Bacteriophage M13: Temperate bacteriophage of the genus INOVIRUS which infects enterobacteria, especially E. coli. It is a filamentous phage consisting of single-stranded DNA and is circularly permuted.Bacteriophages: Viruses whose hosts are bacterial cells.Coliphages: Viruses whose host is Escherichia coli.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.DNA Viruses: Viruses whose nucleic acid is DNA.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.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.Bacteriophage T4: Virulent bacteriophage and type species of the genus T4-like phages, in the family MYOVIRIDAE. It infects E. coli and is the best known of the T-even phages. Its virion contains linear double-stranded DNA, terminally redundant and circularly permuted.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Viral Proteins: Proteins found in any species of virus.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.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Genes, Viral: The functional hereditary units of VIRUSES.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Genome, Mitochondrial: The genetic complement of MITOCHONDRIA as represented in their DNA.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.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.DNA, Single-Stranded: A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.DNA Replication: The process by which a DNA molecule is duplicated.Bacteriophage T7: Virulent bacteriophage and type species of the genus T7-like phages, in the family PODOVIRIDAE, that infects E. coli. It consists of linear double-stranded DNA, terminally redundant, and non-permuted.Lysogeny: The phenomenon by which a temperate phage incorporates itself into the DNA of a bacterial host, establishing a kind of symbiotic relation between PROPHAGE and bacterium which results in the perpetuation of the prophage in all the descendants of the bacterium. Upon induction (VIRUS ACTIVATION) by various agents, such as ultraviolet radiation, the phage is released, which then becomes virulent and lyses the bacterium.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)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.Genome, Fungal: The complete gene complement contained in a set of chromosomes in a fungus.T-Phages: A series of 7 virulent phages which infect E. coli. The T-even phages T2, T4; (BACTERIOPHAGE T4), and T6, and the phage T5 are called "autonomously virulent" because they cause cessation of all bacterial metabolism on infection. Phages T1, T3; (BACTERIOPHAGE T3), and T7; (BACTERIOPHAGE T7) are called "dependent virulent" because they depend on continued bacterial metabolism during the lytic cycle. The T-even phages contain 5-hydroxymethylcytosine in place of ordinary cytosine in their DNA.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).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.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Capsid: The outer protein protective shell of a virus, which protects the viral nucleic acid.Bacteriophage mu: A temperate coliphage, in the genus Mu-like viruses, family MYOVIRIDAE, composed of a linear, double-stranded molecule of DNA, which is able to insert itself randomly at any point on the host chromosome. It frequently causes a mutation by interrupting the continuity of the bacterial OPERON at the site of insertion.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.Siphoviridae: A family of BACTERIOPHAGES and ARCHAEAL VIRUSES which are characterized by long, non-contractile tails.Genome, Archaeal: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.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.Genome Size: The amount of DNA (or RNA) in one copy of a genome.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Bacteriophage phi 6: Virulent bacteriophage and sole member of the genus Cystovirus that infects Pseudomonas species. The virion has a segmented genome consisting of three pieces of doubled-stranded DNA and also a unique lipid-containing envelope.Capsid Proteins: Proteins that form the CAPSID of VIRUSES.Pseudomonas Phages: Viruses whose host is Pseudomonas. A frequently encountered Pseudomonas phage is BACTERIOPHAGE PHI 6.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.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.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Podoviridae: A family of bacteriophages which are characterized by short, non-contractile tails.Bacteriophage phi X 174: The type species of the genus MICROVIRUS. A prototype of the small virulent DNA coliphages, it is composed of a single strand of supercoiled circular DNA, which on infection, is converted to a double-stranded replicative form by a host enzyme.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)Phosphorus Isotopes: Stable phosphorus atoms that have the same atomic number as the element phosphorus, but differ in atomic weight. P-31 is a stable phosphorus isotope.Bacteriophage P2: A species of temperate bacteriophage in the genus P2-like viruses, family MYOVIRIDAE, which infects E. coli. It consists of linear double-stranded DNA with 19-base sticky ends.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.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.Gene Order: The sequential location of genes on a chromosome.Genome, Protozoan: The complete genetic complement contained in a set of CHROMOSOMES in a protozoan.Bacteriophage PRD1: Bacteriophage and type species in the genus Tectivirus, family TECTIVIRIDAE. They are specific for Gram-negative bacteria.Genome, Insect: The genetic complement of an insect (INSECTS) as represented in its DNA.Genome, Chloroplast: The genetic complement of CHLOROPLASTS as represented in their DNA.Bacteriophage T3: Bacteriophage in the genus T7-like phages, of the family PODOVIRIDAE, which is very closely related to BACTERIOPHAGE T7.Myoviridae: A family of BACTERIOPHAGES and ARCHAEAL VIRUSES which are characterized by complex contractile tails.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).Virus Replication: The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.Synteny: The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.Bacteriophage P1: A species of temperate bacteriophage in the genus P1-like viruses, family MYOVIRIDAE, which infects E. coli. It is the largest of the COLIPHAGES and consists of double-stranded DNA, terminally redundant, and circularly permuted.Bacteriophage Typing: A technique of bacterial typing which differentiates between bacteria or strains of bacteria by their susceptibility to one or more bacteriophages.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Salmonella Phages: Viruses whose host is Salmonella. A frequently encountered Salmonella phage is BACTERIOPHAGE P22.Prophages: Genomes of temperate BACTERIOPHAGES integrated into the DNA of their bacterial host cell. The prophages can be duplicated for many cell generations until some stimulus induces its activation and virulence.DNA Packaging: The folding of an organism's DNA molecule into a compact, orderly structure that fits within the limited space of a CELL or VIRUS PARTICLE.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.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.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.Genetic Variation: Genotypic differences observed among individuals in a population.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.Streptococcus Phages: Viruses whose host is Streptococcus.Bacterial Proteins: Proteins found in any species of bacterium.Bacillus Phages: Viruses whose host is Bacillus. Frequently encountered Bacillus phages include bacteriophage phi 29 and bacteriophage phi 105.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).Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.RNA Phages: Bacteriophages whose genetic material is RNA, which is single-stranded in all except the Pseudomonas phage phi 6 (BACTERIOPHAGE PHI 6). All RNA phages infect their host bacteria via the host's surface pili. Some frequently encountered RNA phages are: BF23, F2, R17, fr, PhiCb5, PhiCb12r, PhiCb8r, PhiCb23r, 7s, PP7, Q beta phage, MS2 phage, and BACTERIOPHAGE PHI 6.Bacteriolysis: Rupture of bacterial cells due to mechanical force, chemical action, or the lytic growth of BACTERIOPHAGES.Staphylococcus Phages: Viruses whose host is Staphylococcus.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.Genes, Bacterial: The functional hereditary units of BACTERIA.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Chromosomes, Bacterial: Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.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).Archaeal Viruses: Viruses whose hosts are in the domain ARCHAEA.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Genome, Helminth: The genetic complement of a helminth (HELMINTHS) as represented in its DNA.Genome, Plastid: The genetic complement of PLASTIDS as represented in their DNA.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.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.Human Genome Project: A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.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.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.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.Sequence Homology: The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.Gene Transfer, Horizontal: The naturally occurring transmission of genetic information between organisms, related or unrelated, circumventing parent-to-offspring transmission. Horizontal gene transfer may occur via a variety of naturally occurring processes such as GENETIC CONJUGATION; GENETIC TRANSDUCTION; and TRANSFECTION. It may result in a change of the recipient organism's genetic composition (TRANSFORMATION, GENETIC).Viral Tail Proteins: Proteins found in the tail sections of DNA and RNA viruses. It is believed that these proteins play a role in directing chain folding and assembly of polypeptide chains.Virus Assembly: The assembly of VIRAL STRUCTURAL PROTEINS and nucleic acid (VIRAL DNA or VIRAL RNA) to form a VIRUS PARTICLE.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).Chromosomes, Artificial, Bacterial: DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.Levivirus: A bacteriophage genus of the family LEVIVIRIDAE, whose viruses contain the short version of the genome and have a separate gene for cell lysis.Virion: The infective system of a virus, composed of the viral genome, a protein core, and a protein coat called a capsid, which may be naked or enclosed in a lipoprotein envelope called the peplos.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Contig Mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.Virus Integration: Insertion of viral DNA into host-cell DNA. This includes integration of phage DNA into bacterial DNA; (LYSOGENY); to form a PROPHAGE or integration of retroviral DNA into cellular DNA to form a PROVIRUS.Gene Duplication: Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.Attachment Sites, Microbiological: Specific loci on both the bacterial DNA (attB) and the phage DNA (attP) which delineate the sites where recombination takes place between them, as the phage DNA becomes integrated (inserted) into the BACTERIAL DNA during LYSOGENY.Circoviridae: A family of very small viruses containing circular, single-stranded DNA and possessing no envelope. The modes of transmission are not known.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.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.Viral Structural Proteins: Viral proteins that are components of the mature assembled VIRUS PARTICLES. They may include nucleocapsid core proteins (gag proteins), enzymes packaged within the virus particle (pol proteins), and membrane components (env proteins). These do not include the proteins encoded in the VIRAL GENOME that are produced in infected cells but which are not packaged in the mature virus particle,i.e. the so called non-structural proteins (VIRAL NONSTRUCTURAL PROTEINS).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).Adsorption: The adhesion of gases, liquids, or dissolved solids onto a surface. It includes adsorptive phenomena of bacteria and viruses onto surfaces as well. ABSORPTION into the substance may follow but not necessarily.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Fuselloviridae: A family of lemon-shaped DNA viruses infecting ARCHAEA and containing one genus: Fusellovirus.Bacillus subtilis: A species of gram-positive bacteria that is a common soil and water saprophyte.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Genetics, Microbial: A subdiscipline of genetics which deals with the genetic mechanisms and processes of microorganisms.Viral Plaque Assay: Method for measuring viral infectivity and multiplication in CULTURED CELLS. Clear lysed areas or plaques develop as the VIRAL PARTICLES are released from the infected cells during incubation. With some VIRUSES, the cells are killed by a cytopathic effect; with others, the infected cells are not killed but can be detected by their hemadsorptive ability. Sometimes the plaque cells contain VIRAL ANTIGENS which can be measured by IMMUNOFLUORESCENCE.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.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Inovirus: A genus of filamentous bacteriophages of the family INOVIRIDAE. Organisms of this genus infect enterobacteria, PSEUDOMONAS; VIBRIO; and XANTHOMONAS.Databases, Nucleic Acid: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.Physical Chromosome Mapping: Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Geminiviridae: A family of plant viruses where the VIRION possesses an unusual morphology consisting of a pair of isometric particles. Transmission occurs via leafhoppers or whitefly. Some viruses cause economically important diseases in cultivated plants. There are four genera: Mastrevirus, Curtovirus, Topocuvirus, and BEGOMOVIRUS.Host Specificity: The properties of a pathogen that makes it capable of infecting one or more specific hosts. The pathogen can include PARASITES as well as VIRUSES; BACTERIA; FUNGI; or PLANTS.Acidianus: A genus of facultatively anaerobic coccoid ARCHAEA, in the family SULFOLOBACEAE. Cells are highly irregular in shape and thermoacidophilic. Lithotrophic growth occurs aerobically via sulfur oxidation in some species. Distribution includes solfataric springs and fields, mudholes, and geothermically heated acidic marine environments.Rheiformes: An order of large, long-necked, long-legged, flightless birds, found in South America. Known as rheas, they are sometimes called American ostriches, though they are in a separate order from true OSTRICHES.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.Pseudogenes: Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.Genetic Complementation Test: A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.Transduction, Genetic: The transfer of bacterial DNA by phages from an infected bacterium to another bacterium. This also refers to the transfer of genes into eukaryotic cells by viruses. This naturally occurring process is routinely employed as a GENE TRANSFER TECHNIQUE.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.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.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.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.Genome Components: The parts of a GENOME sequence that are involved with the different functions or properties of genomes as a whole as opposed to those of individual GENES.Virulence: The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its VIRULENCE FACTORS.Chromosomes, Plant: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.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.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.DucksBlotting, 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.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Lipothrixviridae: Family of enveloped, lipid-containing, filamentous DNA viruses that infect ARCHAEA.Plant Diseases: Diseases of plants.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)Halorubrum: A genus of HALOBACTERIACEAE which are chemoorganotrophic and strictly aerobic. They have been isolated from multiple hypersaline environments that vary widely in chemical and physical properties.Oryza sativa: Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.Mutagenesis, Insertional: Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.DNA, Intergenic: Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Genes, Plant: The functional hereditary units of PLANTS.Molecular Weight: The sum of the weight of all the atoms in a molecule.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).Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.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.Retroelements: Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.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.Deoxyribonucleases: Enzymes which catalyze the hydrolases of ester bonds within DNA. EC 3.1.-.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.Hepadnaviridae: A family of hepatotropic DNA viruses which contains double-stranded DNA genomes and causes hepatitis in humans and animals. There are two genera: AVIHEPADNAVIRUS and ORTHOHEPADNAVIRUS. Hepadnaviruses include HEPATITIS B VIRUS, duck hepatitis B virus (HEPATITIS B VIRUS, DUCK), heron hepatitis B virus, ground squirrel hepatitis virus, and woodchuck hepatitis B virus (HEPATITIS B VIRUS, WOODCHUCK).Hepadnaviridae Infections: Virus diseases caused by the HEPADNAVIRIDAE.Symbiosis: The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Chromosomes: In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.Viruses: Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells.Genetic Vectors: DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.Bacteria: One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.RNA Viruses: Viruses whose genetic material is RNA.Metabolic Networks and Pathways: Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.Cystoviridae: A family of bacteriophages containing one genus (Cystovirus) with one member (BACTERIOPHAGE PHI 6).Kinetics: The rate dynamics in chemical or physical systems.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)Interspersed Repetitive Sequences: Copies of transposable elements interspersed throughout the genome, some of which are still active and often referred to as "jumping genes". There are two classes of interspersed repetitive elements. Class I elements (or RETROELEMENTS - such as retrotransposons, retroviruses, LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS) transpose via reverse transcription of an RNA intermediate. Class II elements (or DNA TRANSPOSABLE ELEMENTS - such as transposons, Tn elements, insertion sequence elements and mobile gene cassettes of bacterial integrons) transpose directly from one site in the DNA to another.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.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.Granulovirus: A genus of the family BACULOVIRIDAE, subfamily Eubaculovirinae, characterized by ovicylindrical occlusion bodies. The type species is Cydia pomonella granulovirus.Gene Rearrangement: The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.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.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.Genomic Islands: Distinct units in some bacterial, bacteriophage or plasmid GENOMES that are types of MOBILE GENETIC ELEMENTS. Encoded in them are a variety of fitness conferring genes, such as VIRULENCE FACTORS (in "pathogenicity islands or islets"), ANTIBIOTIC RESISTANCE genes, or genes required for SYMBIOSIS (in "symbiosis islands or islets"). They range in size from 10 - 500 kilobases, and their GC CONTENT and CODON usage differ from the rest of the genome. They typically contain an INTEGRASE gene, although in some cases this gene has been deleted resulting in "anchored genomic islands".Genetic Linkage: The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.Fibroma Virus, Rabbit: A species of LEPORIPOXVIRUS causing subcutaneous localized swellings in rabbits, usually on the feet.
The single stranded DNA of the virus is converted into double stranded DNA by the host machinery. This form is called the ... "Nucleotide sequence and genetic organization of the genome of the N-specific filamentous bacteriophage IKe: Comparison with the ... new ssDNA viral genomes get bound by p5 by interaction with a specific sequence on the DNA called the packing signal. This ... M13, Fd and Fl) Are Not Functionally Interchangeable During Viral Strand Replication" (PDF). Nucleic Acids Research. 14 (12): ...
New viral genomes are produced via the rolling circle mechanism. These new single strand DNA sequences become templates for ... they convert the genome into a double-stranded intermediate form which is then replicated by the host's DNA polymerase. At the ... The phage M13 has been used to make nanosized (10−20 µm in diameter) fibers. "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV ... Welsh LC, Marvin DA, Perham RN (1998). "Analysis of X-ray diffraction from fibres of Pf1 Inovirus (filamentous bacteriophage) ...
Φ29 is a bacteriophage of Bacillus subtilis with a sequenced, linear, 19,285 base pair DNA genome. Each 5' end is covalently ... The enzyme facilitates the "debranching" of double stranded DNA. Deoxyribonucleoside triphoshate cleavage that occurs as part ... of the enzyme to continue to copy the singly primed circular genome of the M13 phage more than tenfold in a single strand (over ... and use of bacteriophage phi29 DNA polymerase for large-scale field sampling and cloning of complete maize streak virus genomes ...
Of the viral families with DNA genomes, only two have single-stranded genomes. Eight of the viral families with DNA genomes ... the result of phage genome acquisition of bacterial host genetic sequences). Evolutionary mechanisms shaping the genomes of ... 169 kbp genome, 200 nm long) T7 phage T12 phage R17 phage M13 phage MS2 phage (23-28 nm in size) G4 phage P1 phage ... The first regulated, randomized, double-blind clinical trial was reported in the Journal of Wound Care in June 2009, which ...
The genome contains 48,490 base pairs of double-stranded, linear DNA, with 12-base single-strand segments at both 5' ends. ... The original B-O-B' sequence is changed by the integration to B-O-P'-phage DNA-P-O-B'. The phage DNA is now part of the host's ... Soon, the phage switches to a rolling circle replication similar to that used by phage M13. The DNA is nicked and the 3' end ... This results (initially) in the excision of any inserted genomes from the host genome. The mRNA from the PL promoter forms a ...
Of the viral families with DNA genomes, only two have single-stranded genomes. Eight of the viral families with DNA genomes ... the result of phage genome acquisition of bacterial host genetic sequences).[41] Evolutionary mechanisms shaping the genomes of ... The first regulated, randomized, double-blind clinical trial was reported in the Journal of Wound Care in June 2009, which ... M13 Leviviridae. Nonenveloped, isometric. Linear ssRNA. MS2, Qβ Microviridae. Nonenveloped, isometric. Circular ssDNA. ΦX174 ...
... strand of the double-stranded replicative form of the phage M13 genome but not the DNA strand that is packaged in the M13 ... Targeting Bacteriophage M13 with Engineered CRISPR Spacer.. Previously, Brouns et al. (17) showed that a plasmid containing an ... 2000) Biological significance of a family of regularly spaced repeats in the genomes of Archaea, bacteria and mitochondria. Mol ... Phage DNA enters the cell as a circular single-stranded DNA ("infecting" or "(+)" strand DNA). This strand is used as a ...
"DNA-binding specificity determinants of replication proteins encoded by eukaryotic ssDNA viruses are adjacent to widely ... Nucleotide sequence of the filamentous bacteriophage M13 DNA genome: comparison with phage fd ... Precise determination, cross-recognition, and functional analysis of the double-strand origins of the rolling-circle ... Beak and feather disease virus and porcine circovirus genomes: intermediates between the geminiviruses and plant circoviruses ...
The single stranded DNA of the virus is converted into double stranded DNA by the host machinery. This form is called the ... "Nucleotide sequence and genetic organization of the genome of the N-specific filamentous bacteriophage IKe: Comparison with the ... new ssDNA viral genomes get bound by p5 by interaction with a specific sequence on the DNA called the packing signal. This ... M13, Fd and Fl) Are Not Functionally Interchangeable During Viral Strand Replication" (PDF). Nucleic Acids Research. 14 (12): ...
... sequence relatedness, and collinearity of the phage genome organization; and (iv) large double-stranded DNA genomes featuring ... The inserts of isolated plasmids were sequenced, using M13 forward and M13 reverse primers. Obtained nucleotide sequences were ... Genome sequencing.For the preparation of phage DNA libraries, purified A511 DNA was fragmented by using a nebulizer (GATC ... DNA treatment with Bal 31, an exonuclease that degrades double-stranded linear DNA from both ends simultaneously, and ...
... plasmid vectors that carry the origin of replication from the genome of a single-stranded filamentous bacteriophage such as M13 ... Most plasmids exist as double-stranded DNA molecules. If both strands of the DNA are intact circles, the molecule is described ... Probes for DNA Sequences: A probe that consists of a single strand of DNA would be able to find and bind to other complementary ... has emerged as an extension of recombinant DNA technology for high resolution mapping and characterization of whole genomes and ...
To obtain a maximally completed sequence, three libraries are cloned into the phage vector, M13, bacteriophage are used: with ... information for computer determination of a sequence of DNA having the complexity of a mammalian genome are obtained in one ... By simultaneous hybridization of DNA molecules applied as dots and bound onto a filter, representing single-stranded phage ... The sequence of a given DNA fragment is read by the hybridization and assembly of positively hybridizing probes through ...
... and it binds to DNA only in the form of a pre-formed homodimer--a pair of identical polypeptide subunits held together by non- ... Native full-length E2 trans-activation protein activates transcription of papillomavirus only through binding to DNA, ... into the filamentous single-stranded DNA bacteriophage M13 strain mp18 (Life Technologies, Inc., Gaithersburg, Md.) and ... Dartmann, K. et al., "The Nucleotide Sequence and Genome Organization of Human Papilloma Virus Type 11", Virology, 151, pp. 124 ...
The present invention relates to a recombinant DNA molecule which contains the telomere and, optionally, the centromere of a ... infection with the M13 bacteriophage can separate the double-stranded DNA into two sets of complementary single-stranded ... They have more DNA and their genomes are composed of different classes of sequences: true gene regions interrupted by numerous ... the Human Genome Southern blots of the genomic DNA prepared from some well-studied animal model systems were probed with pAtT4 ...
Screens conducted in parallel with CRISPRi/a, which do not induce double-stranded DNA breaks, revealed that a distinct set of ... M13 bacteriophage has been used as a scaffold to organize materials for various applications. Building more complex multiphage ... across 44 human tissues by using combined analyses of whole genomes and multi-tissue RNA-sequencing data from the Genotype- ... Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens NATURE COMMUNICATIONS Morgens, D ...
A method of inactivating a proviral DNA integrated into the genome of a host cell latently infected with a retrovirus by ... and other phage DNA, e.g., M13 and filamentous single stranded phage DNA; yeast plasmids such as the 2μ plasmid or derivatives ... In some embodiments, the guide RNA can be a sequence corresponding to a sequence in the genome of the virus harbored by the ... A nucleic acid can be double-stranded or single-stranded (i.e., a sense strand or an antisense strand). Non-limiting examples ...
... carries a single-strand of DNA - not a double helix. In the cell, this single-stranded genome (2.) is used as a template to ... filamentous bacteriophage such as M13, fd, or f1. These origins of replication have two important features: ... Start with a double stranded plasmid containing your DNA insert, the sequence you wish to mutagenize: ... form is used as a template to generate new single-stranded genomes (4.) that are packaged into virions (5.) to generate new ...
The genomes of these viruses consist of double strand DNA (dsDNA), single stranded DNA (ssDNA), double strand RNA (dsRNA), and ... Single-stranded DNA binding protein encoded by the filamentous bacteriophage M13: structural and functional characteristics. ... To obtain high-affinity targets, up to five rounds of biopanning are performed (Figure 5). Finally, DNA sequencing of the ... single strand RNA (ssRNA). The viruses enter host cells via pilli and are involved in genome replication, and virion structure ...
Subclones having sequences specific to cms-T mitochondrial DNA and the DNA and deduced amino acid sequences of ORI3, which is ... The reagent includes a novel nucleic acid segment whose sequence is uniquely arranged in mitochondrial DNA of cms-T maize. The ... 113:237). Single-stranded DNA clones in the bacteriophage M13 were labeled by the backpriming technique of Hu and Messing (1982 ... Target DNA can be added to the PCR as single-stranded or double-stranded molecules. Size is not crucial, but in general, high ...
And Modification Of Dna.The Lifecycle Of M13-M13 Adsorption And Injection.Protection Of The M13 Genome.M13 Dna Replication.M13 ... Double-Stranded Dna.Supercoiling Double-Stranded Dna.Replication Of The Escherichia Coli Chromosome.Constraints That Influence ... Bioinformatics And Proteomics.Bioinformatics.Strategies For Sequencing Genomes.Bacterial Genomes.Analyzing Genomes.The E. Coli ... Life Cycle Of A Bacteriophage.Lytic-Lysogenic Options.The l Lifecycle.l Adsorption.l Dna Injection.Protecting The l Genome In ...
A double stranded Htelo oligonucleotide ligand is made by DNA polymerase primer extension of the C-rich complementary sequence ... DNA may also be replicated by insertion into the host genome. However, the recovery of genomic DNA encodingthe nucleic acid ... A number of methods for site-directed mutagenesis areknown in the art, from methods employing single-stranded phage such as M13 ... such as the minor coat protein pal of bacteriophage ml3 or gene III of bacteriophage Fd, and displayed on the capsid ...
The DNA sequencing of 25 random segments of the φmF genome has indicated that this bacteriophage is related to the Salmonella ... The microvirus genus comprises isometric single-stranded DNA bacteriophage, and includes, as examples, bacteriophages G4 and ... bacteriophages ike, m13 and pf1. The plectrovirus genus comprises bacteriophages that infect Acholeplasma and Spiroplasma. [ ... 0008]The ability to easily sequence entire microbial genomes and to determine the molecular basis of their pathogenicity ...
11 occurring DNA molecules show (a) a fragment of a long, linear double-stranded human chromosome, (b) a circular double- ... Ihssen, recombination between each of the duplicated ends of one T4 genome with homologous sequences in other T4 genomes ... a linear single-stranded parvovirus chromosome, belajar indikator volume forex (d) a circular single-stranded bacteriophage M13 ... Deconstructing the © The McGrawHill Genome DNA at High Companies, the gauge fermion must have ghost number NgΨ 1. Clearly, DDHP ...
... that was modified for double-stranded DNA sequencing (Chen and Seeburg, 1985) by using the Sequenase V2 kit (U.S. Biochemical ... it has been shown that the two genomes do contain islands of conserved organization, despite the fact that the Brassica genome ... Sequence Analysis of Clones. cDNA and YAC inserts of interest were end sequenced using the M13 −20 forward or M13 reverse ... 1994). A new bacteriophage P1-derived vector for the propagation of large human DNA fragments. Nature Genet. 6, 84-89. ...
The complete DNA sequence of the long unique region in the genome of herpes simplex virus type 1. J. Gen. Virol. 69:1531-1574. ... Radiolabeled transcripts were purified and hybridized to single-stranded bacteriophage M13 probes corresponding to the viral gC ... Herpesviruses encompass a large group of medically important, nuclear-replicating double-stranded DNA viruses. Herpes simplex ... It is not known whether the promiscuous run-on transcription seen on replicating viral genomes reflects bona fide transcription ...
Φ2954 was isolated from radish leaves and was found to have a genome of three segments of double-stranded RNA (dsRNA), placing ... The base sequences for many of the genes and for the segment termini were similar but not identical to those of bacteriophage ... Although the pac sequences of Φ2954 show no similarity to those of Φ12, segment M of Φ2954 could be acquired by Φ12 resulting ... We have recently isolated a number of related phages and five showed high similarity to Φ12 in the amino acid sequences of ...
The rate of cytosine deamination in double-stranded DNA is less than 1% of that found in single-stranded DNA. Given that DNA ... Specificity of spontaneous mutation in the lacI gene cloned into bacteriophage M13. Mutat Res 1990 Jan;243(1):21-8 ... Spectrum of spontaneous mutation at the APRT locus of Chinese hamster ovary cells: an analysis at the DNA sequence level. PNAS ... The first revolves around genomic organization, as a drift in the C-to-T direction may play a role in modifying the genomes ...
It also deals with common plasmid DNA procedures, including how to make and transform competent cells, how to culture and ... This section describes considerations for isolation and quantification of both genomic DNA from different sample sources and ... handle plasmid-containing cells, and commonly used techniques for analysis of genomic DNA. ... or double-stranded, linear, or circular. All other organisms have double-stranded DNA genomes. Bacteria have a single, circular ...
Double-stranded (ds) 32P-end-labelled 49-nt DNA containing m1A, m3C, or εA in one strand of the DpnII restriction site GATC was ... AlkB− E. coli expressing the indicated bacterial AlkB proteins were infected with ssDNA bacteriophage M13 that had been treated ... Genomes & Maps*Database of Genomic Structural Variation (dbVar). *GenBank: tbl2asn. *Genome. *Genome Project ... Based on sequence phylogeny, we show that these proteins can be subdivided into four groups: denoted 1A, 1B, 2A and 2B; each ...
"Atomic Force Microscopy of Single-Stranded and Double-Stranded DNA Adsorbed on Chemically Treated Mica," Bull. Am. Phys. Soc. ... "Electron Microscopic Comparison of the Sequences of Single-Stranded Genomes of Mammalian Parvoviruses by Heteroduplex Mapping ... "Electron Microscopic Studies of M13 Bacteriophage DNA Replication," J. Virol. 24, 673-84. ... Research highlights include the development of a procedure to map DNA cosmids, during the Genome project era, using atomic ...
... coli bacterio-phages. M13 is a male-specific lysogenic phage with a circular single-stranded DNA genome 6407 bp in length ... possesses its own genome. The chloroplast genome is a single circular double-stranded DNA molecule, which, in the model ... A. The wild-type DNA sequence of the sense strand of part of exon 2 from the human Pax-3 gene. The sequence shown represents ... Breaking and joining DNA using restriction enzymes and DNA ligase. Linear DNA insert and a closed-circular plasmid DNA vector ...
  • Recombinant DNA technology has revolutionised life sciences, opening new vistas for research in molecular biology. (biologydiscussion.com)
  • The size, number of chromosomes, and nature of genomic DNA varies between different organisms (see table Sizes and molecular weights of various genomic DNAs ). (qiagen.com)
  • Molecular cloning is process of creating an identical copy of DNA fragments. (f-mx.ru)
  • In Biology, it collectively refers to processes used to create copies of DNA fragments (Molecular Cloning), cells (Cell Cloning), or organisms. (f-mx.ru)
  • The molecular analysis of DNA has been made possible by the cloning of DNA. (f-mx.ru)
  • In British patent application no. 8525252 (publication no. 2166445) there are described various DNA sequences which may be used as probes to hybridize individually at a number of polymorphic sites within the human and animal genomes enabling the production of a "fingerprint" composed of marked bands of differing molecular weights. (google.com.au)
  • Figure 1: High resolution AFM and atomistic molecular dynamics simulations reveal the structure of supercoiled DNA to the base pair level. (birs.ca)
  • Here, we show that only protospacer positions proximal to the PAM need to perfectly match the CRISPR spacer sequence in Escherichia coli . (pnas.org)
  • T Hooft, Fermion-Boson Puzzle in a Gauge Theory, and bacteriophage BF23 by Escherichia coli kinetics of phenotypic expression after the introduction of bfe and bfe alleles. (retzepti.ru)
  • The iron(II)- and 2-oxoglutarate (2OG)-dependent dioxygenase AlkB from Escherichia coli (EcAlkB) repairs alkylation damage in DNA by direct reversal. (nih.gov)
  • The DNA of Escherichia coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases, and these are formed by the postreplicative action of three DNA methyltransferases. (asmscience.org)
  • Biological function for 6-methyladenine residues in the DNA of Escherichia coli K12. (asmscience.org)
  • Recombination is essential for viability of an Escherichia coli dam (DNA adenine methyltransferase) mutant. (asmscience.org)
  • Using the type I-E CRISPR-Cas system in Escherichia coli as a model, we found that this effect could be elicited using native or imported systems and was similarly potent regardless of the genomic location, strand, or transcriptional activity of the target sequence. (asm.org)
  • CI binds to two operator regions on the phage genome, designated O R and O L , which are each further divided into three closely spaced binding sites (16 to 18 bp) termed operators O R1/L1 to O R3/L3 (reviewed in reference 27 ). (asm.org)
  • Restriction endonucleases are a class of enzymes that can recognise and bind to specific DNA sequences of four to eight nucleotides, then cleave the sugar-phosphate backbone of each of the two strands at the site of binding. (biologydiscussion.com)
  • Both strands are affected, because the new version is simply copied into its complementary nucleotides on the bottom strand. (escience.ws)
  • One way to appreciate this is to consider the mutagenic effects of deamination among the four nucleotides used by DNA. (wordpress.com)
  • In figure 2, the average substitution rate for each of the four nucleotides is shown as it would be experienced along a hypothetical sequence of ATCGGATGAATCGATCT (red bars). (wordpress.com)
  • Acrylamide gels are especially useful for high resolution separations of DNA in the range of tens to hundreds of nucleotides in length. (umich.edu)
  • To obtain a maximally completed sequence, three libraries are cloned into the phage vector, M13, bacteriophage are used: with the 0.5 kb and 7 kbp insert consisting of two sequences, with the average distance in genomic DNA of 100 kbp. (google.com)
  • While a phage vector limits the size of the insert into pVIII to a few amino acids, a phagemid system limits the number of copies actually displayed at the surface of M13. (stanford.edu)
  • Figure 3.14 shows the overall architecture of a cosmid vector and a cloning scheme for the insertion of foreign DNA. (rrnursingschool.biz)
  • Vector is an agent that can carry out a DNA fragment into a host cell. (f-mx.ru)
  • B) For generation of template DNA for unrelated MiAchE , PCR amplification was performed on pGEM T- MiAchE vector using M13 primers. (bioz.com)
  • Thermally Induced DNA.RNA Hybrid to G-Quadruplex Transitions: Possible Implications for Telomere Synthesis byTelomerase", Biochemistry vol. 35, pp. 16110-16115 (1996). (patentgenius.com)
  • The synthesis of cDNA using modified oligonucleotides to initiate each strand of DNA synthesis allows the insertion of unique restriction enzyme recognition sites at either end of the cDNA so that cloning of the cDNA fragments can only occur in one direction (Figure 5.6). (rrnursingschool.biz)
  • Amplification of a complex mixture of relatively short DNA fragments, derived from mini scale experiments in chromatin immunoprecipitation (ChIP), degraded forensic material, cDNA synthesis, clinical diagnostics, stored tumor or other tissue samples is an area of genome research which has received scant attention. (biomedcentral.com)
  • The strand which came from the virus (VS) is nicked by the viral protein p2 (pII). (wikipedia.org)
  • Engineering and study of protein function by directed evolution has been limited by the technical requirement to use global mutagenesis or introduce DNA libraries. (stanford.edu)
  • The yeast telomere-binding protein RAP1 binds to and promotes the formation of DNA quadruplexes in telomeric DNA", The EMBO J., vol. 13, pp. 2411-2420 (1994). (patentgenius.com)
  • Reverse branch migration of Holliday junctions by RecG protein a new mechanism for resolution of intermediates in recombination and DNA repair. (retzepti.ru)
  • Existence of an intermediate messenger between DNA and protein 1. (retzepti.ru)
  • Approximately half of the cDNAs isolated from the region represent novel expressed sequence tags that do not match entries in the DNA and protein databases. (plantcell.org)
  • I also wish to thank Janet Rogers for DNA sequencing and Dr. Steve Hartson for protein mass determination. (okstate.edu)
  • The CI protein, which is a monomer of 25.3 kDa in solution, specifically binds to a 153-bp DNA fragment that contains two divergent promoters, P L and P R . These promoters mediate transcription from cI and a putative cro , respectively. (asm.org)
  • A region of the DNA which IS transcribed into mRNA and becomes the 3' end or the message, but which does not contain protein coding sequence. (umich.edu)
  • N6-methyl-adenine: an epigenetic signal for DNA-protein interactions. (asmscience.org)
  • For a million bp of genomic DNA, 25,000 subclones of the 0.5 kbp are required as well as 700 subclones 7 kb long and 170 jumping subclones. (google.com)
  • You begin by preparing a small amount of genomic DNA from skin, blood, semen, or other tissue that is easy to obtain from your patient suffering from the novel anemia. (retzepti.ru)
  • Southern blot analysis of M. sexta genomic DNA 66 5. (okstate.edu)
  • The rapid speed of sequencing attained with modern DNA sequencing technology has been instrumental in the sequencing of complete DNA sequences, or genomes of numerous types and species of life, including the human genome and other complete DNA sequences of many animal, plant, and microbial species. (wikidoc.org)
  • Here we describe an improved method for obtaining both phage and microbial DNA from a single skin or wound swab, characterize the yield of DNA in model samples, and demonstrate the utility of this approach with samples collected from a wound clinic. (springer.com)
  • While different antimicrobial strategies, such as antibiotics, antimicrobial peptides, and lytic bacteriophages, offer partial solutions, what remains elusive is a generalized and programmable strategy that can distinguish between even closely related microorganisms and that allows for fine control over the composition of a microbial population. (asm.org)
  • These systems can be employed to selectively and quantitatively remove individual bacterial strains based purely on sequence information, creating opportunities in the treatment of multidrug-resistant infections, the control of industrial fermentations, and the study of microbial consortia. (asm.org)
  • Accordingly, the invention relates to the preparation of this enzyme from various sources by recombinant techniques, to nucleic acid segments which encode the enzyme or which can be used as probes for the selection of related sequences, as well as to assay methods for the identification of candidate substances which will affect the activity of the enzyme. (google.co.uk)
  • A total of 26 genomic and 21 cDNA markers derived from Arabidopsis yeast artificial and bacterial artificial chromosome clones were used to analyze this region in the two genomes. (plantcell.org)
  • The physical maps that we derived by using these markers as well as markers isolated from bacteriophage clones spanning the S 8 haplotype revealed a high degree of synteny at the submegabase scale between the two homeologous regions. (plantcell.org)
  • Mutations in the seed region abolish CRISPR/Cas mediated immunity by reducing the binding affinity of the crRNA-guided Cascade complex to protospacer DNA. (pnas.org)
  • Biologists affiliated with the Intelligent Design movement nail down the distinction by showing that DNA mutations do not create evolution in any significant sense. (antievolution.org)
  • Mutation rates in higher eukaryotes are roughly 0.1-100 per genome per sexual generation but are currently indistinguishable from 1/300 per cell division per effective genome (which excludes the fraction of the genome in which most mutations are neutral). (genetics.org)
  • If adaptive mutations are rare, as seems to be the case, then rates of DNA sequence evolution are driven mainly by mutation and random drift, as K imura ( 1983a ) has argued. (genetics.org)
  • Research highlights include the development of a procedure to map DNA cosmids, during the Genome project era, using atomic force microscopy (AFM). (ornl.gov)
  • It includes any method or technology that is used to determine the order of the four bases- adenine , guanine , cytosine , and thymine -in a strand of DNA. (wikidoc.org)
  • This is the gel of choice for DNA or RNA in the range of thousands of bases in length, or even up to 1 megabase if you are using pulsed field gel electrophoresis. (umich.edu)
  • in this group, therefore, rates per base pair vary inversely and hugely as genome sizes vary from 6 × 10 3 to 4 × 10 7 bases or base pairs. (genetics.org)
  • In 1973, Gilbert and Maxam reported the sequence of 24 basepairs using a method known as wandering-spot analysis. (wikidoc.org)
  • d) repeating steps (a)-(c) with combinations of other unlabeled and labeled oligonucleotide probes until the order of the fragments of the nucleic acid sequence can be determined. (google.com)
  • CsCl gradients), DNA extraction kits are available from many suppliers. (qiagen.com)
  • In contrast to antibiotics, bacteriophages have a number of advantages: they have no side effects and are strictly bacterium-specific so do not disrupt the normal human microbiome. (scfh.ru)