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RAGATH RNA Motifs
RNAs Associated with Genes Associated with Twister and Hammerhead ribozymes (RAGATH) refers to a bioinformatics strategy that was devised to find self-cleaving ribozymes in bacteria. It also refers to candidate RNAs, or RAGATH RNA motifs, discovered using this strategy. With the discovery of the twister ribozyme, it was recognized that many genetic elements in bacteria are often located nearby to twister ribozymes and also to the previously discovered hammerhead ribozymes. These genetic elements include several gene classes, many of which are characteristic of Mu-like phages. The nearby elements also include twister and hammerhead ribozymes. In other words, twister and hammerhead ribozymes are often located in bacteria nearby to other twister or hammerhead ribozymes. Given these observations, researchers hypothesized that other classes of self-cleaving ribozymes would also associate with these genetic elements. Therefore, searches were conducted on the non-coding regions ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Secondary Structure
Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein protein folding, folds into its three dimensional protein tertiary structure, tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the Amine, amino hydrogen and carboxyl oxygen atoms in the peptide backbone chain, backbone. Secondary structure may alternatively be defined based on the regular pattern of backbone Dihedral angle#Dihedral angles of proteins, dihedral angles in a particular region of the Ramachandran plot regardless of whether it has the correct hydrogen bonds. The concept of secondary structure was first introduced by Kaj Ulrik ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Conservation
In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids ( DNA and RNA) or proteins across species ( orthologous sequences), or within a genome ( paralogous sequences), or between donor and receptor taxa ( xenologous sequences). Conservation indicates that a sequence has been maintained by natural selection. A highly conserved sequence is one that has remained relatively unchanged far back up the phylogenetic tree, and hence far back in geological time. Examples of highly conserved sequences include the RNA components of ribosomes present in all domains of life, the homeobox sequences widespread amongst Eukaryotes, and the tmRNA in Bacteria. The study of sequence conservation overlaps with the fields of genomics, proteomics, evolutionary biology, phylogenetics, bioinformatics and mathematics. History The discovery of the role of DNA in heredity, and observations by Frederick Sanger of variation between animal insulins in 1949, promp ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a basic unit of heredity and the molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protein-coding genes and noncoding genes. During gene expression, the DNA is first copied into RNA. The RNA can be directly functional or be the intermediate template for a protein that performs a function. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic traits. These genes make up different DNA sequences called genotypes. Genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes (many different genes) as well as gen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Small RNA
Small RNA (sRNA) are polymeric RNA molecules that are less than 200 nucleotides in length, and are usually non-coding Non-coding DNA (ncDNA) sequences are components of an organism's DNA that do not encode protein sequences. Some non-coding DNA is transcribed into functional non-coding RNA molecules (e.g. transfer RNA, microRNA, piRNA, ribosomal RNA, and regula .... RNA silencing is often a function of these molecules, with the most common and well-studied example being RNA interference (RNAi), in which endogenously expressed microRNA (miRNA) or exogenously derived small interfering RNA (siRNA) induces the degradation of complementarity (molecular biology), complementary messenger RNA. Other classes of small RNA have been identified, including piwi-interacting RNA (piRNA) and its subspecies rasiRNA, repeat associated small interfering RNA (rasiRNA). Small RNA "is unable to induce RNAi alone, and to accomplish the task it must form the core of the RNA–protein complex termed the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ribozyme
Ribozymes (ribonucleic acid enzymes) are RNA molecules that have the ability to catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes. The 1982 discovery of ribozymes demonstrated that RNA can be both genetic material (like DNA) and a biological catalysis, catalyst (like protein enzymes), and contributed to the RNA world hypothesis, which suggests that RNA may have been important in the evolution of prebiotic self-replicating systems. The most common activities of natural or in vitro-evolved ribozymes are the cleavage or ligation of RNA and DNA and peptide bond formation. For example, the smallest ribozyme known (GUGGC-3') can aminoacylate a GCCU-3' sequence in the presence of PheAMP. Within the ribosome, ribozymes function as part of the large subunit ribosomal RNA to link amino acids during Translation (biology), protein synthesis. They also participate in a variety of RNA processing reactions, including RNA ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, and the deep biosphere of Earth's crust. Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of dead bodies; bacteria are responsible for the putrefaction stage in this process. In the biological communities surrounding hydrothermal vents and cold seeps, extremophile bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. Bacteria also live in symbiotic and parasitic relationsh ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Twister Ribozyme
The twister ribozyme is a catalytic RNA structure capable of self- cleavage. The nucleolytic activity of this ribozyme has been demonstrated both ''in vivo'' and ''in vitro'' and has one of the fastest catalytic rates of naturally occurring ribozymes with similar function. The twister ribozyme is considered to be a member of the small self-cleaving ribozyme family which includes the hammerhead, hairpin, hepatitis delta virus (HDV), Varkud satellite (VS), and glmS ribozymes. Discovery In contrast to ''in vitro'' selection methods, which have aided in identifying several classes of catalytic RNA motifs, the twister ribozyme was discovered by a bioinformatics approach as a conserved RNA structure of unknown function. The hypothesis that it functions as a self-cleaving ribozyme was suggested by the similarity between genes nearby to twister ribozymes and genes nearby to hammerhead ribozymes, Indeed, the genes located nearby to these two self-cleaving ribozyme classes overlap ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hammerhead Ribozyme
The hammerhead ribozyme is an RNA motif that catalyzes reversible cleavage and ligation reactions at a specific site within an RNA molecule. It is one of several catalytic RNAs (ribozymes) known to occur in nature. It serves as a model system for research on the Nucleic acid structure, structure and properties of RNA, and is used for targeted RNA cleavage experiments, some with proposed therapeutic applications. Named for the resemblance of early secondary structure diagrams to a hammerhead shark, hammerhead ribozymes were originally discovered in two classes of plant virus-like RNAs: Satellite (biology), satellite RNAs and viroids. They are also known in some classes of Retrotransposon, retrotransposons, including the Retrozyme, retrozymes. The hammerhead ribozyme motif has been ubiquitously reported in lineages across the tree of life. The self-cleavage reactions, first reported in 1986, are part of a rolling circle replication mechanism. The hammerhead sequence is sufficient fo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bacteriophage Mu
Bacteriophage Mu, also known as mu phage or mu bacteriophage, is a muvirus (the first of its kind to be identified) of the family ''Myoviridae'' which has been shown to cause genetic transposition. It is of particular importance as its discovery in ''Escherichia coli'' by Larry Taylor was among the first observations of insertion elements in a genome. This discovery opened up the world to an investigation of transposable elements and their effects on a wide variety of organisms. While Mu was specifically involved in several distinct areas of research (including ''E. coli'', maize, and HIV), the wider implications of transposition and insertion transformed the entire field of genetics. Anatomy Phage Mu is nonenveloped, with a head and a tail. The head has an icosahedral structure of about 54 nm in width. The neck is knob-like, and the tail is contractile with a base plate and six short terminal fibers. The genome has been fully sequenced and consists of 36,717 nucleotides, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Twister Sister Ribozyme
The twister sister ribozyme (TS) is an RNA structure that catalyzes its own cleavage at a specific site. In other words, it is a self-cleaving ribozyme. The twister sister ribozyme was discovered by a bioinformatics strategy as an RNA Associated with Genes Associated with Twister and Hammerhead ribozymes, or RAGATH. The twister sister ribozyme has a possible structural similarity to twister ribozymes. Some striking similarities were noted, but also surprising differences, such as the absence of the two pseudoknot interactions in the twister ribozyme. The exact nature of the structural relationship between twister and twister sister ribozymes, if any, has not be determined. Discovery The twister sister ribozyme was discovered through a bioinformatic search. This study conducted a search for conserved RNA structures near known twister and hammerhead ribozymes as well as certain protein-coding genes based on the fact that many ribozymes are located near to each other and n ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pistol Ribozyme
The pistol ribozyme is an RNA structure that catalyzes its own cleavage at a specific site. In other words, it is a self-cleaving ribozyme. The pistol ribozyme was discovered through comparative genomic analysis. Subsequent biochemical analysis determined further biochemical characteristics of the ribozyme. This understanding was further advanced by an atomic-resolution crystal structure In crystallography, crystal structure is a description of the ordered arrangement of atoms, ions or molecules in a crystal, crystalline material. Ordered structures occur from the intrinsic nature of the constituent particles to form symmetric pat ... of a pistol ribozyme Discovery Pistol ribozyme was discovered by a bioinformatics strategy as an RNA Associated with Genes Associated with Twister and Hammerhead ribozymes, or RAGATH. Physical Properties Comparative analysis of 501 unique samples of pistol ribozyme from ribozyme-associated gene classes and bacterial DNA sequences was done to ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hatchet Ribozyme
Background: The hatchet ribozyme is an RNA structure that catalyzes its own cleavage at a specific site. In other words, it is a self-cleaving ribozyme. Hatchet ribozymes were discovered by a bioinformatics strategy as RNAs Associated with Genes Associated with Twister and Hammerhead ribozymes, or RAGATH. Subsequent biochemical analysis supports the conclusion of a ribozyme function, and determined further characteristics of the chemical reaction catalyzed by the ribozyme. Nucleolytic ribozymes are small RNAs that adopt compact folds capable of site-specific cleavage/ligation reactions. 14 unique nucleolytic ribozymes have been identified to date, including recently discovered twister, pistol, twister-sister, and hatchet ribozymes that were identified based on application of comparative sequence and structural algorithms. The consensus sequence and secondary structure of this class includes 13 highly conserved and numerous other modestly conserved nucleotides inter-dispersed ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
