylation guide function. In total, 51 of the 55 ribose methylated sites in yeast ribosomal RNA were assigned to 41 different guide snoRNAs. (+info)Base pairing of anhydrohexitol nucleosides with 2,6-diaminopurine, 5-methylcytosine and uracil asbase moiety. (2/2613)
Hexitol nucleic acids (HNAs) with modified bases (5-methylcytosine, 2,6-diaminopurine or uracil) were synthesized. The introduction of the 5-methylcytosine base demonstrates that N -benzoylated 5-methylcytosyl-hexitol occurs as the imino tautomer. The base pairing systems (G:CMe, U:D, T:D and U:A) obey Watson-Crick rules. Substituting hT for hU, hCMefor hC and hD for hA generally leads to increased duplex stability. In a single case, replacement of hC by hCMedid not result in duplex stabilization. This sequence-specific effect could be explained by the geometry of the model duplex used for carrying out the thermal stability study. Generally, polypurine HNA sequences give more stable duplexes with their RNA complement than polypyrimidine HNA sequences. This observation supports the hypothesis that, besides changes in stacking pattern, the difference in conformational stress between purine and pyrimidine nucleosides may contribute to duplex stability. Introduction of hCMeand hD in HNA sequences further increases the potential of HNA to function as a steric blocking agent. (+info)Smoothing of the thermal stability of DNA duplexes by using modified nucleosides and chaotropic agents. (3/2613)
The effect of alkyltrimethylammonium ions on the thermostability of natural and modified DNA duplexes has been investigated. We have shown that the use of tetramethylammonium ions TMA+along with the chemical modification of duplexes allow the fine adjustment of T m and the possibility of obtaining several duplex systems with varied isostabilizedtemperatures, some of which show greater stability than those of natural DNA. This approach could be very useful for DNA sequencing by hybridization. (+info)Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. (4/2613)
The complete 184,457-bp sequence of the aromatic catabolic plasmid, pNL1, from Sphingomonas aromaticivorans F199 has been determined. A total of 186 open reading frames (ORFs) are predicted to encode proteins, of which 79 are likely directly associated with catabolism or transport of aromatic compounds. Genes that encode enzymes associated with the degradation of biphenyl, naphthalene, m-xylene, and p-cresol are predicted to be distributed among 15 gene clusters. The unusual coclustering of genes associated with different pathways appears to have evolved in response to similarities in biochemical mechanisms required for the degradation of intermediates in different pathways. A putative efflux pump and several hypothetical membrane-associated proteins were identified and predicted to be involved in the transport of aromatic compounds and/or intermediates in catabolism across the cell wall. Several genes associated with integration and recombination, including two group II intron-associated maturases, were identified in the replication region, suggesting that pNL1 is able to undergo integration and excision events with the chromosome and/or other portions of the plasmid. Conjugative transfer of pNL1 to another Sphingomonas sp. was demonstrated, and genes associated with this function were found in two large clusters. Approximately one-third of the ORFs (59 of them) have no obvious homology to known genes. (+info)Mutated epithelial cadherin is associated with increased tumorigenicity and loss of adhesion and of responsiveness to the motogenic trefoil factor 2 in colon carcinoma cells. (5/2613)
Epithelial (E)-cadherin and its associated cytoplasmic proteins (alpha-, beta-, and gamma-catenins) are important mediators of epithelial cell-cell adhesion and intracellular signaling. Much evidence exists suggesting a tumor/invasion suppressor role for E-cadherin, and loss of expression, as well as mutations, has been described in a number of epithelial cancers. To investigate whether E-cadherin gene (CDH1) mutations occur in colorectal cancer, we screened 49 human colon carcinoma cell lines from 43 patients by single-strand conformation polymorphism (SSCP) analysis and direct sequencing. In addition to silent changes, polymorphisms, and intronic variants in a number of the cell lines, we detected frameshift single-base deletions in repeat regions of exon 3 (codons 120 and 126) causing premature truncations at codon 216 in four replication-error-positive (RER+) cell lines (LS174T, HCT116, GP2d, and GP5d) derived from 3 patients. In LS174T such a mutation inevitably contributes to its lack of E-cadherin protein expression and function. Transfection of full-length E-cadherin cDNA into LS174T cells enhanced intercellular adhesion, induced differentiation, retarded proliferation, inhibited tumorigenicity, and restored responsiveness to the migratory effects induced by the motogenic trefoil factor 2 (human spasmolytic polypeptide). These results indicate that, although inactivating E-cadherin mutations occur relatively infrequently in colorectal cancer cell lines overall (3/43 = 7%), they are more common in cells with an RER+ phenotype (3/10 = 30%) and may contribute to the dysfunction of the E-cadherin-catenin-mediated adhesion/signaling system commonly seen in these tumors. These results also indicate that normal E-cadherin-mediated cell adhesion can restore the ability of colonic tumor cells to respond to trefoil factor 2. (+info)High base pair opening rates in tracts of GC base pairs. (6/2613)
Sequence-dependent structural features of the DNA double helix have a strong influence on the base pair opening dynamics. Here we report a detailed study of the kinetics of base pair breathing in tracts of GC base pairs in DNA duplexes derived from 1H NMR measurements of the imino proton exchange rates upon titration with the exchange catalyst ammonia. In the limit of infinite exchange catalyst concentration, the exchange times of the guanine imino protons of the GC tracts extrapolate to much shorter base pair lifetimes than commonly observed for isolated GC base pairs. The base pair lifetimes in the GC tracts are below 5 ms for almost all of the base pairs. The unusually rapid base pair opening dynamics of GC tracts are in striking contrast to the behavior of AT tracts, where very long base pair lifetimes are observed. The implication of these findings for the structural principles governing spontaneous helix opening as well as the DNA-binding specificity of the cytosine-5-methyltransferases, where flipping of the cytosine base has been observed, are discussed. (+info)How translational accuracy influences reading frame maintenance. (7/2613)
Most missense errors have little effect on protein function, since they only exchange one amino acid for another. However, processivity errors, frameshifting or premature termination result in a synthesis of an incomplete peptide. There may be a connection between missense and processivity errors, since processivity errors now appear to result from a second error occurring after recruitment of an errant aminoacyl-tRNA, either spontaneous dissociation causing premature termination or translational frameshifting. This is clearest in programmed translational frameshifting where the mRNA programs errant reading by a near-cognate tRNA; this error promotes a second frameshifting error (a dual-error model of frameshifting). The same mechanism can explain frameshifting by suppressor tRNAs, even those with expanded anticodon loops. The previous model that suppressor tRNAs induce quadruplet translocation now appears incorrect for most, and perhaps for all of them. We suggest that the 'spontaneous' tRNA-induced frameshifting and 'programmed' mRNA-induced frameshifting use the same mechanism, although the frequency of frameshifting is very different. This new model of frameshifting suggests that the tRNA is not acting as the yardstick to measure out the length of the translocation step. Rather, the translocation of 3 nucleotides may be an inherent feature of the ribosome. (+info)Trans-activation of the Tetrahymena group I intron ribozyme via a non-native RNA-RNA interaction. (8/2613)
The peripheral P2.1 domain of the Tetrahymena group I intron ribozyme has been shown to be non-essential for splicing. We found, however, that separately prepared P2.1 RNA efficiently accelerates the 3' splice-site-specific hydrolysis reaction of a mutant ribozyme lacking both P2.1 and its upstream region in trans. We report here the unusual properties of this trans-activation. Compensatory mutational analysis revealed that non-native long-range base-pairings between the loop region of P2.1 RNA and L5c region of the mutant ribozyme are needed for the activation in spite of the fact that P2.1 forms base-pairings with P9.1 in the Tetrahymena ribozyme. The trans -activation depends on the non-native RNA-RNA interaction together with the higher order structure of P2.1 RNA. This activation is unique among the known trans-activations that utilize native tertiary interactions or RNA chaperons. (+info)
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DNA
A Hoogsteen base pair is a rare variation of base-pairing.[27] As hydrogen bonds are not covalent, they can be broken and ... Base pairing. Further information: Base pair. In a DNA double helix, each type of nucleobase on one strand bonds with just one ... Adenine pairs with thymine and guanine pairs with cytosine, forming A-T and G-C base pairs.[18][19] ... Top, a GC base pair with three hydrogen bonds. Bottom, an AT base pair with two hydrogen bonds. Non-covalent hydrogen bonds ...
Dopamine receptor D4
48-base pair VNTR [edit]. The 48-base pair variable number tandem repeat (VNTR) in exon 3 range from 2 to 11 repeats.[citation ... 13-base pair deletion of bases 235 to 247 in exon 1 ... The 48-base pair VNTR has been the subject of much speculation ... pyridine-based dopamine D4 receptor ligands: discovery of an inverse agonist radioligand for PET". Journal of Medicinal ...
Non-interactive zero-knowledge proof
Pairing-based non-interactive proofs[edit]. Pairing-based cryptography has led to several cryptographic advancements. One of ... Short Pairing-Based Non-interactive Zero-Knowledge Arguments. ASIACRYPT 2010: 321-340 ... Progression-Free Sets and Sublinear Pairing-Based Non-Interactive Zero-Knowledge Arguments. TCC 2012: 169-189 ... external Diffie-Hellman assumption that allow directly proving the pairing product equations that are common in pairing-based ...
DNA synthesis
Base pair synthesis[edit]. New nucleobase pairs can also be synthesized, A-T (adenine - thymine) and G-C (guanine - cytosine). ... A third base pair would expand the number of amino acids that can be encoded by DNA from the existing 20 amino acids to a ... Twist Bioscience developed a silicon-based manufacturing process to industrialize the production of synthetic DNA. By ...
Complementarity (molecular biology)
Base pair. References[edit]. *^ a b c d e f g h Watson, James, Cold Spring Harbor Laboratory, Tania A. Baker, Massachusetts ... The base complement A=T shares two hydrogen bonds, while the base pair G≡C has three hydrogen bonds. All other configurations ... A complementary strand of DNA or RNA may be constructed based on nucleobase complementarity.[2] Each base pair, A=T vs. G≡C, ... Furthermore, various DNA repair functions as well as regulatory functions are based on base pair complementarity. In ...
List of numbers
Pair: 2 (the base of the binary numeral system). *Dozen: 12 (the base of the duodecimal numeral system) ... 10, the number base for most modern counting systems.. *12, the number base for some ancient counting systems and the basis for ... 2, the base of the binary number system, used in almost all modern computers and information systems. Also notable as the only ... 142857, the smallest base 10 cyclic number.. *2147483647, 231 − 1, the maximum value of a 32-bit signed integer using two's ...
Haplogroup Q-M242
Position (base pair): 180. Total size (base pairs): 366. Forward 5′→ 3′: aactcttgataaaccgtgctg. Reverse 5′→ 3′: ... Based on the data above, the average frequency in the whole male population of Mesoamerica and South America is estimated to be ... In another study, Q is found in 4% of Mongols.[22] Based on these studies, the average frequency of Q-M242 in Mongols is ... 2012). "Admixture and population structure in Mexican-Mestizos based on paternal lineages". J. Hum. Genet. 57 (9): 568-74. doi: ...
Transfer RNA
The acceptor stem is a 7- to 9-base pair (bp) stem made by the base pairing of the 5'-terminal nucleotide with the 3'-terminal ... Some anticodons can pair with more than one codon due to a phenomenon known as wobble base pairing. Frequently, the first ... The anticodon forms three complementary base pairs with a codon in mRNA during protein biosynthesis. On the other end of the ... Each tRNA contains a distinct anticodon triplet sequence that can form 3 complementary base pairs to one or more codons for an ...
Francis Crick
The similar structures of guanine:cytosine and adenine:thymine base pairs is illustrated. The base pairs are held together by ... They consulted Jerry Donohue who confirmed the most likely structures of the nucleotide bases.[45] The base pairs are held ... G pairs are structurally similar. In particular, the length of each base pair is the same. Chargaff had also pointed out to ... Identification of the correct base-pairing rules (A-T, G-C) was achieved by Watson "playing" with cardboard cut-out models of ...
Genome size
number of base pairs. =. mass in pg. ×. 9.78. ×. 10. 8. {\displaystyle {\text{number of base pairs}}={\text{mass in pg}}\times ... or as the total number of nucleotide base pairs, usually in megabases (millions of base pairs, abbreviated Mb or Mbp). One ... Conversion from picograms (pg) to base pairs (bp)Edit. Main article: C-value ... The base question behind the process of genome miniaturization is whether is occur trough large steps or due to a constant ...
டி. என். ஏ. - தமிழ் விக்கிப்பீடியா
மனிதனில் உள்ள நிறப்புரிகளில் முதலாவது நிறப்புரி கிட்டத்தட்ட 220 மில்லியன் இணைதாங்கிகளைக் (base pairs) கொண்டது[8]. டி.என்.ஏ ... இணைதாங்கிகளுக்கு (Base pairs) க்கு அண்மையாக உள்ள இந்த பள்ளங்களே இணைப்புப் பகுதிகளாக (binding sites) இருக்கும். இழைகள் ... இவ்வாறாக நிரப்பு இணைதாங்கிகளுக்கிடையே (complementary base pairs) நிகழும் மீள்தகு இடைவினையானது உயிரினங்களில் டி.என்.ஏ யின் ... நியூக்கிளியோடைட்டுக்கள் (nucleotide) எசுத்தர் பிணைப்பால்
RNA world
In eukaryotes, the processing of pre-mRNA and RNA editing take place at sites determined by the base pairing between the target ... However, certain sequences of base pairs have catalytic properties that lower the energy of their chain being created, enabling ... RNA-based evolution. References[edit]. *^ a b Neveu M, Kim HJ, Benner SA (Apr 2013). "The "strong" RNA world hypothesis: fifty ... This 189 base pair ribozyme could polymerize a template of at most 14 nucleotides in length, which is too short for self ...
Substitution
Base-pair substitution or point mutation, a type of mutation. *Substitution reaction, where a functional group in a chemical ...
Codon degeneracy
... and the base-pair formed is called a wobble base pair. The modified bases include inosine and the Non-Watson-Crick U-G basepair ... Degeneracy of codons is the redundancy of the genetic code, exhibited as the multiplicity of three-base pair codon combinations ... These variable codes for amino acids are allowed because of modified bases in the first base of the anticodon of the tRNA, ... "Degeneracy of the genetic code and stability of the base pair at the second position of the anticodon". RNA. 14 (7): 1264-9. ...
Pyrimidine dimer
The photon causes two consecutive bases on one strand to bind together, destroying the normal base-pairing double-strand ... These premutagenic lesions alter the structure and possibly the base-pairing. Up to 50-100 such reactions per second might ... Such dimers interfere with base pairing during DNA replication, leading to mutations. ... Pyrimidine dimers are molecular lesions formed from thymine or cytosine bases in DNA via photochemical reactions.[1][2] ...
Y chromosome
The DNA in the human Y chromosome is composed of about 59 million base pairs.[5] The Y chromosome is passed only from father to ... For example, the platypus relies on an XY sex-determination system based on five pairs of chromosomes.[11] Platypus sex ... They found that human Y chromosome is able to "recombine" with itself, using palindrome base pair sequences.[28] Such a " ... In humans, the Y chromosome spans about 58 million base pairs (the building blocks of DNA) and represents approximately 1% of ...
Intercalation (biochemistry)
In order for an intercalator to fit between base pairs, the DNA must dynamically open a space between its base pairs by ... The base pairs transiently form such openings due to energy absorbed during collisions with solvent molecules. ... on the order of a base pair) was first proposed by Leonard Lerman in 1961.[3][4][5] One proposed mechanism of intercalation is ... This unwinding causes the base pairs to separate, or "rise", creating an opening of about 0.34 nm (3.4 Å). This unwinding ...
Chemical reaction
Lewis definition: Acids are electron-pair acceptors, bases are electron-pair donors; this includes the Brønsted-Lowry ... base. ↽. −. −. ⇀. A. −. conjugated. base. +. HB. +. conjugated. acid. {\displaystyle {\ce {{\underset {acid}{HA}}+{\underset { ... Acid-base reactions. In the Brønsted-Lowry acid-base theory, an acid-base reaction involves a transfer of protons (H+) from one ... and thus the acid/base and conjugated base/acid are always in equilibrium. The equilibrium is determined by the acid and base ...
Category:Molecular biology - Simple English Wikipedia, the free encyclopedia
Base pair. C. *Cellulose. *Central dogma of molecular biology. *Chaperone (protein). *Chlorophyll ...
Promoter (genetics)
CpG islands are generally 200 to 2000 base pairs long, have a C:G base pair content ,50%, and have regions of DNA where a ... On average, only 3 to 4 of the 6 base pairs in each consensus sequence are found in any given promoter. Few natural promoters ... ends of the genes in a bidirectional gene pair.[11] A "bidirectional gene pair" refers to two adjacent genes coded on opposite ... typically within 30 to 40 base pairs). Eukaryotic promoter regulatory sequences typically bind proteins called transcription ...
Spaced repetition
The program schedules pairs based on spaced repetition algorithms. Without a program, the user has to schedule physical ... Automatic generation of pairs (e.g. for vocabulary, it is useful to generate three question-pairs: written foreign word, its ... items to memorize are entered into the program as question-answer pairs. When a pair is due to be reviewed, the question is ... Pavlik, P. I. (2005). The Microeconomics of Learning: Optimizing Paired-Associate Memory. PhD, Carnegie Mellon. ...
Archaeogenetics
Extension occurs when Taq polymerase is added to the sample and matches base pairs to turn the two single strands into two ... This results in samples having strands of DNA measuring around 100 base pairs in length. Contamination is another significant ... "Analysis of one million base pairs of Neanderthal DNA". Nature. 444 (7117): 330-336. Bibcode:2006Natur.444..330G. doi:10.1038/ ... The number of base differences between DNA of an ancient species and that of a closely related extant species can be used to ...
Kv1.1
The edited adenosine is found in a 6-base pair duplex region. Mutation experiment in the region near the 6-base pair duplex ... The double stranded regions of RNA are formed by base-pairing between residues in the region close to the editing site with ... The region that base pairs with the editing region is known as an Editing Complementary Sequence (ECS). ... This region is composed of a 114 base pairs. Similar regions have been identified in mouse and rat. ...
Collagen, type VII, alpha 1
COL7A1 is transcribed into an mRNA of 9,287 base pairs. In the skin, the type VII collagen protein is synthesized by ... The gene is approximately 31,000 base pairs in size and is remarkable for the extreme fragmentation of its coding sequence into ...
Genome - Simple English Wikipedia, the free encyclopedia
Genome size (base pairs) Note Virus, Bacteriophage MS2 3569 First sequenced RNA-genome[4] ...
GenBank
Growth in GenBank base pairs, 1982 to 2018, on a semi-log scale ... the number of bases in GenBank has doubled approximately every ... Direct submissions are made to GenBank using BankIt, which is a Web-based form, or the stand-alone submission program, Sequin. ... Release 194, produced in February 2013, contained over 150 billion nucleotide bases in more than 162 million sequences.[4] ... 18 months".[4][8] As of 15 June 2019[update], GenBank release 232.0 has 213,383,758 loci, 329,835,282,370 bases, from ...
Streptococcus
base pairs. 1,852,442. 2,211,488. 2,160,837. 2,030,921. ORFs. 1792. 2118. 2236. 1963. prophages. yes. no. no. no. ... The United Kingdom has chosen to adopt a risk factor-based protocol, rather than the culture-based protocol followed in the US ... Phylogenetic tree of Streptococcus species, based on data from PATRIC.[18] 16S groups are indicated by brackets and their key ... Species of Streptococcus are classified based on their hemolytic properties.[7] Alpha-hemolytic species cause oxidization of ...
Transfer DNA
As the T-DNA is bordered by 25-base-pair repeats on each end. Transfer is initiated at the right border and terminated at the ... The bacterial T-DNA is about 24,000 base pairs long and contains genes that code for enzymes synthesizing opines and ... Reverse genetics is usually followed as a functional genomics approach based on the dynamic of biological system that aims to ...
Chromosome 16
... spans about 90 million base pairs (the building material of DNA) and represents just under 3% of the total DNA in ... Band length in this diagram is proportional to base-pair length. This type of ideogram is generally used in genome browsers (e. ... a b These values (ISCN start/stop) are based on the length of bands/ideograms from the ISCN book, An International System for ... Chromosome 16 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. ...
Genetics
Figure 3 shows a deletion of the second base pair in the second codon. Figure 4 shows an insertion in the third base pair of ... Each nucleotide in DNA preferentially pairs with its partner nucleotide on the opposite strand: A pairs with T, and C pairs ... Genes are arranged linearly along long chains of DNA base-pair sequences. In bacteria, each cell usually contains a single ... These DNA strands are often extremely long; the largest human chromosome, for example, is about 247 million base pairs in ...
EuroCup Basketball
The survivors were paired into two-legged knockout ties, with the winners advancing to another set of two-legged ties. The ... For this purpose, the clubs from countries participating in the ABA League qualify for the competition based on their ... Clubs qualify for the competition based on their performance in their domestic leagues competitions. ...
Type 2 diabetes
"In Feinglos MN, Bethel MA (eds.). Type 2 diabetes mellitus: an evidence-based approach to practical management. Contemporary ... "The Concordance and Heritability of Type 2 Diabetes in 34,166 Twin Pairs From International Twin Registers: The Discordant ... Sun T, Han X (2019). "Death versus dedifferentiation: The molecular bases of beta cell mass reduction in type 2 diabetes". ... Threshold for diagnosis of diabetes is based on the relationship between results of glucose tolerance tests, fasting glucose or ...
Food web
... which is the number of links connecting to the base. The base of the food chain (primary producers or detritivores) is set at ... between every species pair in a web is averaged to compute the mean distance between all nodes in a web (D)[66] and multiplied ... The base or basal species in a food web are those species without prey and can include autotrophs or saprophytic detritivores ( ... It is the case that the biomass of each trophic level decreases from the base of the chain to the top. This is because energy ...
United States Merchant Marine Academy
In 1992, the academy acquired its largest campus-based training vessel, the T/V Kings Pointer. After 20 years at the academy, ... Midshipmen are typically assigned as pairs to a ship, an engineering cadet and a deck cadet, and operate as part of the crew, ...
Alternative medicine
Science Based Medicine *^ a b c d e f Barrett, Stephen; London, William M.; Kroger, Manfred; Hall, Harriet; Baratz, Robert S. ( ... In 2003, a project funded by the CDC identified 208 condition-treatment pairs, of which 58% had been studied by at least one ... "Science-Based Medicine. Archived from the original on 2013-09-28.. *^ a b Elsevier Science (2002). "Author interview (Edzard ... "Science-Based Medicine. 2016-04-04. Retrieved 2019-02-14.. *^ Atwood, K.C., IV (September-October 2003). "The Ongoing Problem ...
Eurasian magpie
Rossini's opera La gazza ladra and The Adventures of Tintin comic The Castafiore Emerald are based on this theme. However, one ... The European population is estimated to be between 7.5 and 19 million breeding pairs. Allowing for the birds breeding in other ... and the pairs often remain together from one breeding season to the next. They generally occupy the same territory on ... Union decided to treat the black-billed magpie as a separate species based on studies of the vocalization and behaviour that ...
Divisibility rule
Digit pair method of divisibility by 7 This method uses 1, −3, 2 pattern on the digit pairs. That is, the divisibility of any ... For example, in base 10, the factors of 101 include 2, 5, and 10. Therefore, divisibility by 2, 5, and 10 only depend on ... First we separate the number into three digit pairs: 15, 75 and 14.. Then we apply the algorithm: 1 × 15 − 3 × 75 + 2 × 14 = ... Although there are divisibility tests for numbers in any radix, or base, and they are all different, this article presents ...
Chi's Sweet Home
Yamada gets a new pair of jeans, but Chi prefers the old ones. ... Anime series based on manga. *Animated television series about ...
Clave (rhythm)
8 clave-based music is generated from cross-rhythm, it is possible to count or feel the 6. 8 clave in several different ways. ... The following afrobeat guitar part is a variant of the 2-3 onbeat/offbeat motif.[83] Even the melodic contour is guajeo-based. ... The standard bell is the key pattern used in bembé and so with compositions based on triple-pulse rhythms, it is the seven- ... The Congolese called this new music rumba, although it was based on the son. The Africans adapted guajeos to electric guitars ...
Bob Wills
While based in Sacramento, his radio broadcasts over 50,000-watt KFBK were heard all over the West.[43] ... paired with Herman Arnspiger, that he made his first commercial (though unissued) recordings in November 1929 for Brunswick/ ... The Austin-based Western swing band Asleep at the Wheel have honored Wills' music since the band's inception, mostly notably ...
Nowruz
... a pair of thin-soled giveh, and a pair of linen trousers.[138] ... of Religion and Ethics notes that the Purim holiday is based on ...
Maria-sama ga Miteru
Six brief manga one-shots, illustrated by Reine Hibiki and based on some scenes from the novels, were published by Shueisha in ... The fifth and tenth drama CDs by Shueisha were released in limited edition versions each with a slipcase and a pair of ... and Akira Matsushima based the character design used in the anime on Reine Hibiki's original designs. The art director for the ... The drama CDs are based on the stories in the novels. ... Anime and manga based on light novels. *Japanese LGBT-related ...
Phil Lynott
He was good friends with United and Northern Ireland star George Best, and the pair regularly socialised at the Clifton Grange ... He was known for his distinctive plectrum-based style on the bass, and for his imaginative lyrical contributions including ...
Streptococcus pneumoniae
The genome of S. pneumoniae is a closed, circular DNA structure that contains between 2.0 and 2.1 million base pairs depending ... S. pneumoniae can also be distinguished based on its sensitivity to lysis by bile, the so-called "bile solubility test". The ... For instance, the Xisco gene was recently described as a biomarker for PCR-based detection of S. pneumoniae and differentiation ... Diagnosis is generally made based on clinical suspicion along with a positive culture from a sample from virtually any place in ...
Positron emission tomography
Statistical, likelihood-based approaches: Statistical, likelihood-based [37][38] iterative expectation-maximization algorithms ... The system detects pairs of gamma rays emitted indirectly by a positron-emitting radioligand, most commonly fluorine-18, which ... based regularization in a wavelet or other domain), such as via Ulf Grenander's Sieve estimator[41][42] or via Bayes penalty ... Two major sources of noise in PET are scatter (a detected pair of photons, at least one of which was deflected from its ...
Leaf
... attachments are paired at each node and decussate if, as typical, each successive pair is rotated 90° progressing along ... More than one main vein (nerve) at the base. Lateral secondary veins branching from a point above the base of the leaf. Usually ... The leaves on this plant are arranged in pairs opposite one another, with successive pairs at right angles to each other ( ... BaseEdit. Acuminate. Coming to a sharp, narrow, prolonged point.. Acute. Coming to a sharp, but not prolonged point.. ...
I Parachute Battery (Bull's Troop) Royal Horse Artillery
After linking RHA batteries in pairs, just C Battery with 4th Regiment, Royal Horse Artillery in Egypt and K Battery at St ... it has been based in England, initially at Aldershot but latterly at Colchester.[61] ... Rather than disband existing batteries, they were instead linked in pairs. As a result, on 11 May, H Battery (from 8th Field ... currently based in Merville Barracks in Colchester. ...
Matthew Ashford
Ashford's pairing with Melissa Reeves' Jennifer was wildly popular (winning the 7th Soap Opera Digest award for favorite super ... In 2012, Ashford was recruited by the Outside the Box Musical Theatre Company for a new musical based on a Clint Eastwood movie ...
Dunning-Kruger effect
This belief was based on his misunderstanding of the chemical properties of lemon juice as an invisible ink.[3] ... The two papers employed paired, well-aligned instruments of known reliability to examine the evaluation of self-assessment ...
Mallard
... s usually form pairs (in October and November in the Northern Hemisphere) until the female lays eggs at the start of the ... The mallard is omnivorous and very flexible in its choice of food.[61] Its diet may vary based on several factors, including ... The drakes that end up being left out after the others have paired off with mating partners sometimes target an isolated female ...
Mandala
When paired with another mandala depicting the Five Wisdom Kings, this forms the Mandala of the Two Realms. ... The pattern of the dress was based on the Goloka Yantra mandala, shaped as a lotus with eight petals. Visitors were invited to ... The Taima mandala is based on the Contemplation Sutra, but other similar mandalas have been made subsequently. Unlike mandalas ... Mandalas have sometimes been used in Pure Land Buddhism to graphically represent Pure Lands, based on descriptions found in the ...
Level of measurement
Nominal measures are based on sets and depend on categories, a la Aristotle: Chrisman, Nicholas (March 1995). "Beyond Stevens: ... Multiplying together the conjugate pairs of uncertainty limits mentioned, however, I found that they formed invariant products ... Such arguments would be based on the fact that such measures do not really meet the requirements of an interval scale, because ... L. L. Thurstone made progress toward developing a justification for obtaining the interval type, based on the law of ...
Chloroplast DNA
Hypoxanthine can bind to cytosine, and when the XC base pair is replicated, it becomes a GC (thus, an A → G base change).[20] ... Chloroplast DNAs are circular, and are typically 120,000-170,000 base pairs long.[4][7][8] They can have a contour length of ... The inverted repeats vary wildly in length, ranging from 4,000 to 25,000 base pairs long each.[6] Inverted repeats in plants ... During replication, the cytosine will pair with guanine, causing an A → G base change. ...
Transistor
... a base-emitter junction and a base-collector junction, separated by a thin region of semiconductor known as the base region. ( ... A transistor can use a small signal applied between one pair of its terminals to control a much larger signal at another pair ... Also, as the base-emitter voltage (VBE) is increased the base-emitter current and hence the collector-emitter current (ICE) ... A bipolar transistor has terminals labeled base, collector, and emitter. A small current at the base terminal (that is, flowing ...
Black wildebeest
The horns have a broad base in mature males, and are flattened to form a protective shield. In females, the horns are both ... The pair usually separates after copulation, but the female occasionally follows her mate afterwards, touching his rump with ... Features necessary for defending a territory, such as the horns and broad-based skull of the modern black wildebeest, have been ... He based his description on an article written by natural philosopher Jean-Nicolas-Sébastien Allamand in 1776.[2] The generic ...
Barnacle
Free-living barnacles are attached to the substratum by cement glands that form the base of the first pair of antennae; in ... The eight pairs of thoracic limbs are referred to as "cirre", which are feathery and very long, being used to filter food, such ... The ovaries are located in the base or stalk, and may extend into the mantle, while the testes are towards the back of the head ... Larvae assess surfaces based upon their surface texture, chemistry, relative wettability, color, and the presence or absence ...
Hematopoietic stem cell transplantation
In addition, a genetic mismatch as small as a single DNA base pair is significant so perfect matches require knowledge of the ... One study based on a survey of medical teams covered approximately 24,000 peripheral blood HSCT cases between 1993 and 2005, ...
Glossary of graph theory terms
An ordered pair of vertices, such as an edge in a directed graph. An arrow (x, y) has a tail x, a head y, and a direction from ... based on vertex removals.. strong. 1. For strong connectivity and strongly connected components of directed graphs, see ... The line graph L(G) of a graph G is a graph with a vertex for each edge of G and an edge for each pair of edge that share an ... A non-edge or anti-edge is a pair of vertices that are not adjacent; the edges of the complement graph.. null graph. See empty ...
Octopus
The arms can be described based on side and sequence position (such as L1, R1, L2, R2) and divided into four pairs.[23][22] The ... Two possible extant cephalopod phylogenies, based on genetics studies by Strugnell et al. 2007, are shown in the possible ... The incirrate octopuses (the majority of species) lack the cirri and paired swimming fins of the cirrates.[32] In addition, the ... that surround the mouth and are attached to each other near their base by a webbed structure.[22] ...
Caulobacter crescentus
The Caulobacter CB15 genome has 4,016,942 base pairs in a single circular chromosome encoding 3,767 genes.[7] The genome ...
Wobble base pair - Wikipedia
A wobble base pair is a pairing between two nucleotides in RNA molecules that does not follow Watson-Crick base pair rules.[1] ... The thermodynamic stability of a wobble base pair is comparable to that of a Watson-Crick base pair. Wobble base pairs are ... tRNA base pairing schemes[edit]. The original wobble pairing rules, as proposed by Crick. Watson-Crick base pairs are shown in ... base on the mRNA, was not as spatially confined as the other two bases, and could, thus, have non-standard base pairing.[4] ...
A PAIRING-FREE IDENTITY BASED TRIPARTITE SIGNCRYPTION SCHEME
Identity-based cryptography is more efficient than certificate-based… ... The certificate-based cryptosystems is traditional way in providing the system parameters. ... Identity-based cryptography is more efficient than certificate-based cryptosystems. Each user in identity-based cryptography ... Identity-based cryptography is more efficient than certificate-based cryptosystems. Each user in identity-based cryptography ...
DNA Base Pairing Diagram
Apple seeks distance-based pairing, auto contact data patents
... lives easier by letting them pair wireless devices just by bringing them together as well as filling out missing address book ... A pair of filings for US patents made by Apple would make users ... Apple seeks distance-based pairing, auto contact data patents. ... A pair of filings for US patents made by Apple would make users lives easier by letting them pair wireless devices just by ... A representational model of Apples proximity-based wireless pairing patent.. System and method for opportunistic image sharing ...
Pairing-based cryptography - Wikipedia
Pairing-based cryptography is the use of a pairing between elements of two cryptographic groups to a third group with a mapping ... A contemporary example of using bilinear pairings is exemplified in the Boneh-Lynn-Shacham signature scheme. Pairing-based ... Koblitz, Neal; Menezes, Alfred (2005). "Pairing-Based cryptography at high security levels". LNCS. 3796. Galbraith, Steven; ... Lecture on Pairing-Based Cryptography Ben Lynns PBC Library. ... such as identity based encryption or attribute based encryption ...
Efficient Algorithms for Pairing-Based Cryptosystems | SpringerLink
In particular, our techniques improve pairing evaluation speed by a factor of about 55 compared to... ... We describe fast new algorithms to implement recent cryptosystems based on the Tate pairing. ... N.P. Smart, "An Identity Based Authenticated Key Agreement Protocol Based on the Weil Pairing," Electronics Letters, to appear. ... F. Hess, "Exponent Group Signature Schemes and Efficient Identity Based Signature Schemes Based on Pairings," Cryptology ePrint ...
CiteSeerX - Efficient algorithms for pairing-based cryptosystems
We describe fast new algorithms to implement recent cryptosystems based on the Tate pairing. In particular, our techniques ... the latter technique being also useful in contexts other than that of pairing-based cryptography. 1 ... improve pairing evaluation speed by a factor of about 55 compared to previously known methods in characteristic 3, and attain ... pairing-based cryptosystems efficient algorithm square root extraction evaluation speed tate pairing scalar multiplication ...
Base-pair substitution | genetics | Britannica.com
... to single base pairs, called base-pair substitutions. Many of these substitute an incorrect amino acid in the corresponding ... Some base-pair substitutions produce a stop codon. Normally, when a stop codon occurs at the end… ... Other articles where Base-pair substitution is discussed: mutation: … ... to single base pairs, called base-pair substitutions. Many of these substitute an incorrect amino acid in the corresponding ...
Non-canonical base pairing - Wikipedia
The A-U base pair is shown in Figure 5. In the G-C Watson-Crick base pair, like the A-T Hoogsteen base pair, the purine ( ... Wobble base pairing allows for the 5 anticodon to bond to a non-standard base pair. Examples of wobble base pairs are given in ... Hoogsteen base pair Wobble base pair Hermann T, Westhof E (December 1999). "Non-Watson-Crick base pairs in RNA-protein ... of bases in structured RNA participate in canonical Watson-Crick base pairs. Base pairing occurs when two bases form hydrogen ...
The deprotonated guanine-cytosine base pair | PNAS
... to the respective base plus deprotonated base, and GPAs (G-C → anion + H+) for the G-C base pair ... the N-H bond that is cleaved in the isolated base pairs is at the same site as the glycosidic N-C bond between the base pair ... base pairs, as well as the closed shell (13, 27) and H-abstracted (7, 11-13) individual bases. Bera and Schaefer (1) ... The deprotonated guanine-cytosine base pair. Maria C. Lind, Partha P. Bera, Nancy A. Richardson, Steven E. Wheeler, Henry F. ...
Base-pairing dictionary definition | base-pairing defined
... nounThe hydrogen bonding of complementary nitrogenous bases, one purine and one pyrimidine, in DNA and in hybrid molecules ... base-pairing. base-pair·ing. noun. The hydrogen bonding of complementary nitrogenous bases, one purine and one pyrimidine, in ... "base-pairing." YourDictionary, n.d. Web. 16 September 2018. ,http://www.yourdictionary.com/base-pairing,. ... base-pairing. (n.d.). Retrieved September 16th, 2018, from http://www.yourdictionary.com/base-pairing ...
What Are the Base Pairing Rules for DNA? | Reference.com
... in an A-T pairing and cytosine (C) with guanine (G) in a C-G pairing. Conversely, thymine... ... The base pairing rules for DNA are governed by the complementary base pairs: adenine (A) with thymine (T) ... The base pairing rules for DNA are governed by the complementary base pairs: adenine (A) with thymine (T) in an A-T pairing and ... Tired of Endless Searching? Find Base Pairing Rules In Dna on DownloadSearch. ...
What is the term that means base pairing? | Reference.com
... nucleotides are specifically matched to their complementary base pair. According to PBS, DNA resembles a long spiraling ladder ... A: The four steps of DNA replication are the unwinding of two coiled strands of DNA, complementary pairing of nucleotide bases ... During DNA replication, nucleotides are specifically matched to their complementary base pair. According to PBS, DNA resembles ... Cytosine always pairs with guanine, and adenine always pairs with thymine. These two strands of DNA each contain one side of ...
Dynamics of mismatched base pairs in DNA. - PubMed - NCBI
Dynamics of mismatched base pairs in DNA.. Guest CR1, Hochstrasser RA, Sowers LC, Millar DP. ... The interactions are strongest with X = T or C. The ability to discern differences in the strength of base-pairing interactions ... The structural dynamics of mismatched base pairs in duplex DNA have been studied by time-resolved fluorescence anisotropy decay ... These differences are correlated with the strength of base-pairing interactions in the various AP.X mismatches. ...
File Permissions | Pair Knowledge Base
Account Information | Pair Knowledge Base
You can email [email protected]pair.com to request a password reset.. Please do not email the Support team from an account that you will ... Your account username is listed in the Welcome Message you received from Pair Networks upon setting up a new hosting account. ... Your account password is listed in the Welcome Message you received from Pair Networks upon setting up a new hosting account. ... If you have completely forgotten your password, you can request a password reset from Pair Networks Support. Note that Support ...
Base pair - Wikipedia
Top, a G.C base pair with three hydrogen bonds. Bottom, an A.T base pair with two hydrogen bonds. Non-covalent hydrogen bonds ... published that his team designed an unnatural base pair (UBP).[12] The two new artificial nucleotides or Unnatural Base Pair ( ... "Highly specific unnatural base pair systems as a third base pair for PCR amplification". Nucleic Acids Research. 40 (6): 2793- ... "Highly specific unnatural base pair systems as a third base pair for PCR amplification". Nucleic Acids Research. 40 (6): 2793- ...
Base pairing small RNAs and their roles in global regulatory networks. - PubMed - NCBI
Many sRNAs regulate their target mRNAs through limited base-pairing interactions. Ongoing characterization of base-pairing ... Base pairing small RNAs and their roles in global regulatory networks.. Beisel CL1, Storz G. ... In this review, we describe the specific regulatory circuits that incorporate base-pairing sRNAs and the importance of each ... sRNA-based regulation buffers against signal fluctuations due to the time lag when sRNA production is shut off. All axes are ...
Base pair - definition of base pair by The Free Dictionary
base pair synonyms, base pair pronunciation, base pair translation, English dictionary definition of base pair. n. A pair of ... nitrogenous bases, consisting of a purine linked by hydrogen bonds to a pyrimidine, that connects the complementary strands of ... Related to base pair: DNA, complementary base pairing. base pair. n.. A pair of nitrogenous bases, consisting of a purine ... US-based aptamer discovery and development company Base Pair Biotechnologies, Inc has completed a USD 3.. Base Pair ...
AT - Adenine-Thymine (DNA base pairing) | AcronymFinder
DNA base pairing). AT is defined as Adenine-Thymine (DNA base pairing) very frequently. ... DNA base pairing) abbreviated? AT stands for Adenine-Thymine ( ... DNA-base-pairing)-(AT).html,AT,/a,. Citations. *MLA style: "AT ... n.d.) Acronym Finder. (2020). Retrieved December 3 2020 from https://www.acronymfinder.com/Adenine_Thymine-(DNA-base-pairing)-( ... S.v. "AT." Retrieved December 3 2020 from https://www.acronymfinder.com/Adenine_Thymine-(DNA-base-pairing)-(AT).html ...
6KCS: Base Pair Morphology Parameters
Metal Interactions with Nucleobases, Base Pairs, and Oligomer Sequences; Computational Approach | SpringerLink
The structure of metallo-DNA with consecutive T-HgII-T base-pairs ex-plains positive reaction entropy for the metallo-base-pair ... and Co2+ ions on the guanine base in Watson-Crick and reverse Watson-Crick base pairs. Journal of Physical Chemistry B, 113(47 ... Marino, T. (2014). DFT investigation of the mismatched base pairs (T-Hg-T)3, (U-Hg-U)3, d(T-Hg-T)2, and d(U-Hg-U)2. Journal of ... Fortino, M., Marino, T., & Russo, N. (2015). Theoretical study of silver-ion-mediated base pairs: The case of C-Ag-C and C-Ag-A ...
RFC 6767 - Ethernet-Based xDSL Multi-Pair Bonding (G.Bond/Ethernet) MIB
Ethernet-Based xDSL Multi-Pair Bonding (G.Bond/Ethernet) MIB Abstract This document defines a Management Information Base (MIB ... use G.hs-based protocol (default) cpBACP(2) - use frame-based BACP Note that G.hs-based protocol support is mandatory, ... Introduction Ethernet-based xDSL Multi-Pair Bonding, a.k.a. G.Bond/Ethernet, is specified in ITU-T Recommendation G.998.2 [G. ... This document defines an extension to the GBOND-MIB module with a set of objects for managing Ethernet-based multi-pair bonded ...
A Pair of Acupuncture Studies - Science-Based Medicine
BP - Base Pair (nucleic acids) | AcronymFinder
BP stands for Base Pair (nucleic acids). BP is defined as Base Pair (nucleic acids) very frequently. ... T base pair and a G:C base pair.. DNA and RNA structure: nucleic acids as genetic material. lindheimeri, 4 fragments, 202 base- ... We attempted to form a stable triplex DNA structure within an eight base pair bulged/mismatched region of a 32 base pair length ... but now what you have is no longer a Watson-Crick base pair; its something called a Hoogsteen base pair. ...
USER-CGDNA quasi-unique base pairing by ohenrich · Pull Request #1730 · lammps/lammps · GitHub
Implementation Notes (1) Unique base pairing means that a nucleotide can only form a base pair with a specific complementary ... Quasi-unique base pairing means that hybridisation between non-original complementary bases is only prevented over a limited ... Delete lines that dont apply The feature has been verified to work with the CMake based build system ... Summary The changes in this pull request comprise an enhancement in form of quasi-unique base pairing, minor restructuring in ...
Amber Diamond Point Peg Style Votive Cups & Swirl Base Candle Holders - Pair | eBay
Candle holders have a raised base with swirl pattern. This 2 piece candle holder is in great condition. Amber Diamond Point ... Details about Amber Diamond Point Peg Style Votive Cups & Swirl Base Candle Holders - Pair. ... Amber Diamond Point Peg Style Votive Cups & Swirl Base Candle Holders - Pair ... Amber Diamond Point Peg Style Votive Cups & Swirl Base Candle Holders - Pair ...
A retroviral RNA kissing complex containing only two G⋅C base pairs | PNAS
The bases on the ends of the tetraloop (G8, G11) stack on the closing A7⋅U12 base pair; G8 base stacks on A7 base and G11 base ... C base pairs were observed only for the base pair in the loop, not for the base pairs in the stem region. Therefore, only the G ... The stacking between the A9 base and the intermolecular G11⋅C10 base pair (Left). The hydrogen bonds in the G11⋅C10 base pairs ... Second, if G8 formed an intermolecular base pair with C10, it would place an A9⋅A9 mismatch between the two G8⋅C10 base pairs. ...
Earthworks FlexWand FW430 with Cast-Iron Base (Matched Pair) | Musician's Friend
Matched Pair) at Musicians Friend. Get a low price and free shipping on thousands of... ... Get the guaranteed best price on Condenser Microphones like the Earthworks FlexWand FW430 with Cast-Iron Base ( ... Earthworks FlexWand FW430 with Cast-Iron Base (Matched Pair). #preHeaderPromoBar { background-color: #007ba9; min-height: 1.5em ... Dimensions: Stand 47³ (1.39m); Base 12³ (30.5cm) in diameter, 1.1³ (2.7cm) high. Weight: Stand 2 lbs (.9kg); Cast iron base ...
Base Pair Bio to develop POC tests for opioids in newborns
Base Par Biotecnologias, Inc., a empresa da descoberta de Aptamer™, anunciada hoje o recibo de um subsídio de investigação da ... Base Pair Biotechnologies, Inc.. Biotecnologias baixas dos pares para desenvolver testes do ponto--cuidado para opiáceo nos ... Base Pair Biotechnologies, Inc.. Biotecnologias baixas dos pares para desenvolver testes do ponto--cuidado para opiáceo nos ... Base Pair Biotechnologies, Inc.. 2019. Biotecnologias baixas dos pares para desenvolver testes do ponto--cuidado para opiáceo ...
ThymineWatson-CrickCytosineNucleic acidMoleculesInteractionsWobble baseCryptographyNucleotide basesDouble strandedMismatchesCanonicalNucleobasesGenesPurine-pyrimidineNucleotidesCryptosystemsSequenceBillion base pairsComplementary nucleotideMoleculeTRNAComplementarityHoogsteenOccurUracilLigand-receptor pairsStableMRNASpecificityConformationCryptographicTateCodonDuplexElliptic curveAbstractGeometriesGeneticGenomeChiralPyrimidineChargaff'sStructuralIntermolecularNaehrigSecondaryReplicationHydrogen bondInosineSchemeAdvances
Thymine13
- The four nucleotide bases in DNA are guanine, cytosine, adenine and thymine. (reference.com)
- The guanine base is always paired with the complementary cytosine base, and the adenine base is always paired with the complementary thymine base. (reference.com)
- The guanine-cytosine base pair is represented as G-C, and the adenine-thymine base pair is represented as A-T. In a DNA molecule, the G-C base pair is linked by two hydrogen bonds, and the A-T base pair is linked by three hydrogen bonds. (reference.com)
- Non-canonical base pairing occurs when nucleobases hydrogen bond, or base pair, to one another in schemes other than the standard Watson-Crick base pairs (which are adenine (A) -- thymine (T) in DNA, adenine (A) -- uracil (U) in RNA, and guanine (G) -- cytosine (C) in both DNA and RNA). (wikipedia.org)
- The base pairing rules for DNA are governed by the complementary base pairs: adenine (A) with thymine (T) in an A-T pairing and cytosine (C) with guanine (G) in a C-G pairing. (reference.com)
- Conversely, thymine only binds with adenine in a T-A pairing and guanine only binds with cytosine in a G-C pairing. (reference.com)
- Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs ( guanine - cytosine and adenine - thymine ) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence . (wikipedia.org)
- The base pairs are adenine-thymine and guanine-cytosine in DNA, and adenine-uracil and guanine-cytosine in RNA. (thefreedictionary.com)
- The term 'Base pair (bp)' as it applies to the area of gnome research can be defined as 'Two nitrogenous bases (adenine and thymine or guanine and cytosine) held together by weak bonds. (teachmefinance.com)
- In the canonical Watson-Crick base pairing , adenine (A) forms a base pair with thymine (T), as does guanine (G) with cytosine (C) in DNA. (wikidoc.org)
- Computer artwork of an A-T (adenine-thymine) base pair. (sciencephoto.com)
- The pairing of complementary nucleotide bases (adenine and thymine, guanine and cytosine) to each other via hydrogen bonds from opposite strands of a double stranded nucleic acid (such as DNA or RNA), thereby holding the double-stranded nucleic acid together. (healthboard.com)
- DNA has four nitrogenous bases: (A) adenine, (T) thymine, (C) cytosine, and (G) guanine. (enotes.com)
Watson-Crick19
- A wobble base pair is a pairing between two nucleotides in RNA molecules that does not follow Watson-Crick base pair rules. (wikipedia.org)
- The thermodynamic stability of a wobble base pair is comparable to that of a Watson-Crick base pair. (wikipedia.org)
- If each tRNA molecule paired with its complementary mRNA codon using canonical Watson-Crick base pairing, then 64 types (species) of tRNA molecule would be required. (wikipedia.org)
- It is, therefore, possible for non-Watson-Crick base pairing to occur at the third codon position, i.e., the 3' nucleotide of the mRNA codon and the 5' nucleotide of the tRNA anticodon. (wikipedia.org)
- The first two bases in the codon create the coding specificity, for they form strong Watson-Crick base pairs and bond strongly to the anticodon of the tRNA. (wikipedia.org)
- If the first nucleotide in the anticodon is a C or an A pairing is specific and acknowledges original Watson-Crick pairing, that is only one specific codon can be paired to that tRNA. (wikipedia.org)
- James Watson and Francis Crick published the double helical structure of DNA and proposed the canonical Watson-Crick base pairs in 1953. (wikipedia.org)
- Since the structures of the canonical Watson-Crick and non-canonical Hoogsteen base pairs were determined, many other types of non-canonical base pairs have been presented and described. (wikipedia.org)
- An estimated 60% of bases in structured RNA participate in canonical Watson-Crick base pairs. (wikipedia.org)
- Those are known as the Watson-Crick edge(WC), the Hoogsteen edge(H), and the Sugar edge(S). Pyrimidine bases also have three hydrogen-bonding edges. (wikipedia.org)
- Like the puring, there is the Watson-Crick edge(WC) and the Sugar edge(S) but the third edge is referred to as the "C-H" edge(H) on the pyrimidine bases. (wikipedia.org)
- Energetic properties and optimized geometries of 10 radicals and their respective anions derived through hydrogen abstraction from the Watson-Crick guanine-cytosine (G-C) base pair have been studied using reliable theoretical methods. (pnas.org)
- This is particularly important in RNA molecules (e.g., transfer RNA ), where Watson-Crick base pairs (guanine-cytosine and adenine- uracil ) permit the formation of short double-stranded helices, and a wide variety of non-Watson-Crick interactions (e.g. (wikipedia.org)
- The influence of Li+, Na+, Mg2+, Ca2+, and Zn2+ ions on the hydrogen bonds of the Watson-Crick base pair. (springer.com)
- The sequence crystallises as a B-DNA helix with 10 Watson-Crick base-pairs (4 A.T. and 6 G.C) and 2 inosine.adenine (I.A) pairs. (rcsb.org)
- Both duplexes are standard A form, with Watson-Crick base pairing throughout. (rcsb.org)
- The C-based imino-oxo and imino-enol GC tautomers, which can be generated during the UV irradiation of the Watson-Crick base pair, have analogous radiationless energy-decay channels to those of the canonical base pair. (diva-portal.org)
- stacking+Watson-Crick base pairing) in phenix.refine? (phenix-online.org)
- The complementary Watson-Crick base pairs, A-T and G-C. (chemistryexplained.com)
Cytosine3
- In the present study, the CASSCF/CASPT2 methodology is used to map the two-dimensional potential energy surfaces along the stretched NH reaction coordinates of the guanine-cytosine (GC) base pair. (diva-portal.org)
- Here, we study nuclear quantum effects (NQEs) using deuterium isotope-induced changes of nitrogen NMR chemical shifts in a model base pair consisting of two tautomers of isocytosine, which form hydrogen-bonded dimers in the same way as the guanine-cytosine base pair. (rsc.org)
- The presence of an uncomplimentary base in double-stranded DNA caused by spontaneous deamination of cytosine or adenine, mismatching during homologous recombination, or errors in DNA replication. (umassmed.edu)
Nucleic acid5
- Density functional theory study of interaction, bonding and affinity of group IIb transition metal cations with nucleic acid bases. (springer.com)
- Binding of Pt(NH3)3 2+ to nucleic acid bases. (springer.com)
- We use a single molecule computational engine to track individual molecules interacting with and along nucleic acid polymers at single base resolution. (mit.edu)
- All the interactions between nucleic acid molecules that help express genetic information involve base‐pairing between complementary sequences. (cliffsnotes.com)
- The researchers found that the nucleic acid base pairs making up the steps of DNA's spiral staircase are continuously shape-shifting. (thefreedictionary.com)
Molecules15
- These terminate translation by binding to release factors rather than tRNA molecules, so canonical pairing would require 61 species of tRNA. (wikipedia.org)
- The hydrogen bonding of complementary nitrogenous bases, one purine and one pyrimidine, in DNA and in hybrid molecules joining DNA and RNA. (yourdictionary.com)
- purine-purine pairings are energetically unfavorable because the molecules are too close, leading to overlap repulsion. (wikipedia.org)
- Paired DNA and RNA molecules are comparatively stable at room temperature, but the two nucleotide strands will separate above a melting point that is determined by the length of the molecules, the extent of mispairing (if any), and the GC content. (wikipedia.org)
- A pair of nitrogenous bases, consisting of a purine linked by hydrogen bonds to a pyrimidine, that connects the complementary strands of DNA or of hybrid molecules joining DNA and RNA. (thefreedictionary.com)
- Given our current understanding of gene expression, and the goals of biotechnology research, both scientists and engineers would benefit from detailed simulators that can explicitly compute genome-wide expression levels as a function of individual molecular events, including the activities and interactions of molecules on DNA at single base pair resolution. (mit.edu)
- Pairing is also the mechanism by which codons on messenger RNA molecules are recognized by anticodons on transfer RNA during protein translation . (wikidoc.org)
- If the bases don't pair before they are part of polymers, how would the bases have been selected out from the many molecules in the "prebiotic soup" so that RNA polymers could be formed? (bio-medicine.org)
- Researchers at the Georgia Institute of Technology are exploring an alternate theory for the origin of RNA: they think the RNA bases may have evolved from a pair of molecules distinct from the bases we have today. (bio-medicine.org)
- This theory looks increasingly attractive, as the Georgia Tech group was able to achieve efficient, highly ordered self-assembly in water with small molecules that are similar to the bases of RNA. (bio-medicine.org)
- These "proto-RNA bases" spontaneously assemble into gene-length linear stacks, suggesting that the genes of life could have gotten started from these or similar molecules. (bio-medicine.org)
- Learn how DNA molecules are composed of four different types of nucleotides that pair with each other in a very specific, complementary manner. (study.com)
- Complementary base pairing describes the manner in which the nitrogenous bases of the DNA molecules align with each other. (study.com)
- This two-unnatural-base-pair system, combining the Ds - Px and Ds - Pa pairs with modified Pa substrates, provides a powerful tool for the site-specific labeling and modification of desired positions in large RNA molecules. (hindawi.com)
- Thus, several unnatural base pairs that function in polymerase reactions have rapidly been developed for site-specific labeling of RNA molecules [ 7 - 18 ]. (hindawi.com)
Interactions16
- There are three main types of non-canonical base pairs: those stabilized by polar hydrogen bonds, those having interactions among C−H and O/N groups, and those that have hydrogen bonds between the bases themselves. (wikipedia.org)
- The actual number of base-pair combinations is lower because some combinations result in non-favorable interactions. (wikipedia.org)
- These surroundings can consist of adjacent base pairs, adjacent loops, or third interactions (such as a base triple). (wikipedia.org)
- The spatial interactions between the two bases can be classified in 6 rigid-body parameters or intra-base pair parameters (3 translational, 3 rotational) as shown in Figure 4. (wikipedia.org)
- These differences are correlated with the strength of base-pairing interactions in the various AP.X mismatches. (nih.gov)
- The interactions are strongest with X = T or C. The ability to discern differences in the strength of base-pairing interactions at a specific site in DNA by observing their effect on the dynamics of base motion is a novel aspect of the present study. (nih.gov)
- Many sRNAs regulate their target mRNAs through limited base-pairing interactions. (nih.gov)
- The first part focuses on the interactions of isolated bases with metal cations either in bare, hydrated, or ligated forms. (springer.com)
- Cross-strand interactions of the adenines adjacent to the intermolecular G⋅C base pairs, plus unusual strong electrostatic interactions around the base pairs, contribute to the unexpected stability. (pnas.org)
- The pairing observed in this study is presented as a model for I.A base-pairs in RNA codon-anticodon interactions and may help explain the thermodynamic stability of inosine containing base-pairs. (rcsb.org)
- Conformational parameters and base stacking interactions are presented and where appropriate compared with those of the native compound, d(C-G-C-G-A-A-T-T-C-G-C-G) and with other studies of oligonucleotides containing purine.purine base-pairs. (rcsb.org)
- Base stacking interactions between the pi orbitals of the bases' aromatic rings also contribute to stability, and again GC stacking interactions with adjacent bases tend to be more favorable. (wikidoc.org)
- The base pairs that hold together two pieces of RNA, the older cousin of DNA, are some of the most important molecular interactions in living cells. (bio-medicine.org)
- It is important to note that the presence of an incorrect tautomeric form in DNA would engender very different hydrogen bonding interactions, and the structural complementarity of base pairs would, in this instance, not exist. (chemistryexplained.com)
- Therefore, various strategies were followed to identify candidate pairs, such as transcriptional analyses at cellular resolution, microscopic characterization of loss and gain-of-function plants, genetic interaction studies, and biochemical assays demonstrating direct physical interactions (see e.g. (frontiersin.org)
- This novel approach represents a major leap forward regarding ligand-receptor pairing, but does not take the ligand-receptor interactions into account that rely on a protein complex status involving co-receptors and/or interacting proteins. (frontiersin.org)
Wobble base3
- The GU pairing, with two hydrogen bonds, does occur fairly often in RNA (see wobble base pair ). (wikipedia.org)
- A wobble base pair is a G-U and I-U / I-A / I-C pair fundamental in RNA secondary structure . (wikidoc.org)
- The G x U wobble base pair. (wikidoc.org)
Cryptography9
- Pairing-based cryptography is the use of a pairing between elements of two cryptographic groups to a third group with a mapping e : G 1 × G 2 → G T {\displaystyle e:G_{1}\times G_{2}\to G_{T}} to construct or analyze cryptographic systems. (wikipedia.org)
- Pairing-based cryptography relies on hardness assumptions separate from e.g. the Elliptic Curve Discrete Logarithm Problem, which is older and has been studied for a longer time. (wikipedia.org)
- Identity-based cryptography is more efficient than certificate-based cryptosystems. (slideshare.net)
- Each user in identity-based cryptography uses any arbitrary string that uniquely identifies him as his public key. (slideshare.net)
- 1. International Journal on Cryptography and Information Security (IJCIS), Vol.3, No. 4, December 2013 A PAIRING-FREE IDENTITY BASED TRIPARTITE SIGNCRYPTION SCHEME Hassan M. Elkamchouchi 1, Eman F. Abou Elkheir2 and Yasmine Abouelseoud3 1 2 Elec. (slideshare.net)
- In particular, our techniques improve pairing evaluation speed by a factor of about 55 compared to previously known methods in characteristic 3, and attain performance comparable to that of RSA in larger characteristics.We also propose faster algorithms for scalar multiplication in characteristic 3 and square root extraction over F p m , the latter technique being also useful in contexts other than that of pairing-based cryptography. (springer.com)
- We also propose faster algorithms for scalar multiplication in characteristic 3 and square root extraction over Fpm, the latter technique being also useful in contexts other than that of pairing-based cryptography. (psu.edu)
- This book constitutes the refereed proceedings of the 6th International Conference on Pairing-Based Cryptography, Pairing 2013, held in Beijing, China, in November 2013. (springer.com)
- As in previous years, the focus of Pairing 2013 is on all aspects of pairing-based cryptography, including: cryptographic primitives and protocols, mathematical foundations, software and hardware implementation, as well as applied security. (springer.com)
Nucleotide bases4
- Complementary base pairing refers to the structural pairing of nucleotide bases in deoxyribonucleic acid, which is commonly known as DNA. (reference.com)
- DNA is made up of four nucleotide bases, each of which pairs with only one of the other bases. (reference.com)
- A DNA molecule is composed of two connected strands of nucleotide bases, which form a spiraling double helix structure. (reference.com)
- The two strands of nucleotide bases are arranged such that every base in the first strand is paired to its complementary base in the second strand. (reference.com)
Double stranded3
- The presence of non-canonical base pairs in double stranded DNA results in a disrupted double helix. (wikipedia.org)
- The size of an individual gene or an organism's entire genome is often measured in base pairs because DNA is usually double-stranded. (wikipedia.org)
- The following DNA sequences illustrate pair double-stranded patterns. (wikidoc.org)
Mismatches2
- The correlation time and angular range of internal rotation of AP vary among the series of AP.X mismatches, showing that the native DNA bases differ in their ability to influence the motion of AP. (nih.gov)
- these pairings are mismatches because the patterns of hydrogen donors and acceptors do not correspond. (wikipedia.org)
Canonical2
- The first discovered non-canonical base pairs are Hoogsteen base pairs, which were first described by American biochemist Karst Hoogsteen. (wikipedia.org)
- Non-canonical base pairings commonly occur in the secondary structure of RNA (e.g. pairing of G with U), and in tRNA recognition. (wikipedia.org)
Nucleobases2
- A base pair ( bp ) is a unit consisting of two nucleobases bound to each other by hydrogen bonds . (wikipedia.org)
- It has been hypothesised that proton tunnelling between paired nucleobases significantly enhances the formation of rare tautomeric forms and hence leads to errors in DNA replication. (rsc.org)
Genes11
- Many DNA-binding proteins can recognize specific base-pairing patterns that identify particular regulatory regions of genes. (wikipedia.org)
- The haploid human genome (23 chromosomes ) is estimated to be about 3.2 billion bases long and to contain 20,000-25,000 distinct protein-coding genes. (wikipedia.org)
- The sequencing results show that the Aspergillus oryzae genome has about 38 million base pairs and 12,000 genes. (acronymfinder.com)
- for reference, the 39,937 base pair T7 genome encodes 56 genes that are transcribed by two types of RNA polymerases active across 22 promoters. (mit.edu)
- Some DNA- or RNA-binding enzymes can recognize specific base pairing patterns that identify particular regulatory regions of genes. (wikidoc.org)
- Our analysis suggests that the per-base-pair mutation rates at two genes differ significantly (3.80 × 10 −10 at URA3 and 6.44 × 10 −10 at CAN1 ) and we propose a definition for the effective target size of genes (the probability that a mutation inactivates the gene) that acknowledges that the mutation rate is nonuniform across the genome. (genetics.org)
- The identification of ligand-receptor pairs is technically very challenging, as the genes encoding them regularly belong to gene families with multiple members and are often low expressed, and this only in certain cell types or during specific developmental stages. (frontiersin.org)
- However, our understanding of the mechanism of somatic homolog pairing remains unclear, as only a few genes have been implicated in this process. (harvard.edu)
- We identified both candidate "pairing promoting genes" and candidate "anti-pairing genes," providing evidence that pairing is a dynamic process that can be both enhanced and antagonized. (harvard.edu)
- Many of the genes found to be important for promoting pairing are highly enriched for functions associated with mitotic cell division, suggesting a genetic framework for a long-standing link between chromosome dynamics during mitosis and nuclear organization during interphase. (harvard.edu)
- In contrast, several of the candidate anti-pairing genes have known interphase functions associated with S-phase progression, DNA replication, and chromatin compaction, including several components of the condensin II complex. (harvard.edu)
Purine-pyrimidine2
- Consequently, the mechanisms of primary and secondary damage to purine-pyrimidine base pairs have been under intense investigation in recent years ( 1 ⇓ ⇓ ⇓ ⇓ ⇓ ⇓ ⇓ ⇓ ⇓ ⇓ ⇓ ⇓ ⇓ - 15 ). (pnas.org)
- Purine-pyrimidine base-pairing of AT or GC or UA (in RNA) results in proper duplex structure. (wikipedia.org)
Nucleotides6
- When reading 5' to 3' the first nucleotide in the anticodon (which is on the tRNA and pairs with the last nucleotide of the codon on the mRNA) determines how many nucleotides the tRNA actually distinguishes. (wikipedia.org)
- The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA and RNA polymerase transcribes DNA into RNA. (wikipedia.org)
- Hence, the number of total base pairs is equal to the number of nucleotides in one of the strands (with the exception of non-coding single-stranded regions of telomeres ). (wikipedia.org)
- In molecular biology , two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair (often abbreviated bp). (wikidoc.org)
- In case of single stranded DNA/RNA we talk about nucleotides , abbreviated nt (or knt, Mnt, Gnt), rather than base pairs, as they are not paired. (wikidoc.org)
- Students can assemble the nucleotides, feel the hydrogen bonding of the A-T and G-C base pairs, and discover the double helical structure of DNA. (enasco.com)
Cryptosystems2
- The certificate-based cryptosystems is traditional way in providing the system parameters. (slideshare.net)
- We describe fast new algorithms to implement recent cryptosystems based on the Tate pairing. (springer.com)
Sequence10
- Since every nucleotide base is always paired with its complement, you can always deduce the sequence of the second strand if you can identify the sequence of bases in the first strand. (reference.com)
- An oligodeoxynucleotide triplex is formed with a particular base sequence in a pH-dependent manner. (nih.gov)
- In addition, base-pairing between transfer RNA (tRNA) and messenger RNA (mRNA) forms the basis for the molecular recognition events that result in the nucleotide sequence of mRNA becoming translated into the amino acid sequence of proteins via the genetic code . (wikipedia.org)
- note that the two terminal G⋅C base pairs are different from the native sequence. (pnas.org)
- The sequence alignment reinforced the high conservation of the trnL intron, and it showed a few random base pair substitutions. (thefreedictionary.com)
- Sequence specific assembly of two PNA /peptide hybrids can be achieved by PNA base pairing. (cuvillier.de)
- Formation of esters between phenols and benzoic acids has been used as a base-pairing strategy for sequence information transfer in template-directed synthesis of linear oligomers, but the copy strand produced by this process has the complementary sequence to the template strand. (rsc.org)
- Although many ligands were predicted based on sequence signatures, ligands of shorter sequences have not been identified, together with many "orphan" receptors without known ligands. (nih.gov)
- A DNA strand has the base sequence of ACGT. (enotes.com)
- So if all of the bases we sequenced were from the same organism, in principle, we have collected enough data to sequence the virus genome 20,000 times over, the bacterial genome about 200 times over, and about a quarter of the mouse genome. (nasa.gov)
Billion base pairs3
- The human genome is approximately three billion letters (or base pairs) long, and in a typical experiment we generate seven or eight billion base pairs of raw sequencing data. (bms.com)
- Each human cell contains approximately 3 billion base pairs. (ehd.org)
- I [have a] genomics background, [so] I get really excited about that kind of stuff," Rubins said in a downlink shortly after reaching the one billion base pairs sequenced goal. (nasa.gov)
Complementary nucleotide1
- 1) Unique base pairing means that a nucleotide can only form a base pair with a specific complementary nucleotide, usually the original hybridisation partner in a duplex during initialisation. (github.com)
Molecule4
- We attempted to form a stable triplex DNA structure within an eight base pair bulged/mismatched region of a 32 base pair length DNA duplex using coralyne as a stabilizing intercalating molecule for the triplex. (acronymfinder.com)
- We confirm that single molecule, base-pair resolved simulation using TABASCO (Tabasco) can accurately compute gene expression dynamics and, moving beyond previous simulators, provide for the direct representation of intermolecular events such as polymerase collisions and promoter occlusion. (mit.edu)
- Conclusion Tabasco enables genome-scale simulation of transcription and translation at individual molecule and single base-pair resolution. (mit.edu)
- only some of the nitrogenous bases of DNA can interact to form a stable DNA molecule. (study.com)
TRNA4
- Since most organisms have fewer than 45 species of tRNA, [3] some tRNA species must pair with more than one codon. (wikipedia.org)
- Movement ("wobble") of the base in the 5' anticodon position is necessary for small conformational adjustments that affect the overall pairing geometry of anticodons of tRNA. (wikipedia.org)
- If the first nucleotide is U or G, the pairing is less specific and in fact two bases can be interchangeably recognized by the tRNA. (wikipedia.org)
- Inosine displays the true qualities of wobble, in that if that is the first nucleotide in the anticodon then any of three bases in the original codon can be matched with the tRNA. (wikipedia.org)
Complementarity1
- In the case of nucleic acids, complementarity generally involves base pairing. (cliffsnotes.com)
Hoogsteen3
- The G-C Hoogsteen base pair was first observed via X-ray crystallography years later, in 1986, by co-crystallizing DNA with triostin A (an antibiotic). (wikipedia.org)
- it's something called a Hoogsteen base pair . (acronymfinder.com)
- common such patterns are Hoogsteen base pairs . (wikidoc.org)
Occur3
- Intramolecular base pairs can occur within single-stranded nucleic acids. (wikipedia.org)
- It should be noted that the GU pairing, with two hydrogen bonds, does occur fairly often in RNA but rarely in DNA . (wikidoc.org)
- What is the complementary RNA base pairing that would occur during transcription? (enotes.com)
Uracil1
- RNA contains three of these bases - (A),(C), and (G) but not (T). Uracil (U) is found in its place and complements adenine (A) instead. (enotes.com)
Ligand-receptor pairs2
- Based on the conserved signaling among paralogous receptors and common knock-out phenotypes of ligand-receptor pairs, relationships between relaxin family peptides and leucine-rich repeat-containing, G protein-coupled receptors (LGR) were revealed. (nih.gov)
- Future development of tools for predicting ligands and high throughput assays to identify ligand-receptor pairs based on ligand binding and/or signal transduction could advance hormone-based physiology and pathophysiology. (nih.gov)
Stable5
- They are typically less stable than standard base pairings. (wikipedia.org)
- The most stable deprotonated base pair corresponds to the radical with the largest adiabatic electron affinity, 3.65 eV. (pnas.org)
- Surprisingly, it forms a stable, homodimeric kissing complex through only two intermolecular G⋅C base pairs. (pnas.org)
- as a consequence, the GC pair is more stable. (wikidoc.org)
- In addition, the C-based imino-enol GC tautomer is thermally less stable. (diva-portal.org)
MRNA2
- He postulated that the 5' base on the anticodon, which binds to the 3' base on the mRNA , was not as spatially confined as the other two bases, and could, thus, have non-standard base pairing. (wikipedia.org)
- The resulting new strand of mRNA has complementary base pairs to the original DNA template. (enotes.com)
Specificity2
- Aside from the obvious necessity of wobble, that our bodies have a limited amount of tRNAs and wobble allows for broad specificity, wobble base pairs have been shown to facilitate many biological functions, most clearly proven in the bacterium Escherichia coli . (wikipedia.org)
- In particular, a modified Px base, 4-(4,5-dihydroxypent-1-yn-1-yl)-2-nitropyrrole (Diol1 -Px , Figure 1 ), has extremely high specificity as a pairing partner of Ds , and thus the misincorporation rates of Diol1 - d Px TP and d Ds TP opposite the natural bases in templates during PCR amplification are as low as 0.005% per base pair per replication [ 20 ]. (hindawi.com)
Conformation3
- These parameters describe the base pairs' three dimensional conformation. (wikipedia.org)
- Two hydrogen bonds link the I.A. base-pair, one between N-1(I) and N-7(A), the other between O-6(I) and N-6(A). This bulky purine.purine base-pair is incorporated in the double helix at two positions with little distortion of either local or global conformation. (rcsb.org)
- Perhaps surprisingly, these crystals of the 18 base pair RNA exhibit a 36-fold static disorder, resulting in a structure with a single sugar-phosphate backbone conformation and an averaged base composition at each residue. (rcsb.org)
Cryptographic1
- While first used for cryptanalysis, pairings have also been used to construct many cryptographic systems for which no other efficient implementation is known, such as identity based encryption or attribute based encryption schemes. (wikipedia.org)
Tate2
- For example, in groups equipped with a bilinear mapping such as the Weil pairing or Tate pairing, generalizations of the computational Diffie-Hellman problem are believed to be infeasible while the simpler decisional Diffie-Hellman problem can be easily solved using the pairing function. (wikipedia.org)
- S. Galbraith, K. Harrison and D. Soldera, "Implementing the Tate pairing," Algorithm Number Theory Symposium - ANTS V, Lecture Notes in Computer Science 2369 , Springer-Verlag, to appear. (springer.com)
Codon3
- Some base-pair substitution s produce a stop codon. (britannica.com)
- The genetic code makes up for disparities in the number of amino acids (20) for codons (64), by using modified base pairs in the first base of the anti-codon . (wikidoc.org)
- He postulated that the 5' base on the anti-codon was not as spatially confined as the other two bases, and could thus have non-standard base pairing. (wikidoc.org)
Duplex2
- It is possible to form a base-pair between two benzoic acids by using a hydroquinone linker, which is eliminated when the product duplex is hydrolysed. (rsc.org)
- duplexes showed only minor changes in the backbone structure and revealed a structural switch around the base-linker unit to be responsible for the generation of enantiomorphic duplex structures. (epfl.ch)
Elliptic curve1
- This paper proposes a new identity-based tripartite signcryption scheme based on the elliptic curve discrete logarithm problem. (slideshare.net)
Abstract1
- Internet Engineering Task Force (IETF) E. Beili Request for Comments: 6767 Actelis Networks Category: Standards Track M. Morgenstern ISSN: 2070-1721 ECI Telecom February 2013 Ethernet-Based xDSL Multi-Pair Bonding (G.Bond/Ethernet) MIB Abstract This document defines a Management Information Base (MIB) module for use with network management protocols in TCP/IP-based internets. (ietf.org)
Geometries1
- Therefore, with the cis/trans forms and the 3 hydrogen bond edges, there are 12 basic types of base pairing geometries which can be found in RNA structures. (wikipedia.org)
Genetic4
- Wobble base pairs are fundamental in RNA secondary structure and are critical for the proper translation of the genetic code . (wikipedia.org)
- [1] The complementary nature of this based-paired structure provides a redundant copy of the genetic information encoded within each strand of DNA. (wikipedia.org)
- The positioning of these base pairs along the DNA chain is what is known as the genetic code. (sciencephoto.com)
- His next goal is to determine whether the proto-RNA bases can be linked by a backbone to form a polymer that could have functioned as a genetic material. (bio-medicine.org)
Genome7
- In the Human genome, it is about 1 million base pairs [2] [3] . (wikidoc.org)
- Although mutation rates are a key determinant of the rate of evolution they are difficult to measure precisely and global mutations rates (mutations per genome per generation) are often extrapolated from the per-base-pair mutation rate assuming that mutation rate is uniform across the genome. (genetics.org)
- Estimating this parameter is typically a three-step process: determining the mutation rate to a particular phenotype, converting this phenotypic rate into a per-base-pair mutation rate in a particular gene, and extrapolating this local rate to the entire genome. (genetics.org)
- The block, known as a base pair , was used in the 33ft-high model which represents a chromosome, one of the human genome. (thefreedictionary.com)
- To commemorate this anniversary in a fashion that showcases the rich history of the Human Genome Project and the field of genomics over the last quarter-century, the NHGRI History of Genomics Program is hosting a seminar series entitled "A Quarter Century after the Human Genome Project's Launch: Lessons Beyond the Base Pairs. (genome.gov)
- For reference, the genome of the virus DNA we sent up is 48,000 bases, the genome of the E. Coli DNA we sent up is 4.6 million bases, and the length of the human genome is 3.2 billion bases," Burton said. (nasa.gov)
- In this study, we introduce a novel high-throughput fluorescent in situ hybridization (FISH) technology that enabled us to conduct a genome-wide RNAi screen for factors involved in the robust somatic pairing observed in Drosophila. (harvard.edu)
Chiral1
- PUTJD115 'Asymmetric frustrated Lewis pair catalyzed hydrogenation using chiral Lewis bases (1.03.2015−29.02.2016)', Karl Kaupmees, University of Tartu, Faculty of Science and Technology, Institute of Chemistry. (etis.ee)
Pyrimidine2
- The various edges for the purine and pyrimidine bases are shown in Figure 2. (wikipedia.org)
- The 20-angstrom (7.9 × 10 −8 -inch) diameter of the helix was consistent with the presence of two adjacent strands and supported the hypothesis that a purine base resided on one strand and a pyrimidine base on the equivalent (homologous) site of the complementary strand. (chemistryexplained.com)
Chargaff's2
- In one of his experiments, Chargaff illustrated that the quantity of A is equal to that of T, while the quantity of C is equal to that of G. He then concluded that the complementary base of A must be T and the complementary base of C must be G. Chargaff's findings formed the basis for the base pairing principle of DNA. (reference.com)
- Erwin Chargaff's rules on DNA equivalence paved the way for the discovery of base pairing in DNA. (jove.com)
Structural1
- Polymerase chain reaction (PCR)-amplification with a thermal cycler (MJ Research PTC--200-DNA Engine, San Francisco, CA) was used to obtain a 2,122 base pair gene fragment consisting of the carbapenemase structural gene nmcA and its regulatory gene nmcR (12,13). (thefreedictionary.com)
Intermolecular1
- Unusually, the dimer interface, in which six unpaired adenosines break overall two-fold symmetry, lacks any intermolecular base pairs. (sigmaaldrich.com)
Naehrig1
- Barreto, P.S.L.M., Naehrig, M.: Pairing-friendly elliptic curves of prime order. (springer.com)
Secondary3
- Start with 'main.secondary_structure_restraints=True', and it will attempt to find existing base pairs by analyzing hydrogen bonds. (phenix-online.org)
- If your geometry is still a little screwy, the parameter syntax is like this: refinement.secondary_structure.nucleic_acids { base_pair { base1 = chain 'A' and resseq 1 base2 = chain 'B' and resseq 10 } } One piece of advice: make sure your structure has either all hydrogen atoms where they should be, or none at all - if you're missing any, the secondary structure restraints will probably break. (phenix-online.org)
- In combination with a variety of secondary assays, these results provide insights into the mechanism and dynamics of somatic pairing. (harvard.edu)
Replication1
- Replication, transcription, and translation all involve base‐pairing at several levels. (cliffsnotes.com)
Hydrogen bond2
- The Purine bases have 3 edges which are able to hydrogen bond. (wikipedia.org)
- Appropriate geometrical correspondence of hydrogen bond donors and acceptors allows only the "right" pairs to form stably. (wikipedia.org)
Inosine1
- The present work shows that in the purine.purine base-pairs the adenine adopts syn orientation with respect to the furanose moiety while the inosine is in the trans (anti) orientation. (rcsb.org)
Scheme2
- A contemporary example of using bilinear pairings is exemplified in the Boneh-Lynn-Shacham signature scheme. (wikipedia.org)
- The proposed id-based tripartite signcryption scheme does not use the bilinear pairings in both the Signcryption and unsigncryption phases. (slideshare.net)
Advances2
- D. Boneh and M. Franklin, "Identity-based encryption from the Weil pairing," Advances in Cryptology - Crypto'2001, Lecture Notes in Computer Science 2139 , pp. 213-229, Springer-Verlag, 2001. (springer.com)
- Nanowerk News ) By mapping uneven patterns of electrons in iron-based superconductors, RIKEN researchers have found evidence that electrons can pair up in two different ways, depending on the crystal structure ( Science Advances , 'Two distinct superconducting pairing states divided by the nematic end point in FeSe 1-x S x ' ). (nanowerk.com)