Base Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.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).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 Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Nucleic Acid Denaturation: Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.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).Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Oligonucleotides: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)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)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.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Nucleic Acid Renaturation: The reformation of all, or part of, the native conformation of a nucleic acid molecule after the molecule has undergone denaturation.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Polydeoxyribonucleotides: A group of 13 or more deoxyribonucleotides in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Skull Base: The inferior region of the skull consisting of an internal (cerebral), and an external (basilar) surface.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Schiff Bases: Condensation products of aromatic amines and aldehydes forming azomethines substituted on the N atom, containing the general formula R-N:CHR. (From Grant & Hackh's Chemical Dictionary, 5th ed)GuanineDNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.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)Adenine: A purine base and a fundamental unit of ADENINE NUCLEOTIDES.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).Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Poly dA-dT: Polydeoxyribonucleotides made up of deoxyadenine nucleotides and thymine nucleotides. Present in DNA preparations isolated from crab species. Synthetic preparations have been used extensively in the study of DNA.Intercalating Agents: Agents that are capable of inserting themselves between the successive bases in DNA, thus kinking, uncoiling or otherwise deforming it and therefore preventing its proper functioning. They are used in the study of DNA.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.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)Aminacrine: A highly fluorescent anti-infective dye used clinically as a topical antiseptic and experimentally as a mutagen, due to its interaction with DNA. It is also used as an intracellular pH indicator.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)Kinetics: The rate dynamics in chemical or physical systems.DNA, Circular: Any of the covalently closed DNA molecules found in bacteria, many viruses, mitochondria, plastids, and plasmids. Small, polydisperse circular DNA's have also been observed in a number of eukaryotic organisms and are suggested to have homology with chromosomal DNA and the capacity to be inserted into, and excised from, chromosomal DNA. It is a fragment of DNA formed by a process of looping out and deletion, containing a constant region of the mu heavy chain and the 3'-part of the mu switch region. Circular DNA is a normal product of rearrangement among gene segments encoding the variable regions of immunoglobulin light and heavy chains, as well as the T-cell receptor. (Riger et al., Glossary of Genetics, 5th ed & Segen, Dictionary of Modern Medicine, 1992)Hydrogen Bonding: A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.Genes, Bacterial: The functional hereditary units of BACTERIA.RNA, Ribosomal, 18S: Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Magnetic Resonance Spectroscopy: Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).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.Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.DNA, Recombinant: Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.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.Nucleotides: The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.DNA, Single-Stranded: A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.ThymineCell Line: Established cell cultures that have the potential to propagate indefinitely.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Saccharomyces: A genus of ascomycetous fungi of the family Saccharomycetaceae, order SACCHAROMYCETALES.DNA Replication: The process by which a DNA molecule is duplicated.Poly A: A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Genes, Viral: The functional hereditary units of VIRUSES.Deoxyribonucleotides: A purine or pyrimidine base bonded to a DEOXYRIBOSE containing a bond to a phosphate group.Structure-Activity Relationship: The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.Templates, Genetic: Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.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.Oligoribonucleotides: A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Saccharomycetales: An order of fungi in the phylum Ascomycota that multiply by budding. They include the telomorphic ascomycetous yeasts which are found in a very wide range of habitats.Skull Base Neoplasms: Neoplasms of the base of the skull specifically, differentiated from neoplasms of unspecified sites or bones of the skull (SKULL NEOPLASMS).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.Coliphages: Viruses whose host is Escherichia coli.Chemistry: A basic science concerned with the composition, structure, and properties of matter; and the reactions that occur between substances and the associated energy exchange.Bacterial Proteins: Proteins found in any species of bacterium.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Chemical Phenomena: The composition, conformation, and properties of atoms and molecules, and their reaction and interaction processes.Endonucleases: Enzymes that catalyze the hydrolysis of the internal bonds and thereby the formation of polynucleotides or oligonucleotides from ribo- or deoxyribonucleotide chains. EC 3.1.-.Molecular Weight: The sum of the weight of all the atoms in a molecule.RNA, Fungal: Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.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.Models, Chemical: Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.Hot Temperature: Presence of warmth or heat or a temperature notably higher than an accustomed norm.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Cytosine: A pyrimidine base that is a fundamental unit of nucleic acids.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.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).Transformation, Genetic: Change brought about to an organisms genetic composition by unidirectional transfer (TRANSFECTION; TRANSDUCTION, GENETIC; CONJUGATION, GENETIC, etc.) and incorporation of foreign DNA into prokaryotic or eukaryotic cells by recombination of part or all of that DNA into the cell's genome.TritiumCircular Dichroism: A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Denture Bases: The part of a denture that overlies the soft tissue and supports the supplied teeth and is supported in turn by abutment teeth or the residual alveolar ridge. It is usually made of resins or metal or their combination.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Hybridization, Genetic: The genetic process of crossbreeding between genetically dissimilar parents to produce a hybrid.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.UracilDNA 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.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Ribonucleases: Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.Viral Proteins: Proteins found in any species of virus.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.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).2-Aminopurine: A purine that is an isomer of ADENINE (6-aminopurine).Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.Microscopy, Electron: Microscopy using an electron beam, instead of light, to visualize the sample, thereby allowing much greater magnification. The interactions of ELECTRONS with specimens are used to provide information about the fine structure of that specimen. In TRANSMISSION ELECTRON MICROSCOPY the reactions of the electrons that are transmitted through the specimen are imaged. In SCANNING ELECTRON MICROSCOPY an electron beam falls at a non-normal angle on the specimen and the image is derived from the reactions occurring above the plane of the specimen.Operon: In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.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.Chromosome Deletion: Actual loss of portion of a chromosome.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.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.Anticodon: The sequential set of three nucleotides in TRANSFER RNA that interacts with its complement in MESSENGER RNA, the CODON, during translation in the ribosome.Molecular Structure: The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.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.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.Centrifugation, Density Gradient: Separation of particles according to density by employing a gradient of varying densities. At equilibrium each particle settles in the gradient at a point equal to its density. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.DNA Damage: Injuries to DNA that introduce deviations from its normal, intact structure and which may, if left unrepaired, result in a MUTATION or a block of DNA REPLICATION. These deviations may be caused by physical or chemical agents and occur by natural or unnatural, introduced circumstances. They include the introduction of illegitimate bases during replication or by deamination or other modification of bases; the loss of a base from the DNA backbone leaving an abasic site; single-strand breaks; double strand breaks; and intrastrand (PYRIMIDINE DIMERS) or interstrand crosslinking. Damage can often be repaired (DNA REPAIR). If the damage is extensive, it can induce APOPTOSIS.Transfection: The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.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.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.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 18.104.22.168.Genes, Regulator: Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.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 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.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Nuclear Magnetic Resonance, Biomolecular: NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Recombination, Genetic: Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.Purines: A series of heterocyclic compounds that are variously substituted in nature and are known also as purine bases. They include ADENINE and GUANINE, constituents of nucleic acids, as well as many alkaloids such as CAFFEINE and THEOPHYLLINE. Uric acid is the metabolic end product of purine metabolism.Echinomycin: A cytotoxic polypeptide quinoxaline antibiotic isolated from Streptomyces echinatus that binds to DNA and inhibits RNA synthesis.Point Mutation: A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.RNA, Transfer, Ala: A transfer RNA which is specific for carrying alanine to sites on the ribosomes in preparation for protein synthesis.Bacteriophage lambda: A temperate inducible phage and type species of the genus lambda-like viruses, in the family SIPHOVIRIDAE. Its natural host is E. coli K12. Its VIRION contains linear double-stranded DNA with single-stranded 12-base 5' sticky ends. The DNA circularizes on infection.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.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 22.214.171.124.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.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).Protons: Stable elementary particles having the smallest known positive charge, found in the nuclei of all elements. The proton mass is less than that of a neutron. A proton is the nucleus of the light hydrogen atom, i.e., the hydrogen ion.Enhancer Elements, Genetic: Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Netropsin: A basic polypeptide isolated from Streptomyces netropsis. It is cytotoxic and its strong, specific binding to A-T areas of DNA is useful to genetics research.Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.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.Operator Regions, Genetic: The regulatory elements of an OPERON to which activators or repressors bind thereby effecting the transcription of GENES in the operon.Nucleotide Mapping: Two-dimensional separation and analysis of nucleotides.Knowledge Bases: Collections of facts, assumptions, beliefs, and heuristics that are used in combination with databases to achieve desired results, such as a diagnosis, an interpretation, or a solution to a problem (From McGraw Hill Dictionary of Scientific and Technical Terms, 6th ed).Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.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.Genomic Library: A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).Genetic Code: The meaning ascribed to the BASE SEQUENCE with respect to how it is translated into AMINO ACID SEQUENCE. The start, stop, and order of amino acids of a protein is specified by consecutive triplets of nucleotides called codons (CODON).Mannich Bases: Ketonic amines prepared from the condensation of a ketone with formaldehyde and ammonia or a primary or secondary amine. A Mannich base can act as the equivalent of an alpha,beta unsaturated ketone in synthesis or can be reduced to form physiologically active amino alcohols.Hydrogen-Ion Concentration: The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.Cattle: Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.DNA Adducts: The products of chemical reactions that result in the addition of extraneous chemical groups to DNA.Blotting, Northern: Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.RNA, Transfer, Amino Acid-Specific: A group of transfer RNAs which are specific for carrying each one of the 20 amino acids to the ribosome in preparation for protein synthesis.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.HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.DNA Footprinting: A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Genetic Variation: Genotypic differences observed among individuals in a population.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Genes, Fungal: The functional hereditary units of FUNGI.Endodeoxyribonucleases: A group of enzymes catalyzing the endonucleolytic cleavage of DNA. They include members of EC 3.1.21.-, EC 3.1.22.-, EC 3.1.23.- (DNA RESTRICTION ENZYMES), EC 3.1.24.- (DNA RESTRICTION ENZYMES), and EC 3.1.25.-.DNA, B-Form: The most common form of DNA found in nature. It is a right-handed helix with 10 base pairs per turn, a pitch of 0.338 nm per base pair and a helical diameter of 1.9 nm.RNA Splicing: The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.Deoxyribonuclease EcoRI: One of the Type II site-specific deoxyribonucleases (EC 126.96.36.199). It recognizes and cleaves the sequence G/AATTC at the slash. EcoRI is from E coliRY13. Several isoschizomers have been identified. EC 3.1.21.-.Heteroduplex Analysis: A method of detecting gene mutation by mixing PCR-amplified mutant and wild-type DNA followed by denaturation and reannealing. The resultant products are resolved by gel electrophoresis, with single base substitutions detectable under optimal electrophoretic conditions and gel formulations. Large base pair mismatches may also be analyzed by using electron microscopy to visualize heteroduplex regions.Osmium Tetroxide: (T-4)-Osmium oxide (OsO4). A highly toxic and volatile oxide of osmium used in industry as an oxidizing agent. It is also used as a histological fixative and stain and as a synovectomy agent in arthritic joints. Its vapor can cause eye, skin, and lung damage.N-Glycosyl Hydrolases: A class of enzymes involved in the hydrolysis of the N-glycosidic bond of nitrogen-linked sugars.Repressor Proteins: Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.Electrophoresis, Agar Gel: Electrophoresis in which agar or agarose gel is used as the diffusion medium.DNA, Superhelical: Circular duplex DNA isolated from viruses, bacteria and mitochondria in supercoiled or supertwisted form. This superhelical DNA is endowed with free energy. During transcription, the magnitude of RNA initiation is proportional to the DNA superhelicity.Deoxyguanosine: A nucleoside consisting of the base guanine and the sugar deoxyribose.Micrococcal Nuclease: An enzyme that catalyzes the endonucleolytic cleavage to 3'-phosphomononucleotide and 3'-phospholigonucleotide end-products. It can cause hydrolysis of double- or single-stranded DNA or RNA. (From Enzyme Nomenclature, 1992) EC 188.8.131.52.DNA Polymerase beta: A DNA repair enzyme that catalyzes DNA synthesis during base excision DNA repair. EC 184.108.40.206.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Chickens: Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.Spectrophotometry, Ultraviolet: Determination of the spectra of ultraviolet absorption by specific molecules in gases or liquids, for example Cl2, SO2, NO2, CS2, ozone, mercury vapor, and various unsaturated compounds. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Gene Expression Regulation, Enzymologic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.Methylation: Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.DNA, Mitochondrial: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.Macromolecular Substances: Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.Pentoxyl: 5-Hydroxymethyl-6-methyl- 2,4-(1H,3H)-pyrimidinedione. Uracil derivative used in combination with toxic antibiotics to lessen their toxicity; also to stimulate leukopoiesis and immunity. Synonyms: pentoksil; hydroxymethylmethyluracil.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.
The double stranded regions of RNA are formed by base-pairing between residues in the close to region of the editing site with ... The region that base pairs with the editing region is known as an Editing Complementary Sequence (ECS). ADARs bind interact ... site F has also been located in the exon complementary sequence (ECS) of intron 5. The ECS required for formation of double ... that specifically recognize adenosines within double-stranded regions of pre-mRNAs and deaminate them to inosine. Inosines are ...
... but can be an exonic sequence. The region that base-pairs with the editing region is known as an Editing Complementary Sequence ... The double-stranded regions of RNA are formed by base-pairing between residues in the close to region of the editing site, with ... that specifically recognize adenosines within double-stranded regions of pre-mRNAs and deaminate them to inosine. Inosines are ... A to I editing occurs in a noncoding RNA sequences such as introns, untranslated regions (UTRs), LINEs, SINEs( especially Alu ...
... but can be an exonic sequence. The region that base pairs with the editing region is known as an Editing Complementary Sequence ... The double-stranded regions of RNA are formed by base-pairing between residues in the close to region of the editing site, with ... All editing in glutamate receptors occurs in double-stranded RNAs (dsRNAs), which form due to complementary base pairing ... that specifically recognize adenosines within double-stranded regions of pre-mRNAs and deaminate them to inosine. Inosines are ...
The double-stranded regions of RNA are formed by base-pairing between residues in the close to region of the editing site, with ... The region that base pairs with the editing region is known as an Editing Complementary Sequence (ECS). The editing site was ... The double-stranded region is 22 base pairs in length. As with editing of the KCNA1 gene product, the editing region and the ... that specifically recognize adenosines within double-stranded regions of pre-mRNAs and deaminate them to inosine. Inosines are ...
The editing region is predicted to form a double stranded region of 32 base pairs in length with a complementary sequence about ... The double stranded regions of RNA are formed by base-pairing between residues in a region complementary to the region of the ... The region that base pairs with the editing region is known as an Editing Complentary Sequence (ECS). The one editing site of ... This complementary region is usually found in a neighbouring intron but can also be located in an exonic sequence. ...
The double-stranded regions of RNA are formed by base-pairing between residues in a region complementary to the region of the ... The region that pairs with the editing region is known as an Editing Complementary Sequence (ECS). The candidate editing sites ... This complementary region is usually found in a neighbouring intron but can also be located in an exonic sequence. ... that specifically recognize adenosines within double-stranded regions of pre-mRNAs and deaminate them to inosine. Inosines are ...
The double stranded regions of RNA are formed by base-pairing between residues in the close to region of the editing site with ... The region that base pairs with the editing region is known as an Editing Complementary Sequence (ECS). An editing site was ... No double stranded region required by ADARs has predicted.Immunoprecipitation experiments and RNA interference have shown that ... The substitution occurs within amino acid position 320 in humans and also in mice.A possible double stranded RNA region has not ...
The double-stranded regions of RNA are formed by base-pairing between residues in the close to region of the editing site with ... The region that base pairs with the editing region is known as an Editing Complementary Sequence (ECS) ADARs bind interact ... This sequence is necessary for editing at the site to occur. The possible editing complementary sequence was observed from ... that specifically recognize adenosines within double-stranded regions of pre-mRNAs and deaminate them to inosine. Inosines are ...
... which contains complementary sequences to the regions around the insertion/deletion points. The newly formed double-stranded ... those formed in an mRNA where intronic sequence base pairs with a complementary exonic sequence), while promiscuous editing ... A-to-I editing is the main form of RNA editing in mammals and occurs in regions of double-stranded RNA (dsRNA). Adenosine ... Editing can restore the essential base-pairing sequences of tRNAs, restoring functionality. It has also been linked to the ...
The double stranded regions of RNA are formed by base-pairing between residues in the close to region of the editing site with ... The region that base pairs with the editing region is known as an Editing Complementary Sequence (ECS). The editing sites are ... that specifically recognize adenosines within double-stranded regions of pre-mRNAs and deaminate them to inosine. Inosines are ... UTR while exon 2 includes the remaining sequence of the 5′UTR, the coding region and the 3′UTR. The coding sequence of the ...
The intronic sequence includes a 5' splice site, and the predicted double-stranded region is 30 base pairs in length. The ... The region that base pairs with the editing region is known as an Editing Complementary Sequence (ECS). The pre-mRNA of this ... The double-stranded regions of RNA are formed by base-pairing between residues in the close to region of the editing site with ... that specifically recognize adenosines within double-stranded regions of pre-mRNAs and deaminate them to inosine. Inosines are ...
... but can be an exonic sequence.The region that base pairs with the editing region is known as an Editing Complementary Sequence( ... ADAR 3 is restricted to the brain.The double stranded regions of RNA are formed by base-pairing between residues in the region ... that specifically recognize adenosines within double-stranded regions of pre-mRNAs and deaminate them to inosine.Inosines are ... Editing at this site results in a codon changed from a Lysine to an Arginine.This occurs in a highly basic region of the ...
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). The modified residue is ... The edited adenosine is found in a 6-base pair duplex region. Mutation experiment in the region near the 6-base pair duplex ... This region is composed of a 114 base pairs. Similar regions have been identified in mouse and rat. ...
... is held onto a region of double-stranded DNA by the telomere strand disrupting the double-helical DNA and base pairing to ... Here, the two strands are separated and then each strand's complementary DNA sequence is recreated by an enzyme called DNA ... This enzyme makes the complementary strand by finding the correct base through complementary base pairing and bonding it onto ... Adenine pairs with thymine and guanine pairs with cytosine. It was represented by A-T base pairs and G-C base pairs. The ...
Complementarity (molecular biology)
A complementary strand of DNA or RNA may be constructed based on nucleobase complementarity. Each base pair, A=T vs. G≡C, takes ... These short strands bind to a RISC complex. They match up with sequences in the upstream region of a transcribed gene due to ... the complementary bases of the two strands form up and begin to unwind the hairpins until a double-stranded RNA (dsRNA) complex ... Two strands of complementary sequence are referred to as sense and anti-sense. The sense strand is, generally, the transcribed ...
The following DNA sequences illustrate pair double-stranded patterns. By convention, the top strand is written from the 5' end ... The complementary nature of this based-paired structure provides a backup copy of all genetic information encoded within double ... Many DNA-binding proteins can recognize specific base pairing patterns that identify particular regulatory regions of genes. ... kb (= kbp) = kilo base pairs = 1,000 bp Mb (= Mbp) = mega base pairs = 1,000,000 bp Gb = giga base pairs = 1,000,000,000 bp. ...
The third strand has a base sequence which is complementary to one of the main strands and pairs with it, thus displacing the ... other complementary main strand in the region. Within that region the structure is thus a form of triple-stranded DNA. A ... When a double-stranded DNA molecule has suffered a break in both strands, one repair mechanism available in diploid eukaryotic ... This is a loop of both strands of the chromosome which are joined to an earlier point in the double-stranded DNA by the 3' ...
Nucleic acid secondary structure
A double helix is formed by regions of many consecutive base pairs. The nucleic acid double helix is a spiral polymer, usually ... two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair ( ... The base pairing in pseudoknots is not well nested; that is, base pairs occur that "overlap" one another in sequence position. ... Hybridization is the process of complementary base pairs binding to form a double helix. Melting is the process by which the ...
... which can recognize and specifically base-pair with regions of inserting complementary foreign DNA. The crRNA-foreign nucleic ... the Cas9 protein has been heavily utilized as a genome engineering tool to induce site-directed double strand breaks in DNA. ... is responsible for complementary sequence cleavage of target DNA and RuvC is responsible for the non-complementary sequence. ... Cas9 performs this interrogation by unwinding foreign DNA and checking for sites complementary to the 20 basepair spacer region ...
... usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an ... It occurs when two regions of the same strand, ... and the base composition of the paired region. Pairings between ... Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The ... The first prerequisite is the presence of a sequence that can fold back on itself to form a paired double helix. The stability ...
Nucleic acid double helix
T and A rich regions are more easily melted than C and G rich regions. Some base steps (pairs) are also susceptible to DNA ... As a result, proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make ... Hybridization is the process of complementary base pairs binding to form a double helix. Melting is the process by which the ... For each base pair, considered relative to its predecessor, there are the following base pair geometries to consider: Shear ...
... makes it possible to catalyze a DNA synapsis reaction between a DNA double helix and a complementary region of single stranded ... producing a region of heteroduplex DNA that is thousands of base pairs long. Since it is a DNA-dependent ATPase, RecA contains ... The RecA-ssDNA filament searches for sequence similarity along the dsDNA. The search process induces stretching of the DNA ... In branch migration an unpaired region of one of the single strands displaces a paired region of the other single strand, ...
The guide RNA can be engineered to match a desired DNA sequence through simple complementary base pairing, as opposed to the ... are currently three methods in use that involve precisely targeting a DNA sequence in order to introduce a double-stranded ... DNA binding region consists of amino acid repeats that each recognize a single base pair of the desired targeted DNA sequence.[ ... Fig 1. Frameshift mutation resulting from a single base pair deletion, causing altered amino acid sequence and premature stop ...
Complementarity (molecular biology)
A complementary strand of DNA or RNA may be constructed based on nucleobase complementarity. Each base pair, A=T vs. G≡C, ... These short strands bind to a RISC complex. They match up with sequences in the upstream region of a transcribed gene due to ... Left: the nucleotide base pairs that can form in double-stranded DNA. Between A and T there are two hydrogen bonds, while there ... DNA and RNA base pair complementarity. Complementarity between two antiparallel strands of DNA. The top strand goes from ...
Because a DNA sequence is double stranded, the base pairs are read, (not just the bases on one strand), to determine a ... forward on one strand matches the sequence reading 5' to 3' on the complementary strand with which it forms a double helix. ... been suggested that the existence of palindromes in peptides might be related to the prevalence of low-complexity regions in ... A palindromic sequence is a nucleic acid sequence on double-stranded DNA or RNA wherein reading 5' (five-prime) to 3' (three ...
... which occurs when the guide strand pairs with a complementary sequence in a messenger RNA molecule and induces cleavage by ... Dicer cleaves long double-stranded RNA molecules into short double stranded fragments of around 20 nucleotide siRNAs. The dsRNA ... But only one of the two single-stranded RNA here will be utilized to base pair with target mRNA. It is known as the guide ... In animals, Argonaute associated with miRNA binds to the 3'-untranslated region of mRNA and prevents the production of proteins ...
The editing complementary sequence (ECS) is located in a region within the coding sequence about 200 base pairs upstream from ... restricted to the brain.The double stranded regions of RNA are formed by base-pairing between residues in the close to region ... but can be an exonic sequence.The region that base pairs with the editing region is known as an Editing Complentary Sequence ( ... that specifically recognize adenosines within double-stranded regions of pre-mRNAs and deaminate them to inosine.Inosines are ...
Glossary of genetics
... base pair A pair of nucleotide bases on complementary DNA or RNA strands organized in a double helix. Contents: Top 0-9 A B C D ... classical genetics cloning codominance codon A series of three nucleotides in a coding region of a nucleid acid sequence which ... The "rungs" of the ladder are made of base pairs, or nucleotides with complementary hydrogen bonding patterns. DNA condensation ... mitosis mobile genetic element monosomy mosaic mutagen mutation Any change in the base pair sequence of DNA or RNA. Contents: ...
Single-stranded DNA (ssDNA) folds into a tertiary structure. The conformation is sequence dependent and most single base pair ... The oligonucleotide is designed such that there are complementary regions at each end and a probe sequence located in between. ... The double-stranded PCR products are denatured using heat and formaldehyde to produce ssDNA. The ssDNA is applied to a non- ... If on the other hand, the probe sequence encounters a target sequence with as little as one non-complementary nucleotide, the ...
Nucleotide excision repair
The undamaged single-stranded DNA remains and DNA polymerase uses it as a template to synthesize a short complementary sequence ... Similarly, the MMR pathway only targets mismatched Watson-Crick base pairs. Nucleotide excision repair (NER) is a particularly ... they help unwind DNA and generate a junction between the double-stranded and single-stranded DNA around the transcription ... there is a difference in NER efficiency between transcriptionally silent and transcriptionally active regions of the genome. ...
5-HT2C receptor - Wikipedia
The double stranded regions of RNA are formed by base-pairing between residues in the close to region of the editing site with ... The region that base pairs with the editing region is known as an Editing Complementary Sequence (ECS). ADARs bind interact ... site F has also been located in the exon complementary sequence (ECS) of intron 5. The ECS required for formation of double ... that specifically recognize adenosines within double-stranded regions of pre-mRNAs and deaminate them to inosine. Inosines are ...
GRIK1 - Wikipedia
... but can be an exonic sequence. The region that base-pairs with the editing region is known as an Editing Complementary Sequence ... The double-stranded regions of RNA are formed by base-pairing between residues in the close to region of the editing site, with ... that specifically recognize adenosines within double-stranded regions of pre-mRNAs and deaminate them to inosine. Inosines are ... A to I editing occurs in a noncoding RNA sequences such as introns, untranslated regions (UTRs), LINEs, SINEs( especially Alu ...
Role of Saccharomyces cerevisiae Msh2 and Msh3 repair proteins in double-strand break-induced recombination | PNAS
Similarly, in SSA, complementary strands of homologous regions flanking a DSB can anneal, producing an intermediate that has ... plasmid where a 60-bp HO endonuclease recognition site was introduced into one of a pair of inverted repeated LacZ sequences ( ... However, for this to occur, any nonhomologous bases at the 3′ end must be removed, so that the primer end may basepair with the ... 3 both duplicated regions were shown by sequencing to be identical to the URA3 sequence derived from strain +D4 (32), except ...
Kv1.1 - Wikipedia
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). ... The edited adenosine is found in a 6-base pair duplex region. Mutation experiment in the region near the 6-base pair duplex ... This region is composed of a 114 base pairs. Similar regions have been identified in mouse and rat. ...
Patent EP2287307A2 - Materials and methods for identifying and analyzing intermediate tandem ... - Google Patents
... sequence is a region of a DNA sequence containing at least one five to seven base repeat unit appearing in tandem at least two ... invention is directed to materials and methods for the identification and analysis of intermediate tandem repeat sequences in ... is an oligonucleotide primer comprising a sequence complementary to a strand of a double-stranded DNA marker in a region of the ... base pairs repeated in tandem at least two (2) times, wherein the double-stranded DNA marker sequence is SEQ ID NO:26. ...
... perfectly base-paired RNAs that initiate RNAi yields both sense and antisense, or potentially double-stranded siRNAs, only one ... they interact with their targets by imperfect base-pairing to mRNA sequences within the 3 untranslated region (3 UTR). ... The ARE-complementary sequence in miR16 is indeed required for miR16 function in destabilizing ARE-RNA. However, pairing with ... RNase III enzymes cleave perfectly paired dsRNA on both strands, producing a pair of cuts, one on each strand, displaced by two ...
2422-Nucleotide and/or Amino Acid Sequence Disclosures in Patent Applications
hairpin; a double-helical region formed by base-pairing between adjacent (inverted) complementary sequences in a single strand ... uncertainties in the sequence; used to describe region(s) of a sequence for which the authors are unsure about the sequence ... author is unsure of exact sequence in this region V_region. variable region of immunoglobulin light and heavy chains, and T- ... However, when a sequence is presented in a drawing, the sequence must still be included in the sequence listing if the sequence ...
Frontiers | The Glycolytic Versatility of Bacteroides uniformis CECT 7771 and Its Genome Response to Oligo and Polysaccharides ...
We have also used massive sequencing approaches to distinguish the genome expression patterns in response to carbon sources of ... We have also used massive sequencing approaches to distinguish the genome expression patterns in response to carbon sources of ... We have used the cutting-edge nanopore-based technology to sequence the genome of B. uniformis CECT 7771, a human symbiont with ... We have used the cutting-edge nanopore-based technology to sequence the genome of B. uniformis CECT 7771, a human symbiont with ...
CMTr1-DXH15 interactions in RNA capping | Philosophical Transactions of the Royal Society B: Biological Sciences
... beyond the base-paired region). In our experiments, CMTr1 did not show any strand displacement activity on its own (electronic ... terminus was base-paired to a short complementary oligo, and RNAs in which the base-pairing was intra-molecular. This could be ... proximal 52 nt region are base-paired. Furthermore, as many as 24.38% of sequences in the dataset analysed had the first ten ... 2012 Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activity. Nucleic Acids Res. ...
Patent US7267948 - SERS diagnostic platforms, methods and systems microarrays, biosensors and ... - Google Patents
... labeled DNA and allowed to hybridize by reestablishing a double-stranded molecule with the complementary target sequences. ... the degree of mismatch between the base pairs, and the length and concentration of the target and probe sequences. ... The code-containing regions of the gene (exons), however, are often separated by much noncoding DNA (introns). A cDNA molecule ... Nucleic acids strands tend to be paired to their complements in the corresponding double-stranded structure. Therefore, a ...
US5686238A - Method and device for testing blood units for viral contamination - Google Patents
By repeating these cycles of denaturation-annealing-extension, a single sequence of a few hundred base pairs can be amplified. ... Initially, to denature the double-stranded DNA under study, the temperature of the reaction is rapidly increased. The ... a thermostable DNA polymerase and oligonucleotide primers complementary to the ends of a region of DNA of interest. ... Although nucleic acid sequencing techniques are very sensitive, they are also sample specific. Moreover, the samples of the ...
Community Academic Profiles - Faculty & Researchers - Stanford Medicine
The TALEN pairs were designed to induce double-strand DNA break near the starting codon of each gene that either disrupted the ... Multiplexing 11 samples per sequencing run resulted in a mean base pair coverage of 420, of which 97% had >20 coverage and >99 ... and cost.We used double-stranded probes (complementary long padlock probes), an inexpensive and customizable capture technology ... to efficiently capture and amplify the entire coding region and flanking intronic and regulatory sequences of 88 genes and 40 ...
Community Academic Profiles - Faculty & Researchers - Stanford Medicine
Multiplexing 11 samples per sequencing run resulted in a mean base pair coverage of 420, of which 97% had >20 coverage and >99 ... and cost.We used double-stranded probes (complementary long padlock probes), an inexpensive and customizable capture technology ... to efficiently capture and amplify the entire coding region and flanking intronic and regulatory sequences of 88 genes and 40 ... However, options for sequencing this rapidly evolving gene set are limited because many sequencing services and off-the-shelf ...
IJMS | Free Full-Text | A DNA Network as an Information Processing System | HTML
Watson-Crick double helix is formed by linking together two antiparallel strands of DNA that have complementary base sequences ... Pairs of domains (X,x) and (Y,y) are complementary. The double-stranded complex S1•S2 is formed by hybridization of domains X ... Strand displacement occurs by means of a random walk of the branch point separating regions of S2 hybridized to S1 and to S3, ... Pairs of domains (X,x) and (Y,y) are complementary. The double-stranded complex S1•S2 is formed by hybridization of domains X ...
... pairing patterns that identify particular regulatory regions of genes.. Hydrogen bonding in base pairs. ... The complementary nature of this based-paired structure provides a backup copy of all genetic information encoded within double ... stranded DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of ... is subtly dependent on its nucleotide sequence. ... Base pairs, which form between specific nucleobases (also ...
UniProt release 2015 06
Once homology has been found, each DNA strand is extended from the base-paired region using the opposing overhang as a template ... homologous DNA sequences in overhangs to form base pairs. The homology can be either terminal, or internal, as far as 5 ... DNA double-strand breaks (DSBs) are our worse cellular enemy, yet they do occur all the time, often accidentally, as a result ... RAD51 proteins bind to the resulting 3 single-stranded overhangs and help them to recognize complementary (homologous) DNA in ...
chapter 7 - www.sumanasinc.com Chapter 7 Genomes and Chromosomes*Read this chapter Genetics Molecule of heredity...
The 2 DNA polynucleotide strands have base sequences that are complementary: - Adenine always pairs with Guanine (A=T) - ... DNA is a double-stranded helix (twisted ladder) • The two strands in the double helix are antiparallel (run in opposite ... Two major differences: 1. Eukaryotes contain non-coding regions called introns - introns are later spliced out and exons are ... Watson-Crick base pairing) Size of DNA • Expressed as number of thousands of nucleotides bases or base pairs per molecule • ...
Kühn Lab | Max Delbrück Center for Molecular Medicine
sgRNAs are bound by the generic nuclease Cas9 and guide the complex to the complementary DNA sequence, followed by the ... induction of a double-strand break (DSB). DSBs are fixed in mammalian cells mainly by the NHEJ repair pathway which reconnects ... open DNA ends imprecisely and frequently leads to the loss of multiple base pairs at the target site. ... Mutations in disordered regions can cause disease by creating dileucine motifs K. Meyer et al. ...
Patent and Trademark Office Consolidated Notices December 31, 2013 1397 Item cons157
... a double-helical region formed by base-pairing between adjacent (inverted) complementary sequences in a single strand of RNA or ... into an amino acid sequence unsure author is unsure of exact sequence in this region V_region Variable region of immunoglobulin ... region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the ... Uncertainties in the sequence. Used to describe region(s) of a sequence for which the authors are unsure about the sequence ...
US4725537A - Assay, reagent and kit employing nucleic acid strand displacement and restriction endonuclease cleavage -...
... probe polynucleotide containing a target binding region which is substantially complementary to the target nucleotide sequence ... displaces the second polynucleotide from the target nucleotide region and forms the unique restriction site in double-stranded ... The labeled probe polynucleotide is then cleaved at the unique restriction site in double-stranded form to form labeled ... contains a unique half-restriction site completely complementary to the half-restriction site of the target nucleotide sequence ...
Transcription | Encyclopedia.com
Transcription Transcription is the process in which genetic information stored in a strand of DNA is copied into a strand of ... However, rather than matching the DNA sequence, the polymerase pairs up complementary base pairs. G is always paired with C, so ... which are located ten and thirty-five base pairs respectively upstream of the transcription start site. DNA is double-stranded ... Transcription is initiated at regions of DNA called promoters, which are typically 20 to 150 base pairs long, depending on the ...
2 Introduction | Mapping and Sequencing the Human Genome | The National Academies Press
There is growing enthusiasm in the scientific community about the prospect of mapping and sequencing the human genome, a mon... ... The information on one DNA strand is therefore redundant to that on the other (that is because of complementary base pairing ... 17 DNA is a double helix: Each nucleotide on a strand of DNA has a complementary nucleotide on the other strand. ... Only such a sequence reveals all or nearly all the information in the human genome. A number of specific regions of human DNA ...
The DDBJ/ENA/GenBank Feature Table Definition | INSDC
... a double-helical region formed by base-pairing between adjacent (inverted) complementary sequences in a single strand of RNA or ... Start at the base complementary to 126 and finish at the base complementary to base 34 (the feature is on the strand ... This numbering designates the first base (5 end) of the presented sequence as base 1. Base locations beyond the range of the ... Qualifier /mod_base= Definition abbreviation for a modified nucleotide base Value format modified_base Example /mod_base=m5c ...
... better illustrated in the base pair opening profile.. The two complementary strands comprising the double helix can be ... These stability map and base pair association opening provide unique information about the roles of specific regions in various ... nucleotides sequences.. The concomitant advances in theory, measuring systems, and DNA sequencing techniques bring new ... This double stranded structure is maintained by two main forces hydrogen bonds between complementary pairs on opposite strands ...
A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity | Science
... the complementary strand) is cleaved at a site three base pairs upstream of the PAM (Fig. 1, D and E, and fig. S5, B and C). ... complementary to the repeat sequences in pre-crRNA triggers processing by the double-stranded (ds) RNA-specific ribonuclease ... The bulk of the tracrRNA downstream of the crRNA base-pairing region is free to form additional RNA structure(s) and/or to ... C base pairs that occur one base pair downstream of the crRNA binding sequence, within the target DNA (4). Transformation ...
MicroRNA Role in Thyroid Cancer Development
... through direct base pairing between miR-369-3 "seed" region and complementary ARE regions, under cell cycle arrest conditions. ... the other strand is degraded. The incorporate guide strand leads the RISC to the complementary sequence in the 3′-UTR of target ... These double-stranded products are unwound by a still unidentified helicase and incorporated as single-stranded RNAs (guide ... Which of the two RNA strands is incorporated in the RISC is determined by the stability of the base pairs at the 5′ end of the ...
Nucleic Acid Crystallography - MyBioSource Learning Center
DNA templates for T7 RNA polymerase are designed to contain a double-stranded 17 base pair T7 promoter with a downstream single ... The coding region typically contains a 2-5 nt sequence complementary to the target RNA, followed by a "stalling" nucleotide ... oligonucleotides containing a complementary or bottom strand of the T7 promoter with an RNA coding sequence depicted by a ... and single-stranded synthetic templates containing a double-stranded T7 promoter. Therefore, a DNA template can be easily ...
A cooperative-binding split aptamer assay for rapid, specific and ultra-sensitive fluorescence detection of cocaine in saliva ...
The cocaine-CBSA-5325 complex features four complementary double-stranded regions (A-D) and a duplexed AP site. (B) In the ... 2B, right). The resulting CBSA-5325/cocaine complex contains four complementary base-paired segments (Fig. 2A, right; segments ... in which we replaced one of the binding domains with fully complementary sequences (Fig. 3A, LSA). The LSA fragments quenched ... In the absence of cocaine, the quenching of ATMND fluorescence increased as the number of base-pairs between the two CBSA ...
An Introduction to Molecular Biology/Gene Expression - Wikibooks, open books for an open world
... but the forward and backward sequences are found in complementary DNA strands (i.e., double stranded) as in GTATAC (Notice that ... This means its 5 end is created first in base pairing. Although DNA is arranged as two antiparallel strands in a double helix ... The regulatory sequence before (upstream from) the coding sequence is called the 5UTR (five prime untranslated region) , and ... as opposed to double-stranded DNA. The other DNA strand is called the coding strand, because its sequence is the same as the ...
Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells | Development
... complexes that utilize the incorporated RNA to generate sequence-specific double-strand breaks at a complementary DNA sequence ... can be guided to specific sites in the human genome through base-pair complementation between a 20-nucleotide guide region of ... 2013). Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173-1183. ... Total RNA (2 μg for SOX17 analysis, or 250 ng for OCT4 analysis) was reverse-transcribed using SuperScript III First-Strand ...
AdenineGeneMoleculesPolymeraseRNAsHydrogen bondsGuanineCytosineProteinsCas9HomologyPolynucleotideIntronsCrRNAPrimersGeneticPromoter sequencesBindsAntiparallel to one anotherSgRNARecognizeMRNA sequenceTarget sequenceIntramolecularCleavesHighly conservedAmplificationAssayComplementarityChromosomesAntisenseTemplate strandAmino acidsSiRNAConformationPrimerFully sequencedApproximately 20 baseExonsSingle stranded armsFormRiboseRestriction endonuclease
- The sequence of the four bases in DNA, which are adenine (A), cytosine (C), guanine (G), and thymine (T), is preserved in the sequence of the four bases in RNA, which are A, C, G, and uracil (U). (encyclopedia.com)
- Each strand is made of a sequence of four much smaller molecules, adenine (A), guanine (G), cytosine (C) and thymine (T). The strands are complementary, so that an A on one strand is matched by a T on the other strand, and a C is matched by a G. The human genome consists of more than 3 billion of these pairs, called base pairs, packaged into 23 pairs of chromosomes. (bioedonline.org)
- Ribonucleic acid or RNA is a polymer or chain of nucleotide units, each comprising a nitrogenous base ( adenine , cytosine , guanine , or uracil ), a five-carbon sugar ( ribose ), and a phosphate group. (newworldencyclopedia.org)
- The bases always complement one another with adenine and thymine pairing together and cytosine and guanine pairing together. (isogg.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 base - often adenine , cytosine , guanine or uracil - is attached to the 1' position. (wikidoc.org)
- Thirdly, the complementary nucleotide to adenine is not thymine , as it is in DNA, but rather uracil , which is an unmethylated form of thymine. (wikidoc.org)
- The mRNA sequence is complementary to the DNA, however, uracil (U) is used in the mRNA as the complementary nucleotide for adenine (A). During translation, a triplet of nucleotides in the mRNA, termed a codon, are used to direct the synthesis of the protein. (psu.edu)
- The normal rules of complementary base pairing apply, except uracil (U) substitutes for thymine (T) in the RNA and is complementary to adenine (A). Synthesis of mRNA occurs in the 5' to 3'direction, reading the template strand in the 3' to 5' direction. (psu.edu)
- When gene conversion is initiated by a double-strand break (DSB), any nonhomologous DNA that may be present at the ends must be removed before new DNA synthesis can be initiated. (pnas.org)
- In Saccharomyces cerevisiae , homologous recombination initiated by double-strand breaks (DSBs) can occur by at least two distinct pathways: gene conversion and single-strand annealing (SSA) ( 1 - 6 ). (pnas.org)
- In gene conversion, these tails invade a homologous donor sequence and act as primers of new DNA synthesis. (pnas.org)
- The gene is located on the Watson (plus) strand of the short arm of chromosome 12 (12p13.32). (wikipedia.org)
- Since critical sequence elements are conserved, it is suggested that dimerization might be a general feature of dsRBD proteins in gene silencing. (sdbonline.org)
- Such small, randomly sized deletions are often used for the creation of frame shift mutations within coding regions leading to gene inactivation (knockout). (mdc-berlin.de)
- The generation of precise modifications such as nucleotide replacements by gene targeting requires the alternative pathway of homology directed repair (HDR), able to read new sequences from externally delivered, DNA templates into the DSB site (knock-in). (mdc-berlin.de)
- MicroRNAs (miRNAs) are endogenous noncoding RNAs that negatively regulate gene expression by binding the 3′ noncoding region of the messenger RNA targets inducing their cleavage or blocking the protein translation. (hindawi.com)
- MicroRNAs (miRNAs) are endogenous single-stranded noncoding RNAs of about 22 nucleotides which suppress gene expression by selectively binding to the complementary 3′ untranslated region (3′-UTR) of messenger RNAs (mRNAs) through base-pairing. (hindawi.com)
- The genetic code stored in DNA in form of nucleotide sequence is "interpreted" by gene expression, and the properties of the expression products give rise to the organism's phenotype. (wikibooks.org)
- 8 Epigenetic regulation, which can alter gene expression without changing the nucleotide base sequence of gene, may result from environment-gene interactions. (nature.com)
- Epigenetic phenomena are defined as heritable mechanisms that establish and maintain mitotically stable patterns of gene expression without modifying the base sequence of DNA. (nature.com)
- Generally, the transcribed region accounts for more than one gene. (rug.nl)
- Loss-of-function or "knockout" mutations require complete destruction of gene function, which can be obtained from a variety of possible insertional or deletional events at the start of the coding sequence. (stemcell.com)
- In this method, CRISPR-Cas9 is used to create a targeted a double-strand DNA break in the gene of interest. (stemcell.com)
- Alternatively, one might use CRISPR-Cas9 to generate double-strand breaks at two sites within the gene, thereby creating a large deletion spanning the two targets. (stemcell.com)
- Originally, naturally occurring mutations were identified and then gene loss or inactivation had to be established by DNA sequencing or other methods. (wikipedia.org)
- This results in the sequence of the gene being altered, and most cases the gene will be translated into a nonfunctional protein , if it is translated at all. (wikipedia.org)
- An average single coding gene sequence might be about 10,000 bases long. (coursehero.com)
- 1 kb) insertion/deletion (I/D) heterologies during double-strand-break repair (DSBR) was investigated using a gene-targeting assay that permits efficient recovery of sequence insertion events at the haploid chromosomal immunoglobulin (Ig) μ-locus in mouse hybridoma cells. (genetics.org)
- Spliceosomal RNAs help discard intervening sequences (introns) from pre-mRNA transcripts and splice together the mRNA segments (exons) to create what can be a complex assortment of distinct protein-coding mRNAs from a single gene. (umassmed.edu)
- In prokaryotes (for example, bacteria), small antisense RNAs exert a variety of gene regulatory activities by base pairing specifically to their target mRNAs. (umassmed.edu)
- Gene conversion (conversion), the unidirectional transfer of DNA sequence information, occurs as a byproduct of recombinational repair of broken or damaged DNA molecules. (nih.gov)
- These noncoding regions have other functions, including preserving important gene sequences and regulation of gene functions. (bioedonline.org)
- A novel intrinsic HIV-1 antisense gene was previously described with RNA initiating from the region of an HIV-1 antisense initiator promoter element (HIVaINR). (biomedcentral.com)
- Thus the proposed intrinsic HIVaINR antisense RNA microRNAs (HAAmiRNAs) of the human immunodeficiency virus form complementary targets with mRNAs of a key human gene in adaptive immunity, the IL-2Rγc, in which genetic defects are known to cause an X-linked severe combined immunodeficiency syndrome (X-SCID), as well as mRNAs of genes important in innate immunity. (biomedcentral.com)
- Trichomonas vaginalis , a sexually transmitted human parasite, was detected by performing PCR with primers from a region of the 18S rRNA gene that produce a 312 base pair product. (cdc.gov)
- In it's simplest form, genome editing involves generation of gene knockouts, where expression is eliminated through insertion or a removal of a region of genomic DNA, or knockins, where a new coding region is inserted to produce a novel gene product. (openwetware.org)
- Because very few cells undergo successful recombination, the inserted sequence must contain a selectable marker, such as an antibiotic resistance gene, to facilitate selection of modified cells. (openwetware.org)
- Once in the cell, the shRNA can decrease the expression of a gene with complementary sequences by RNAi. (thermofisher.com)
- The effect may be mediated by the sense strand of an siRNA, which may initiate a loss-of-function response from an unrelated gene. (thermofisher.com)
- Off-target effects can also occur as a secondary effect of the antisense strand of a specific siRNA, if it has sufficient homology to knock down the expression of a non-target gene. (thermofisher.com)
- MicroRNA (miRNA) molecules, on the other hand, are naturally occurring single-stranded RNAs 19-22 nucleotides long, which regulate gene expression by binding to the 3' untranslated regions (UTRs) of target mRNAs and inhibiting their translation (Ambros, 2004). (thermofisher.com)
- The sites of genomic rearrangement are specified by recombination signal sequences (RSS) that immediately flank each immune gene segment. (jimmunol.org)
- The DNA is subsequently cleaved generating double-strand breaks at the borders between the coding gene segments and the RSS. (jimmunol.org)
- Goggins LW, Vass JK, Stinson MA, Lanyon WG, Paul J (1982) A B1 repetitive sequence near the mouse β-major globin gene. (springer.com)
- Koop BF, Miyamoto MM, Embury JE, Goodman M, Czelusniak J, Slightom JL (1986) Nucleotide sequences and evolution of the orangutan epsilon globin gene region and surrounding Alu repeats. (springer.com)
- An allele (pronounced UH-leel is one of multiple alternative forms of a single gene , each of which is a viable DNA sequence occupying a given position, or locus on a chromosome . (isogg.org)
- Autosomal dominant inheritance - a gene on one of the first 22 pairs of chromosomes, which, when present in one copy, causes a trait or disease to be expressed. (lymphedemapeople.com)
- The base pairing region can be altered in each case to target a specific gene and guide the dCas9. (news-medical.net)
- In conclusion, the use of CRISPRi technique would greatly help in the field of germline gene therapy and in developing sequence-targeted precision medicines. (news-medical.net)
- Similar number of conversion events with two different chimeras indicates the absence of restricting influence of genomic target sequence on the gene repair in tobacco. (plantphysiol.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)
- 18. The applicant proposes to release 25 categories of GM sugarcane with gene sequences from a total of 19 genes of interest, two marker genes and one reporter gene (Table 2). (health.gov.au)
- With three exceptions, each category is based upon one full or partial sequence from a gene of interest, which would be combined with different regulatory elements. (health.gov.au)
- Within each category, a group of expression cassettes would be made consisting of the gene(s) of interest in combination with up to five promoters, up to three terminators and up to two targeting sequences (Table 3, Table 4). (health.gov.au)
- 20. Six categories of GM sugarcane would contain partial or complete gene sequences expected to alter plant growth of the GM sugarcane plants, with expected phenotypes including decreased or increased height and decreased or increased tillering. (health.gov.au)
- 23. Seven categories of GM sugarcane would contain partial gene sequences expected to alter sucrose accumulation by modifying sucrose transport, carbohydrate metabolism or osmotic stress tolerance. (health.gov.au)
- The partial gene sequences are derived from a common plant species, and are incorporated into constructs designed to decrease expression of homologous genes in sugarcane. (health.gov.au)
- If the base sequence of the DNA of the gene under study is known, two synthetic oligonucleotides complementary to sequences flanking the region of interest can be prepared. (jefferson.edu)
- Gene expression is the process by which a DNA sequence yields a functional product such as, for example, protein. (conservapedia.com)
- Gene expression refers to all the processes involved in converting genetic information from a DNA sequence, or protein . (conservapedia.com)
- However, options for sequencing this rapidly evolving gene set are limited because many sequencing services and off-the-shelf kits suffer from slow turnaround, inefficient capture of genomic DNA, and high cost. (cdc.gov)
- We sought to develop a custom high throughput, clinical-grade next-generation sequencing assay for detecting cardiac disease gene mutations with improved accuracy, flexibility, turnaround, and cost. (cdc.gov)
- RNA-seq is a next generation sequencing method with a wide range of applications including single nucleotide polymorphism (SNP) detection, splice junction identification, and gene expression level measurement. (beds.ac.uk)
- However, the RNA-seq sequence data can be biased during library constructions resulting in incorrect data for SNP, splice junction, and gene expression studies. (beds.ac.uk)
- The enumeration of tetrameric and other sequence motifs that are positively or negatively correlated with in vivo antisense DNA effects has been a useful addition to the arsenal of information needed to predict effective targets for antisense DNA control of gene expression. (biomedcentral.com)
- Antisense oligodeoxynucleotides are typically targeted to bind mRNA sequences, leading to inhibition of gene expression by activation of RNase H to cleave the mRNA, obstruction of translation, alteration of splicing, or other mechanisms. (biomedcentral.com)
- The experimental determination of an effective antisense DNA to inhibit the expression of a particular gene product is expensive and time-consuming, and efforts have long been made to develop a procedure for the rational design of antisense DNA sequences based on properties such as the DNA:RNA hybrid stability, the region of the mRNA being targeted, and the secondary structures of the mRNA and DNA (reviewed by Chan et al. (biomedcentral.com)
- 10. The plant of claim 9, wherein the signal sequence is derived from the signal sequence of a vacuolar targeted gene. (patentgenius.com)
- Expected eye and brain phenotypes were observed when inducing mutations in the six3 coding regions, as well as when deleting the gene promoter by dual targeting. (xenbase.org)
- The six3 gene was furthermore targeted in the proximal promoter region with two sgRNAs simultaneously to cause deletion of the promoter region. (xenbase.org)
- The range of features to be represented is diverse, including regions which: * perform a biological function, * affect or are the result of the expression of a biological function, * interact with other molecules, * affect replication of a sequence, * affect or are the result of recombination of different sequences, * are a recognizable repeated unit, * have secondary or tertiary structure, * exhibit variation, or have been revised or corrected. (insdc.org)
- In the expression and interference phases, transcription of the repeat-spacer element into precursor CRISPR RNA (pre-crRNA) molecules followed by enzymatic cleavage yields the short crRNAs that can pair with complementary protospacer sequences of invading viral or plasmid targets ( 4 - 11 ). (sciencemag.org)
- Aptamers are single-stranded oligonucleotides isolated via in vitro systematic evolution of ligands by exponential enrichment (SELEX), 1,2 which can specifically bind to a wide range of targets including proteins, small molecules and metal ions. (rsc.org)
- The crRNA and tracrRNA molecules form a duplex via a short homologous region. (stemcell.com)
- Amplification -- any process by which specific DNA sequences are replicated disproportionately greater than their representation in the parent molecules. (kumc.edu)
- In the next step, The reaction mixture is cooled (about 50-65 o C) for 20-40 seconds, to allow primers to select and bind (hybridize) to their complementary positions on the ssDNA template molecules. (mybiosource.com)
- PCR increases the concentration of DNA by copying millions upon millions of DNA molecules in a sequence specific manner allowing the invisible to be seen. (dwbio.com)
- In addition to heat, chemicals, proteins, and competition from other ssDNA molecules can disrupt base pairing. (dwbio.com)
- DNA, and RNA, molecules can also form intramolecular double strands where local regions in a sequence fold together to form stem-loop structures. (dwbio.com)
- At such temperatures, hybridized DNA molecules, of any length, often melt into single stranded molecules, unless they are protected by protein. (dwbio.com)
- Cas9 forms a complex with two small RNA molecules, a crRNA and a trans-activating crRNA (tracRNA) complementary to the pre-crRNA. (openwetware.org)
- and 3) extension of the primers in the 5′ to 3′ direction by heat-stable DNA polymerase to produce double-stranded DNA molecules. (cdc.gov)
- The copy number of DNA molecules is doubled in each extension step, generating millions of copies of the original DNA molecules when PCR is completed. (cdc.gov)
- Non-specific detection systems use a fluorescent dye that intercalates into any double-stranded DNA molecules and emits enhanced fluorescence. (cdc.gov)
- A molecular "package" for carrying DNA in cells, organized as two double-helical DNA molecules that encode many genes. (isogg.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)
- High on the list of RNA regulatory activities is RNA interference (RNAi), a mechanism by which certain double-stranded small RNA (sRNA) molecules suppress the expression of specific genes. (asmblog.org)
- The degree of base-pairing (A opposite U or T, G opposite C) between two sequences of DNA and/or RNA molecules. (thefreedictionary.com)
- The sequence of bases at a promoter is recognized by RNA polymerase, the enzyme that synthesizes RNA. (encyclopedia.com)
- However, in eukaryotes and Archaea, other proteins, called initiation factors, recognize the promoter sequence, "recruit" RNA polymerase and other proteins, help the RNA polymerase bind to the DNA, and regulate the enzyme's activity. (encyclopedia.com)
- The RNA polymerase, as it builds the chain of nucleotides, processes only one of the two complementary strands of DNA. (encyclopedia.com)
- At precise locations, determined by the promotor DNA sequence, the first and second RNA bases bind to the complex, and RNA polymerase catalyzes the formation of a covalent bond between them. (encyclopedia.com)
- First, the polymerase is able to transcribe in vitro from both supercoiled and linear DNA templates and is highly effective with double- and single-stranded synthetic templates containing a double-stranded T7 promoter. (mybiosource.com)
- During transcription, a DNA sequence is read by RNA polymerase , which produces a complementary, antiparallel RNA strand. (wikibooks.org)
- RNA polymerase then binds to DNA at a region called the promoter via binding to the transcription factors. (reference.com)
- Bacterial transcription is the process in which a segment of bacterial DNA is copied into a newly synthesized strand of messenger RNA (mRNA) with use of the enzyme RNA polymerase . (rug.nl)
- Transcription is carried out by RNA polymerase but its specificity is controlled by sequence-specific DNA binding proteins called transcription factors . (rug.nl)
- Furthermore, RNA polymerase also displays exonuclease activities, meaning that if improper base pairing is detected, it can cut out the incorrect bases and replace them with the proper, correct one. (rug.nl)
- Generally, this nucleotide sequence consists of about twelve base pairs and aids in contributing to the stability of RNA polymerase so it is able to continue along the strand of DNA. (rug.nl)
- the more similar the promoter region is to the consensus sequence, the tighter RNA polymerase will be able to bind. (rug.nl)
- cDNA -- complementary DNA produced from a RNA template by the action of RNA- dependent DNA polymerase. (kumc.edu)
- It uses thermal cycler including repeated heating and cooling mechanisms for melting of DNA and replication using thermo stable DNA polymerase, primer with specific complementary sequence of the target region and dNTPs. (mybiosource.com)
- During PCR testing, Taq polymerase and DNA primers complementary to a unique sequence of target DNA were used to greatly amplify that region if the target was present in the sample. (cdc.gov)
- In contrast, miRNAs are excised from precursors that are transcribed by RNA polymerase II as single-stranded precursors. (plantphysiol.org)
- In addition to DNA polymerase, the enzyme that synthesizes the new DNA by adding nucleotides matched to the template strand, a number of other proteins are associated with the fork and assist in the initiation and continuation of DNA synthesis. (wikibooks.org)
- The leading strand is formed along the leading strand template as a polymerase "reads" the template DNA and continuously adds nucleotides to the 3' end of the elongating strand. (wikibooks.org)
- Just as before, DNA Polymerase reads 3'-5' on the original DNA to produce a 5'-3' nascent strand. (wikibooks.org)
- The polymerase chain reaction exploits this double stranded structure and the naturally occurring process of copying an existing DNA strand by DNA polymerase. (jefferson.edu)
- If these are the only oligonucleotides present in the reaction mixture, then the DNA polymerase can only generate, i.e. "copy", daughter strands of DNA downstream from those oligonucleotides that are identical to the target DNA. (jefferson.edu)
- The first two rNTPs complementary to the DNA bind to the active site of RNA polymerase and the first phosphodiester bond is formed. (conservapedia.com)
- 1) RNA polymerase binds DNA in the promoter region (pink-shaded area) and unwinds the DNA in front of it. (psu.edu)
- RNA polymerase]] cannot bind to the promoter region unless a sigma factor is present. (ncl.ac.uk)
- RNA polymerase]] binds to the correct promoter region, this is another method in which transcription is regulated. (ncl.ac.uk)
- The function of A to I editing in these regions is thought to involve creation of splice sites and retention of RNAs in the nucleus, among others. (wikipedia.org)
- The latest generation of nucleases is provided by the CRISPR/Cas9 bacterial defense system that uses short, single guide (sg) RNAs for DNA sequence recognition and can be programmed towards new targets by adaption of the sgRNA first 20 nucleotides. (mdc-berlin.de)
- These defense systems rely on small RNAs for sequence-specific detection and silencing of foreign nucleic acids. (sciencemag.org)
- The three areas of epigenetics: DNA base modifications (including DNA methylation and DNA hydroxymethylation), histone modification and RNA-based mechanisms (including long non-coding RNAs and short RNAs). (nature.com)
- Messenger RNAs (mRNAs) are copies of individual protein-coding genes, and serve as an amplified read-out of each gene's nucleic acid sequence. (umassmed.edu)
- Transfer RNAs (tRNAs) use complementary base pairing to decode the three-letter "words" in the mRNA, each corresponding to an amino acid to be sequentially incorporated into a growing protein chain. (umassmed.edu)
- These modifications are introduced by protein enzymes in conjunction with specialized noncoding RNAs (called snoRNAs) that base pair with the rRNA and guide the modifying enzymes to precise locations on the rRNA. (umassmed.edu)
- For example, microRNAs (miRNAs) are regulatory RNAs approximately 22 nt long that are produced from longer transcripts that contain a certain kind of double-stranded "hairpin" structure. (umassmed.edu)
- MicroRNAs (miRNAs) interact in a sequence-specific manner with target messenger RNAs (mRNAs) to induce either cleavage of the message or impede translation. (biomedcentral.com)
- miRNAs are 19-23 nt single-stranded RNAs, originating from single-stranded precursor transcripts that are characterized by imperfectly base-paired hairpins. (thermofisher.com)
- To allow specific genes to be targeted, synthesis single guide RNAs (sgRNA) can be manufactured, composed of chimeric noncoding RNA sequences. (news-medical.net)
- Like DNA, most biologically active RNAs including tRNA, rRNA, snRNAs and other non-coding RNAs are extensively base paired to form double stranded helices. (wikidoc.org)
- This double stranded structure is maintained by two main forces hydrogen bonds between complementary pairs on opposite strands, and stacking interactions between neighboring base pairs. (wseas.us)
- At this point, the holoenzyme is referred to as the closed complex because the DNA is still double stranded (connected by hydrogen bonds). (rug.nl)
- When paired, A and T form two hydrogen bonds and C and G form three, so CG base pairs are stronger than AT (or AU) base pairs. (dwbio.com)
- As hydrogen bonds are weak bonds, base pairing can be disrupted by heat and other factors. (dwbio.com)
- A base pair ( bp ) is a unit consisting of two nucleobases bound to each other by hydrogen bonds . (wikipedia.org)
- Top, a G.C base pair with three hydrogen bonds . (wikipedia.org)
- Bottom, an A.T base pair with two hydrogen bonds. (wikipedia.org)
- The GU pairing, with two hydrogen bonds, does occur fairly often in RNA (see wobble base pair ). (wikipedia.org)
- Ideally, the very last nucleotide region is gc-rich, as these have 3 hydrogen bonds instead of the 2 that A-T pairs have, and this will decrease nonspecific amplification. (igem.org)
- 10 The field can be broadly categorized into three areas: DNA base modifications (including cytosine methylation and cytosine hydroxymethylation), posttranslational modifications of histone proteins and RNA-based mechanisms that operate in the nucleus, which collectively enable the cell to respond quickly to environment changes ( Figure 1 ). (nature.com)
- We were interested in whether other proteins were required to attract Rad1/Rad10 to the sites of strand invasion or strand annealing. (pnas.org)
- For efficient processing, double-stranded RNA-binding proteins support Dicer proteins. (sdbonline.org)
- Double-stranded RNA-binding domains (dsRBDs) are commonly found in modular proteins that interact with RNA. (sdbonline.org)
- The RNA polymerases in bacteria, as well as in viruses in bacteria, are able to recognize particular promoter sequences without the help of any other cellular proteins. (encyclopedia.com)
- Many RNA-binding proteins recognize specifically or semi-specifically short RNA sequences. (mybiosource.com)
- This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. (newworldencyclopedia.org)
- Proteins can either bind to a DNA sequence, or initiate the copying of it. (coursehero.com)
- Ribosomal RNA (rRNA) constitutes the core structural and enzymatic framework of the ribosome, the machine that synthesizes proteins according to the instructions contained in the sequence of an mRNA. (umassmed.edu)
- A nuclease complex composed of proteins and siRNA that targets and cleaves endogenous mRNAs complementary to the siRNA within the RISC complex. (thermofisher.com)
- These long double-stranded precursors are processed into 21- to 24- nt siRNAs by a member of the DICER-LIKE (DCL) family of proteins, typically DCL2, DCL3, or DCL4. (plantphysiol.org)
- 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)
- Whereas charge distributions of the extramembranous regions are crucial for the membrane topology of cytoplasmic membrane proteins ( 10 , 27 ), it is unknown whether the extramembranous regions of outer membrane proteins play a similar role. (asm.org)
- Unlike DNA, this structure is not just limited to long double-stranded helices but rather collections of short helices packed together into structures akin to proteins. (wikidoc.org)
- Thermodynamic data have been typically obtained for standard Watson-Crick base pairs in unmodified nucleic acids under non-physiological solution conditions, such as in the presence of 1 M NaCl and in the absence of proteins and enzymes that bind to nucleic acids. (biomedcentral.com)
- sgRNAs are bound by the generic nuclease Cas9 and guide the complex to the complementary DNA sequence, followed by the induction of a double-strand break (DSB). (mdc-berlin.de)
- We show here that in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. (sciencemag.org)
- At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand, whereas the Cas9 RuvC-like domain cleaves the noncomplementary strand. (sciencemag.org)
- The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. (sciencemag.org)
- Association of the crRNA:trRNA duplex with Cas9 causes a conformational change in the nuclease, allowing it to bind DNA at the nearby PAM site and implement the double-strand cut. (stemcell.com)
- When a Cas9, tracrRNA, crRNA complex is formed, 20 nucleotides of the crRNA are oriented to directly base-pair with a strand of the target DNA. (openwetware.org)
- It was recently demonstrated that a single, synthetic RNA, dubbed sgRNA, containing elements of both the crRNA and tracrRNA could be used to stimulate Cas9 cleavage at a site determined by the sequence of the DNA-base pairing region from the crRNA portion. (openwetware.org)
- The Cas9 protein uses a gRNA (guide RNA) sequence to cut DNA at a complementary site. (news-medical.net)
- These mutations ensured that the transcribed Cas9 endonuclease could not cut through the double-stranded DNA, but allowed it to be guided using RNA. (news-medical.net)
- The sgRNA guides the Cas9 endonuclease to a specific genomic locus via base pairing between the crRNA sequence and the target sequence, and cleaves the DNA to create a double-strand break. (zellbio.eu)
- Briefly, the sgRNA forms a complex with the Cas9 protein and identifies the target site via complementary base-pairing. (xenbase.org)
- The Cas9 nuclease subsequently cleaves the genomic DNA at the target site, just upstream of the PAM sequence. (xenbase.org)
- Once homology has been found, each DNA strand is extended from the base-paired region using the opposing overhang as a template, and, in case of internal homology, the terminal unpaired regions are removed. (uniprot.org)
- The construct will also contain a minimum of 2kb of homology to the target sequence. (wikipedia.org)
- Resolution of the two Holliday junctions in opposite planes results in crossover, integrating the vector into the chromosome and duplicating the region of shared homology ( Figure 1D ). (genetics.org)
- To carry this out, the cells are transformed with exogenous DNA (usually on a plasmid) containing the desired insertion sequence flanked by homology regions complementary to the target site sequences. (openwetware.org)
- The 5' sequence can be completely different, and in fact, what we WANT is for the homology to be to a DIFFERENT sequence - the sequence preceding the target sequence in the final plasmid product. (igem.org)
- 4 . The probe of claim 3 , wherein said nucleotide clamp region base-pairs with a nucleotide label moiety present at a 3′ end of said target polynucleotide. (google.com.au)
- 8. The method of claim 4 wherein the polynucleotide comprises a promoter that is expressible in the colorectal cancer cell and that is operably linked to a sequence encoding a member of the group consisting of an siRNA, an antisense polynucleotide and a ribozyme. (freepatentsonline.com)
- 9. The plant of claim 1, wherein the signal sequence is upstream of the 5' end of the ferulic acid esterase encoding polynucleotide. (patentgenius.com)
- 14. The plant of claim 1, wherein the signal sequence is downstream of the 3' end of the ferulic acid esterase encoding polynucleotide. (patentgenius.com)
- 15. The plant of claim 14, wherein the polynucleotide sequence further comprises a stop codon. (patentgenius.com)
- 16. The plant of claim 14, wherein the polynucleotide sequence further comprises an extension of the ferulic acid esterase reading frame to provide a linker to KDEL (SEQ ID NO: 97). (patentgenius.com)
- These stored sequences can then be transcribed to form crRNA and used to detect future infections by binding to complementary sequences and allowing them to be cleaved. (news-medical.net)
- The CRISPR system consists of a short non-coding guide RNA (sgRNA) made up of a target complementary CRISPR RNA (crRNA) and an auxiliary transactivating crRNA (tracrRNA). (zellbio.eu)
- The two primers (primer pair) can then be synthesized chemically and will then serve as leaders or initiators of the replication step. (mybiosource.com)
- This allows the primers access to the single stranded DNA (ssDNA) templates. (mybiosource.com)
- At the end of one such cycle, the net effect is synthesis of one more copy for each instance of the DNA sequence bounded by the two used primers: this effectively doubles the number of copies of the DNA region of interest with each cycle. (jefferson.edu)
- Subsequent denaturation of DNA by heat allows hybridization (annealing) of the now-single-stranded daughter strands to the available primers in preparation for elongation and the completion of one more cycle. (jefferson.edu)
- How do we design primers with overlapping sequences? (igem.org)
- However, the 5' primer end does not have to match the target sequence, and this is what comes in handy when designing these gibson-assembly primers. (igem.org)
- Transcription is the process in which genetic information stored in a strand of DNA is copied into a strand of RNA. (encyclopedia.com)
- A particular sequence of nucleotides says the same thing to one organism as it does to another, differences between organisms reflect genetic programs of different nucleotides sequences. (wseas.us)
- Chromosome -- in the eukaryotic nucleus, one of the threadlike structures consisting of chromatin and carry genetic information arranged in a linear sequence. (kumc.edu)
- Deoxyribonucleic acid (DNA) A chemical consisting of a sequence of hundreds of millions of nucleotides found in the nuclei of cells containing the genetic information about an individual. (isogg.org)
- Using these sequences, scientists have recently developed a new genetic technique called CRISPR interference (CRISPRi), which allows the suppression of genetic transcription. (news-medical.net)
- This is particularly helping in identifying genetic sequences involved in hereditary diseases such as certain forms of cancer. (news-medical.net)
- The complementary nature of this based-paired structure provides a redundant copy of the genetic information encoded within each strand of DNA. (wikipedia.org)
Antiparallel to one another1
- The PAM sequence, NGG, must follow the targeted region on the opposite strand of the DNA with respect to the region complementary sgRNA sequence. (zellbio.eu)
- instead all sgRNAs used in this study are transcribed in vitro from double-stranded DNA templates that were made by PCR (except the sgRNA for tyr target site 1, which used a cloned template, pDR274-Xt-tyr). (xenbase.org)
- note the genomic target sequence must begin with a G for proper transcriptional initiation using the T7 promoter) and a 3′ oligonucleotide (primer) that partly overlaps the 5′ primer and contains the sgRNA backbone sequence required for proper folding of sgRNAs. (xenbase.org)
- Transcription factors work to recognize specific DNA sequences and based on the cells needs, promote or inhibit additional transcription. (rug.nl)
- Specific detection systems rely on fluorescent resonance energy transfer probes that specifically recognize target sequences, thus making them the systems of choice for the molecular detection assays described here. (cdc.gov)
- A key player is Dicer , an RNase III-type endonuclease that can recognize and cleave dsRNA from viruses into short fragments (20-25 base pairs long) to yield sRNAs. (asmblog.org)
- A strong Pol III-type promoter is used to drive transcription of a target sequence designed to form hairpins and loops of variable length, which are processed by cellular siRNA machinery. (thermofisher.com)
- You need approximately 20 base pairs of your target sequence on the 3' END. (igem.org)
- Subsequent calculations of the antisense inhibitory parameters for any mRNA target sequence automatically take into account the effects of all possible overlapping combinations of nearest-neighbors in the sequence. (biomedcentral.com)
- All these results in amplification of particular sequence of DNA in the range of upto - 10Kb or in some instances upto -40Kb. (mybiosource.com)
- After a series of successive cycles of amplification, the presence of double stranded DNA product was visualized on agarose gels stained with ethidium bromide. (cdc.gov)
- It is designed to permit selective amplification of a specific target DNA sequence(s) within a heterogeneous collection of DNA sequences (e.g., total genomic DNA). (cdc.gov)
- PCR results in the selective amplification of a region of interest that can yield micrograms of product from a significantly smaller initial amount. (jefferson.edu)
- There is a high degree of sequence conservation between the two chromosomes. (biomedcentral.com)
- Human species has in total 46 chromosomes, which are grouped into 23 pairs, each pair consisting of one chromosome from our mother and one from our father. (prezi.com)
- One of the first 22 pairs of chromosomes. (lymphedemapeople.com)
- Such retrospective information derived from in vivo cellular experiments characterizes aspects of the sequence dependence of antisense inhibition that are not predicted by nearest-neighbor (NN) thermodynamic parameters derived from in vitro experiments. (biomedcentral.com)
- Data were fitted using a NNN model, neglecting end effects, to derive NNN inhibition parameters that could be combined to give parameters for a set of 49 sequences that represents the inhibitory effects of all possible overlapping triplet interactions in the cellular targets of these antisense S-DNAs. (biomedcentral.com)
- a) Nucleotide and/or amino acid sequences as used in §§ 1.821 through 1.825 are interpreted to mean an unbranched sequence of four or more amino acids or an unbranched sequence of ten or more nucleotides. (uspto.gov)
- Sequences with fewer than four specifically defined nucleotides or amino acids are specifically excluded from this section. (uspto.gov)
- Those amino acid sequences containing D-amino acids are not intended to be embraced by this definition. (uspto.gov)
- Sequences which contain fewer than four specifically identified nucleotides or amino acids will no longer be required to be submitted in computer readable form. (uspto.gov)
- β2-β2 strand amino acids mediate A3H dimerization. (bioz.com)
- This region contains a stretch of 7 amino acids that is repeated between 26 and 52 times (differences in the number of repeats occur in a species specific manner). (conservapedia.com)
- The method of claim 2 wherein the oligonucleotide primer used in amplifying the target intermediate tandem repeat sequence has a fluorescent label covalently attached thereto. (google.com.au)
- The method of claim 4, wherein the oligonucleotide primer provided in step (a) comprises a sequence selected from one of the groups of sequences consisting of: SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110 and SEQ ID NO: 111. (google.com.au)
- It is important to match the primer sequence with the single stranded DNA closely to form stable hydrogen bond. (mybiosource.com)
- In principle, the primer sequences are designed to be placed in 3' region of DNA strand which is supposed to get amplified. (mybiosource.com)
- An RNA primer is placed on the DNA strand 3' to the origin of replication. (wikibooks.org)
- An Okazaki fragment is a relatively short fragment of DNA (with no RNA primer at the 5' terminus) created on the lagging strand during DNA replication. (wikibooks.org)
- The required ingredients comprise an existing denatured strand of DNA, which is used as the template, and a primer. (jefferson.edu)
- When designing a primer, it is ABSOLUTELY VITAL that the 3' primer end has the identical sequence of the DNA you want to copy. (igem.org)
Approximately 20 base1
Single stranded arms3
- A single monomer is composed of double DNA strands that share a complementary central region of similar sequence, with four single stranded arms. (labcritics.com)
- In this two-layer 3DNA scaffold the number of free single-stranded arms increases to 36. (genisphere.com)
- similarly, the addition of a fourth set of monomers leaves 324 single-stranded arms on the surface of the 4-layer structure. (genisphere.com)
- The MFOLD programme predicted that the minimum region required for editing would form an imperfect inverted repeat hairpin . (wikipedia.org)
- e) A copy of the "Sequence Listing" referred to in paragraph (c) of this section must also be submitted in computer readable form in accordance with the requirements of § 1.824 . (uspto.gov)
- ACTION: Final Rule SUMMARY: The Patent and Trademark Office (PTO) is amending the rules for submitting nucleotide or amino acid sequences in computer readable form (CRF) for patent applications.These amendments simplify the requirements of the rules, rearrange portions of the rules for better understanding and establish consistent rules to permit a single internationally acceptable computer readable form. (uspto.gov)
- Under the previous PCT Regulations, each International Searching Authority, each International Preliminary Examining Authority and each designated/elected office was free to set the requirements for submission of sequence listings in paper and electronic form. (uspto.gov)
- Under ordinary condition, native DNA in an aqueous solution takes a double stranded structure, known as B-form. (wseas.us)
- 1032) /product="T-cell receptor beta-chain" which might be read as: This feature, which is a partial coding sequence, is formed by joining elements indicated to form one contiguous sequence encoding a product called T- cell receptor beta-chain. (insdc.org)
- Appropriate geometrical correspondence of hydrogen bond donors and acceptors allows only the "right" pairs to form stably. (wikipedia.org)
- An aldehyde group comprises a carbon atom bonded to a hydrogen atom and double-bonded to an oxygen atom (chemical formula O=CH-). Ribose forms a five-member ring with four carbon atoms and one oxygen. (newworldencyclopedia.org)
- Each nucleotide consists of a nitrogenous base , a ribose sugar, and a phosphate . (wikidoc.org)