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Pseudoknot
__NOTOC__ A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow mosaic virus in 1982. Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knots. These structures are categorized as cross (X) topology within the circuit topology framework, which, in contrast to knot theory, is a contact-based approach. Prediction and identification The structural configuration of pseudoknots does not lend itself well to bio-computational detection due to its context-sensitivity or "overlapping" nature. The base pairing in pseudoknots is not well nested; that is, base pairs occur that "overlap" one another in sequence position. This makes the presence of pseudoknots in RNA sequences more difficult to predict by the standard method of dynamic programming, which use a recur ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pseudoknot 1YMO
__NOTOC__ A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow mosaic virus in 1982. Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knots. These structures are categorized as cross (X) topology within the circuit topology framework, which, in contrast to knot theory, is a contact-based approach. Prediction and identification The structural configuration of pseudoknots does not lend itself well to bio-computational detection due to its context-sensitivity or "overlapping" nature. The base pairing in pseudoknots is not well nested; that is, base pairs occur that "overlap" one another in sequence position. This makes the presence of pseudoknots in RNA sequences more difficult to predict by the standard method of dynamic programming, which use a recursiv ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleic Acid Structure Prediction
Nucleic acid structure prediction is a computational method to determine ''secondary'' and ''tertiary'' nucleic acid structure from its sequence. Secondary structure can be predicted from one or several nucleic acid sequences. Tertiary structure can be predicted from the sequence, or by comparative modeling (when the structure of a homologous sequence is known). The problem of predicting nucleic acid secondary structure is dependent mainly on base pairing and base stacking interactions; many molecules have several possible three-dimensional structures, so predicting these structures remains out of reach unless obvious sequence and functional similarity to a known class of nucleic acid molecules, such as transfer RNA (tRNA) or microRNA (miRNA), is observed. Many secondary structure prediction methods rely on variations of dynamic programming and therefore are unable to efficiently identify pseudoknots. While the methods are similar, there are slight differences in the approach ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleic Acid Secondary Structure
Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. It can be represented as a list of bases which are paired in a nucleic acid molecule. The secondary structures of biological DNAs and RNAs tend to be different: biological DNA mostly exists as fully base paired double helices, while biological RNA is single stranded and often forms complex and intricate base-pairing interactions due to its increased ability to form hydrogen bonds stemming from the extra hydroxyl group in the ribose sugar. In a non-biological context, secondary structure is a vital consideration in the nucleic acid design of nucleic acid structures for DNA nanotechnology and DNA computing, since the pattern of basepairing ultimately determines the overall structure of the molecules. Fundamental concepts Base pairing In molecular biology, two nucleotides on opposite complementary DNA or RNA strands that are connected via hydroge ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Long Range Pseudoknots
A long range pseudoknot is a pseudoknot containing a long loop region, and may be a mechanism of translational control. A long range pseudoknot is thought to negatively regulate the translation of the IF3-L35-L20 operon in ''E. coli''. This operon encodes the translation initiation factor IF-3 and ribosomal proteins L35 and L20. In this example, the RNA-RNA interaction occurs between nucleotides separated by a 300 nucleotide loop region. A long range pseudoknot is also believed to be required for the activity of the ''Neurospora'' VS ribozyme Ribozymes (ribonucleic acid enzymes) are RNA molecules that have the ability to Catalysis, catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes. The 1982 discovery of ribozy .... References External links Rfam entry for Long range pseudoknots{dead link, date=January 2018 , bot=InternetArchiveBot , fix-attempted=yes Non-coding RNA ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RNA Tertiary Structure
Nucleic acid tertiary structure is the Biomolecular structure#Tertiary structure, three-dimensional shape of a nucleic acid polymer. RNA and DNA molecules are capable of diverse functions ranging from molecular recognition to catalysis. Such functions require a precise three-dimensional structure. While such structures are diverse and seemingly complex, they are composed of recurring, easily recognizable tertiary structural motifs that serve as molecular building blocks. Some of the most common motifs for RNA and DNA tertiary structure are described below, but this information is based on a limited number of solved structures. Many more tertiary structural motifs will be revealed as new RNA and DNA molecules are structurally characterized. Helical structures Double helix The double helix is the dominant tertiary structure for biological DNA, and is also a possible structure for RNA. Three DNA conformations are believed to be found in nature, A-DNA, B-DNA, and Z-DNA. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Stem-loop
Stem-loops are nucleic acid Biomolecular structure, secondary structural elements which form via intramolecular base pairing in single-stranded DNA or RNA. They are also referred to as hairpins or hairpin loops. A stem-loop occurs when two regions of the same nucleic acid strand, usually Complementarity (molecular biology), complementary in nucleotide sequence, base-pair to form a double helix that ends in a loop of unpaired nucleotides. Stem-loops are most commonly found in RNA, and are a key building block of many RNA biomolecular structure#Secondary structure, secondary structures. Stem-loops can direct RNA folding, protect structural stability for messenger RNA (mRNA), provide recognition sites for RNA-binding protein, RNA binding proteins, and serve as a Substrate (chemistry), substrate for Enzyme catalysis, enzymatic reactions. Formation and stability The formation of a stem-loop is dependent on the stability of the helix and loop regions. The first prerequisite is the p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Telomerase RNA Component
Telomerase RNA component, also known as TR, TER or TERC, is an Non-coding RNA, ncRNA found in eukaryotes that is a component of telomerase, the enzyme used to extend telomeres. TERC serves as a template for telomere DNA replication, replication (Reverse transcriptase, reverse transcription) by telomerase. Telomerase RNAs differ greatly in sequence and structure between vertebrates, ciliates and yeasts, but they share a 5' pseudoknot structure close to the template sequence. The vertebrate telomerase RNAs have a 3' Small nucleolar RNA#H/ACA box, H/ACA snoRNA-like domain. Structure TERC is a Long non-coding RNA (lncRNA) ranging in length from ~150nt in ciliates to 400-600nt in vertebrates, and 1,300nt in yeast (Alnafakh). Mature human TERC (hTR) is 451nt in length. TERC has extensive secondary structural features over 4 principal conserved domains. The core domain, the largest domain at the 5’ end of TERC, contains the CUAAC Telomere template sequence. Its secondary structu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Stochastic Context-free Grammar
In theoretical linguistics and computational linguistics, probabilistic context free grammars (PCFGs) extend context-free grammars, similar to how hidden Markov models extend regular grammars. Each Formal grammar#The syntax of grammars, production is assigned a probability. The probability of a derivation (parse) is the product of the probabilities of the productions used in that derivation. These probabilities can be viewed as parameters of the model, and for large problems it is convenient to learn these parameters via machine learning. A probabilistic grammar's validity is constrained by context of its training dataset. PCFGs originated from grammar theory, and have application in areas as diverse as natural language processing to the study the structure of RNA molecules and design of programming languages. Designing efficient PCFGs has to weigh factors of scalability and generality. Issues such as grammar ambiguity must be resolved. The grammar design affects results accuracy. Gr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Knot (mathematics)
In mathematics, a knot is an embedding of the circle () into three-dimensional Euclidean space, (also known as ). Often two knots are considered equivalent if they are ambient isotopic, that is, if there exists a continuous deformation of which takes one knot to the other. A crucial difference between the standard mathematical and conventional notions of a knot is that mathematical knots are closed — there are no ends to tie or untie on a mathematical knot. Physical properties such as friction and thickness also do not apply, although there are mathematical definitions of a knot that take such properties into account. The term ''knot'' is also applied to embeddings of in , especially in the case . The branch of mathematics that studies knots is known as knot theory and has many relations to graph theory. Formal definition A knot is an embedding of the circle () into three-dimensional Euclidean space (), or the 3-sphere (), since the 3-sphere is compact. Two knots ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Circuit Topology
The circuit topology of a folded linear polymer refers to the arrangement of its intra-molecular contacts. Examples of linear polymers with intra-molecular contacts are nucleic acids and proteins. Proteins fold via the formation of contacts of various natures, including hydrogen bonds, disulfide bonds, and beta-beta interactions. RNA molecules fold by forming hydrogen bonds between nucleotides, forming nested or non-nested structures. Contacts in the genome are established via protein bridges including CTCF and cohesins and are measured by technologies including Chromosome conformation capture, Hi-C. Circuit topology categorises the topological arrangement of these physical contacts, that are referred to as hard contacts (or h-contacts). Furthermore, chains can fold via knotting (or the formation of "soft" contacts (s-contacts)). Circuit topology uses a similar language to categorise both "soft" and "hard" contacts, and provides a full description of a folded linear chain. In this ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Base Pair
A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, "Watson–Crick" (or "Watson–Crick–Franklin") base pairs (guanine–cytosine and adenine–thymine) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. The Complementarity (molecular biology), complementary nature of this based-paired structure provides a Redundancy (information theory), redundant copy of the genetic information encoded within each strand of DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
