Double-stranded RNA (dsRNA) is RNA with two complementary strands, similar to the DNA found in all cells, but with the replacement of thymine by uracil. dsRNA forms the genetic material of some viruses (double-stranded RNA viruses). Double-stranded RNA, such as viral RNA or siRNA, can trigger RNA interference in eukaryotes, as well as interferon response in vertebrates.
Double-stranded RNA
RNA
RNA | Double-stranded RNA
Yes, Double-stranded RNA is RNA with two complementary strands Yes, RNA with two complementary strands. Yes. Yes.
rna consists of how many chains of subunits
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Small RNAs mainly include 5.8S ribosomal RNA (rRNA), 5S rRNA, transfer RNA (tRNA), microRNA (miRNA), small interfering RNA (siRNA), small nucleolar RNA (snoRNAs), Piwi-interacting RNA (piRNA), tRNA-derived small RNA (tsRNA) and small rDNA-derived RNA (srRNA)
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are they also double-stranded?
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Double-stranded RNA (dsRNA) is RNA with two complementary strands, similar to the DNA found in all cells, but with the replacement of thymine by uracil. dsRNA forms the genetic material of some viruses (double-stranded RNA viruses). Double-stranded RNA, such as viral RNA or siRNA, can trigger RNA interference in eukaryotes, as well as interferon response in vertebrates.
RNA | Double-stranded RNA
Double-stranded RNA viruses (dsRNA viruses) are a polyphyletic group of viruses that have double-stranded genomes made of ribonucleic acid. The double-stranded genome is used to transcribe a positive-strand RNA by the viral RNA-dependent RNA polymerase (RdRp). The positive-strand RNA may be used as messenger RNA (mRNA) which can be translated into viral proteins by the host cell's ribosomes. The positive-strand RNA can also be replicated by the RdRp to create a new double-stranded viral genome. Double-stranded RNA viruses are classified in two separate phyla "Duplornaviricota" and "Pisuviricota" (specifically class "Duplopiviricetes"), which are in the kingdom "Orthornavirae" and realm "Riboviria". The two groups do not share a common dsRNA virus ancestor.
Double-stranded RNA viruses | Introduction
The same helical conformation occurs in double-stranded RNAs, and in DNA-RNA hybrid double helices.
A-DNA | Introduction
The majority of fungal viruses are double-stranded RNA viruses. A small number of positive-strand RNA viruses have been described. One report has suggested the possibility of a negative stranded virus.
RNA virus | Notes
The absence of the 2′ hydroxyl group in deoxyribose is apparently responsible for the increased mechanical flexibility of DNA compared to RNA, which allows it to assume the double-helix conformation, and also (in the eukaryotes) to be compactly coiled within the small cell nucleus. The double-stranded DNA molecules are also typically much longer than RNA molecules. The backbone of RNA and DNA are structurally similar, but RNA is single stranded, and made from ribose as opposed to deoxyribose. Other biologically important derivatives of deoxyribose include mono-, di-, and triphosphates, as well as 3′-5′ cyclic monophosphates.
Deoxyribose | Biological importance
This interaction is a unique adaptation for the shape of an RNA double helix as it involves 2'-hydroxyls and phosphate oxygen. Despite the common structural features among dsRBMs, they exhibit distinct chemical frameworks, which permits specificity for a variety for RNA structures including stem-loops, internal loops, bulges or helices containing mismatches.
RNA-binding protein | Double-stranded RNA-binding motif
Because of the double-stranded nature of DNA, essentially all of the nucleotides take the form of Watson-Crick base pairs between nucleotides on the two complementary strands of the double-helix. In contrast, both RNA and proteins are normally single-stranded. Therefore, they are not constrained by the regular geometry of the DNA double helix, and so fold into complex three-dimensional shapes dependent on their sequence. These different shapes are responsible for many of the common properties of RNA and proteins, including the formation of specific binding pockets, and the ability to catalyse biochemical reactions.
Macromolecule | Structural features
For dsRNA viruses, RdRp transcribes mRNA by using the negative strand as a template. Positive strands may also be used as templates to synthesize negative strands for the construction of genomic dsRNA. dsRNA is not a molecule produced by cells, so cellular life has evolved mechanisms to detect and inactive viral dsRNA. To counter this, dsRNA viruses typically retain their genomes inside of viral capsid in order to evade the host's immune system.
Orthornavirae | Double-stranded RNA viruses
The class "Duplopiviricetes" is the second clade of dsRNA viruses and is in the phylum "Pisuviricota", which also contains positive-sense single-stranded RNA viruses. "Duplopiviricetes" mostly contains plant and fungal viruses and includes the following four families: "Amalgaviridae", "Hypoviridae", "Partitiviridae", and "Picobirnaviridae".
Double-stranded RNA viruses | "Duplopiviricetes"
Other viruses use a RNA-dependent RNAP (an RNAP that employs RNA as a template instead of DNA). This occurs in negative strand RNA viruses and dsRNA viruses, both of which exist for a portion of their life cycle as double-stranded RNA. However, some positive strand RNA viruses, such as poliovirus, also contain RNA-dependent RNAP.
RNA polymerase | Viruses
Moreover, the structural and functional similarities with dsRNA viruses of mammals has made it useful to consider these entities as viruses.
Double-stranded RNA viruses | "Saccharomyces cerevisiae" virus L-A
Thus, the two dsRNA pathways, exogenous and endogenous, converge at the RISC. Exogenous dsRNA initiates RNAi by activating the ribonuclease protein Dicer, which binds and cleaves double-stranded RNAs (dsRNAs) in plants, or short hairpin RNAs (shRNAs) in humans, to produce double-stranded fragments of 20–25 base pairs with a 2-nucleotide overhang at the 3' end. Bioinformatics studies on the genomes of multiple organisms suggest this length maximizes target-gene specificity and minimizes non-specific effects. These short double-stranded fragments are called small interfering RNAs (siRNAs). These siRNAs are then separated into single strands and integrated into an active RISC, by RISC-Loading Complex (RLC).
RNA interference | Cellular mechanism
RNA, ribosomal 2, also known as RNR2, is a human gene coding for ribosomal RNA. Genes for ribosomal RNA are clustered on the short arms of chromosomes 13 (RNR1), 14 (RNR2), 15 (RNR3), 20 (RNR4), 21 (RNR5). The gene for RNR2 exists in multiple copies on chromosome 14. Each gene cluster contains 30–40 copies and encodes a 45S RNA product that is then processed to form 18S, 5.8S and 28S rRNA.
RNR2 | Introduction
The other strand of the double-stranded DNA molecule is referred to as negative-sense (also negative (-) or antisense), and is reverse complementary to both the positive-sense strand and the RNA transcript. It is actually the antisense strand that is used as the template from which RNA polymerases construct the RNA transcript, but the complementary base-pairing by which nucleic acid polymerization occurs means that the sequence of the RNA transcript will look identical to the sense strand, apart from the RNA transcript's use of uracil instead of thymine. Sometimes the phrases coding strand and template strand are encountered in place of sense and antisense, respectively, and in the context of a double-stranded DNA molecule the usage of these terms is essentially equivalent.
Sense (molecular biology) | DNA sense
The eleven dsRNA strands remain within the protection of the two protein shells and the viral RNA-dependent RNA polymerasecreates mRNA transcripts of the double-stranded viral genome. By remaining in the core, the viral RNA evades innate host immune responses called RNA interference that are triggered by the presence of double-stranded RNA.
Rotaviral gastroenteritis | Replication
However, there is no other evidence to suggest that the RNA is transcribed from the opposite strand.
GntR-DTE RNA motif | Introduction
Most recent work has identified that repeat RNA transcripts from the major satellite repeats largely remain chromatin associated and form an RNA-nucleosome scaffold that is supported by RNA:DNA hybrids.
Thomas Jenuwein | Career and research
The double-stranded RNA-binding motif (dsRM, dsRBD), a 70–75 amino-acid domain, plays a critical role in RNA processing, RNA localization, RNA interference, RNA editing, and translational repression. All three structures of the domain solved as of 2005 possess uniting features that explain how dsRMs only bind to dsRNA instead of dsDNA. The dsRMs were found to interact along the RNA duplex via both α-helices and β1-β2 loop. Moreover, all three dsRBM structures make contact with the sugar-phosphate backbone of the major groove and of one minor groove, which is mediated by the β1-β2 loop along with the N-terminus region of the alpha helix 2.
RNA-binding protein | Double-stranded RNA-binding motif
Many RNAs are shipped to the cytoplasm where the proteins are assembled, including a large number of empty capsids. Reverse transcription by the viral polymerase protein re-creates the relaxed, partially double-stranded circular DNA genome.
Woolly monkey hepatitis B virus | Replication and transcription
(Plant Dcl2 may play a role in rasi/piRNA biogenesis.) Double-stranded RNAs capable of silencing repeat elements, then known as repeat associated small interfering RNA (rasiRNA), were proposed in "Drosophila" in 2001. By 2008, it was still unclear how piRNAs are generated, but potential methods had been suggested, and it was certain their biogenesis pathway is distinct from miRNA and siRNA, while rasiRNA is now considered a piRNA subspecies.
Piwi-interacting RNA | Introduction
According to the length of RNA chain, RNA includes small RNA and long RNA. Usually, small RNAs are shorter than 200 nt in length, and long RNAs are greater than 200 nt long. Long RNAs, also called large RNAs, mainly include long non-coding RNA (lncRNA) and mRNA. Small RNAs mainly include 5.8S ribosomal RNA (rRNA), 5S rRNA, transfer RNA (tRNA), microRNA (miRNA), small interfering RNA (siRNA), small nucleolar RNA (snoRNAs), Piwi-interacting RNA (piRNA), tRNA-derived small RNA (tsRNA) and small rDNA-derived RNA (srRNA). There are certain exceptions as in the case of the 5S rRNA of the members of the genus Halococcus (Archaea), which have an insertion, thus increasing its size.
RNA | In length
Many double-helical forms are possible; for DNA the three biologically relevant forms are A-DNA, B-DNA, and Z-DNA, while RNA double helices have structures similar to the A form of DNA.
Nucleic acid secondary structure | Double helix
An optimized mixture of oligo-dT and random hexamer primers increases the chance of obtaining full-length cDNA while reducing 5' or 3' bias. Ribosomal RNA may also be depleted to enrich both mRNA and non-poly-adenylated transcripts such as some non-coding RNA.
Complementary DNA | First-strand synthesis
Like DNA, most biologically active RNAs, including mRNA, tRNA, rRNA, snRNAs, and other non-coding RNAs, contain self-complementary sequences that allow parts of the RNA to fold and pair with itself to form double helices. Analysis of these RNAs has revealed that they are highly structured. Unlike DNA, their structures do not consist of long double helices, but rather collections of short helices packed together into structures akin to proteins. In this fashion, RNAs can achieve chemical catalysis (like enzymes). For instance, determination of the structure of the ribosome—an RNA-protein complex that catalyzes peptide bond formation—revealed that its active site is composed entirely of RNA.
RNA | Comparison with DNA
Two clades of dsRNA viruses exist: the phylum "Duplornaviricota" and the class "Duplopiviricetes", which is in the phylum "Pisuviricota". Both are included in the kingdom "Orthornavirae" in the realm "Riboviria". Based on phylogenetic analysis of RdRp, the two clades do not share a common dsRNA ancestor but are instead separately descended from different positive-sense, single-stranded RNA viruses. In the Baltimore classification system, which groups viruses together based on their manner of mRNA synthesis, dsRNA viruses are group III.
Double-stranded RNA viruses | Classification
Their conclusion was that 98% of scrambled isoforms represented circRNAs. Zhang et al. 2014
Circular RNA | Salzman et al. 2012
Triple-stranded DNA (also known as H-DNA or Triplex-DNA) is a DNA structure in which three oligonucleotides wind around each other and form a triple helix. In triple-stranded DNA, the third strand binds to a B-form DNA (via Watson–Crick base-pairing) double helix by forming Hoogsteen base pairs or reversed Hoogsteen hydrogen bonds.
Triple-stranded DNA | Introduction
RHBV is a single stranded, negative-sense RNA virus of the genus "Tenuivirus", derived from the Latin ""tenui"", meaning thin or weak. This comes from the nature of "Tenuiviruses" to form thin, filamentous viral particles. Other viruses in the genus "Tenuivirus" include maize stripe virus (MSV), rice stripe virus (RSV), and rice grassy stunt virus (RGSV). While RHBV and other "Tenuiviruses" have single stranded RNA genomes, it is interesting to note that examination of non-denaturing gel electrophoresis performed with "Tenuiviruses" has yielded both single stranded and double stranded RNA. Because it is unlikely that both single stranded and double stranded RNA's are encapsidated within the viral ribonucleoprotein, it is theorized that the double stranded RNA sometimes present in gel electrophoresis results comes from the annealing in vitro of single stranded RNA's that possess opposite polarities.
Rice hoja blanca tenuivirus | Viral Classification
The TD-2 RNA motif is a conserved RNA structure found in "Treponema denticola", as well as metagenome sequences extracted from a termite hindgut, which is known to be enriched for Spirochaetes. Since TD-2 RNAs are not typically positioned in 5′ UTRs, the motif is presumed to correspond to a non-coding RNA. The TD-2 RNA's secondary structure is supported by covariation (see secondary structure prediction), and one stem typically has terminal GNRA tetraloops, which are known to be especially stable. Surprisingly, however, the motif has an unusual number of stems containing runs of adenosines that base pair with coordinate runs of uridines.
TD-2 RNA motif | Introduction
All viruses in "Negarnaviricota" are negative-sense, single-stranded RNA (-ssRNA) viruses. They have genomes made of RNA, which are single instead of double-stranded. Their genomes are negative sense, meaning that messenger RNA (mRNA) can be synthesized directly from the genome by the viral enzyme RNA-dependent RNA polymerase (RdRp), also called RNA replicase, which is encoded by all -ssRNA viruses. Excluding viruses in the genus "Tenuivirus" and some in the family "Chuviridae", all -ssRNA viruses have linear rather than circular genomes, and the genomes may be segmented or non-segmented. All -ssRNA genomes contain terminal inverted repeats, which are palindromic nucleotide sequences at each end of the genome.
Negative-strand RNA virus | Genome
Here, the single-stranded DNA curls around in a long circle stabilized by telomere-binding proteins. At the very end of the T-loop, the single-stranded telomere DNA is held onto a region of double-stranded DNA by the telomere strand disrupting the double-helical DNA and base pairing to one of the two strands. This triple-stranded structure is called a displacement loop or D-loop.
DNA | Quadruplex structures
Non-canonical base pairings commonly occur in the secondary structure of RNA (e.g. pairing of G with U), and in tRNA recognition. They are typically less stable than standard base pairings. The presence of non-canonical base pairs in double stranded DNA results in a disrupted double helix.
Non-canonical base pairing | Introduction
In eukaryotic RTs, the RNase H domain lies on the wrist below the base of the thumb, but retron RTs lack RNase H activity. The nucleic acid binding cleft, extending from the polymerase active site to the RNase H active site, is about 60 Å in length in eukaryotic RTs, corresponding to nearly two helical turns. When eukaryotic RT extends a conventional primer, the growing DNA/RNA double helix spirals along the cleft, and as the double helix passes the RNase H domain, the template RNA is digested to release the nascent strand of cDNA. In the case of msDNA primer extension, however, a long strand of RNA remains attached to the 3'-OH of the priming G.
Multicopy single-stranded DNA | Biosynthesis
The structure of 6S RNA was defined in 1971. It is a small RNA strand consisting of 184 nucleotides. 6S RNA is a long double-stranded structure and has a single strand loop. Its structure is similar to an open promoter complex of DNA structure. Varies analyses discovered that 6S RNAs are capable of forming a secondary structure. The secondary structure consists of two irregular helical stem regions, making a large core loop which is called a central knot.
6S / SsrS RNA | Structure
The double-stranded regions of RNA are formed by base-pairing between residues in a region complementary to the region of the editing site. This complementary region is usually found in a neighbouring intron but can also be located in an exonic sequence. The region that pairs with the editing region is known as an Editing Complementary Sequence (ECS).
C1QL1 | Editing type
The double-stranded regions of RNA are formed by base-pairing between residues close to region of the editing site, with residues usually in a neighboring intron, though they can occasionally be located in an exonic sequence. The region that forms base pairs with the editing region is known as an Editing Complementary Sequence (ECS). ADARs bind interact directly with the dsRNA substrate via their double-stranded RNA binding domains. If an editing site occurs within a coding sequence, the result could be a codon change. This can lead to translation of a protein isoform due to a change in its primary protein structure.
GRIK2 | Type
Despite DNA being a double stranded molecule, only one of the strands acts as a template for pre-mRNA synthesis - this strand is known as the template strand. The other DNA strand (which is complementary to the template strand) is known as the coding strand. Both DNA and RNA have intrinsic directionality, meaning there are two distinct ends of the molecule. This property of directionality is due to the asymmetrical underlying nucleotide subunits, with a phosphate group on one side of the pentose sugar and a base on the other. The five carbons in the pentose sugar are numbered from 1' (where ' means prime) to 5'.
Protein biosynthesis | Transcription
Ambisense RNA viruses resemble negative-sense RNA viruses, except they also translate genes from the positive strand.
RNA virus | Single-stranded RNA viruses and RNA Sense
These viruses have double stranded DNA genomes with no RNA intermediate.
Mardivirus | Introduction
Where the helix is unwound, the coding strand consists of unpaired bases, while the template strand consists of an RNA:DNA composite, followed by a number of unpaired bases at the rear. This hybrid consists of the most recently added nucleotides of the RNA transcript, complementary base-paired to the template strand. The number of base-pairs in the hybrid is under investigation, but it has been suggested that the hybrid is formed from the last 10 nucleotides added.
Coding strand | RNA-DNA hybrid
This frequency of twist (known as the helical "pitch") depends largely on stacking forces that each base exerts on its neighbours in the chain. Double-helical RNA adopts a conformation similar to the A-form structure. Other conformations are possible; in fact, only the letters F, Q, U, V, and Y are now available to describe any new DNA structure that may appear in the future. However, most of these forms have been created synthetically and have not been observed in naturally occurring biological systems.
Nucleic acid tertiary structure | Double helix
In the late 1970s, it was shown that there is a single stranded covalently closed, i.e. circular form of RNA expressed throughout the animal and plant kingdom (see circRNA). circRNAs are thought to arise via a "back-splice" reaction where the spliceosome joins a downstream donor to an upstream acceptor splice site. So far the function of circRNAs is largely unknown, although for few examples a microRNA sponging activity has been demonstrated.
RNA | Circular RNA
2'-O-methylation also helps to increase base stacking forces, stabilizing the secondary and tertiary structure of rRNA even further. Collectively, these modifications in rRNA are indispensable to ribosomal function.
Epitranscriptome | Ribosomal RNA (rRNA)
The lengths of these runs do correspond, thus comprising part of the covariation evidence in support of the motif's assignment as a conserved RNA. The first (5′-most) stem in the TD-2 RNA motif exhibits covariation, but also appears to be lost in some TD-2 RNAs. Seven TD-2 RNAs overlap predicted representatives of the TD-1 RNA motif, but it is unknown whether these two motifs can somehow be merged.
TD-2 RNA motif | Introduction
These small RNAs are predicted to fold into a conserved stem formed by the RNA's 3′ and 5′ ends and characterized by a single bulged cytosine, which are the known requirements for Ro binding.
Y RNA | Structure
The stacking of turret protein functional domains and the presence of constrictions and A spikes along the mRNA release pathway indicate a mechanism that uses pores and channels to regulate the highly coordinated steps of RNA transcription, processing, and release.
Double-stranded RNA viruses | Cypovirus
It is not clear how the cell determines the locations of "de novo" DNA methylation, but evidence suggests that for many (though not all) locations, RNA-directed DNA methylation (RdDM) is involved. In RdDM, specific RNA transcripts are produced from a genomic DNA template, and this RNA forms secondary structures called double-stranded RNA molecules. The double-stranded RNAs, through either the small interfering RNA (siRNA) or microRNA (miRNA) pathways direct de-novo DNA methylation of the original genomic location that produced the RNA. This sort of mechanism is thought to be important in cellular defense against RNA viruses and/or transposons, both of which often form a double-stranded RNA that can be mutagenic to the host genome.
DNA methylation | In plants
The conversion from single-stranded to double-stranded form is carried out by the host's own DNA polymerase. The host's RNA polymerase binds to the viral genome and syntheses RNA. Some of this RNA is translated and the remainder is used to initiate DNA replication.
Plectrovirus | Conversion to double stranded form
Double-stranded nucleic acids are made up of complementary sequences, in which extensive Watson-Crick base pairing results in a highly repeated and quite uniform double-helical three-dimensional structure. In contrast, single-stranded RNA and DNA molecules are not constrained to a regular double helix, and can adopt highly complex three-dimensional structures that are based on short stretches of intramolecular base-paired sequences including both Watson-Crick and noncanonical base pairs, and a wide range of complex tertiary interactions. Nucleic acid molecules are usually unbranched and may occur as linear and circular molecules. For example, bacterial chromosomes, plasmids, mitochondrial DNA, and chloroplast DNA are usually circular double-stranded DNA molecules, while chromosomes of the eukaryotic nucleus are usually linear double-stranded DNA molecules.
Nucleic acid | Topology
Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded RNA non-coding RNA molecules, typically 20-27 base pairs in length, similar to miRNA, and operating within the RNA interference (RNAi) pathway. It interferes with the expression of specific genes with complementary nucleotide sequences by degrading mRNA after transcription, preventing translation.
Small interfering RNA | Introduction
Additionally, a single RNA gene may not be able to provide enough RNA, but tandem repeats of the gene allow sufficient RNA to be produced. For example, cells in a human embryo contain between five and ten million ribosomes, and cell number doubles within 24 hours. In order to provide the necessary ribosomes, multiple RNA polymerases must consecutively transcribe multiple rRNA genes. In some species, such as Arabidopsis thaliana and Oryza sativa, most TAGs are the result of unequal chromosomal crossover during genetic recombination.
Tandemly arrayed genes | Introduction
The secondary structure of RNA consists of a single polynucleotide. Base pairing in RNA occurs when RNA folds between complementarity regions. Both single- and double-stranded regions are often found in RNA molecules. The four basic elements in the secondary structure of RNA are: The antiparallel strands form a helical shape. Bulges and internal loops are formed by separation of the double helical tract on either one strand (bulge) or on both strands (internal loops) by unpaired nucleotides.
Nucleic acid structure | RNA
"Reoviridae" are currently classified into nine genera. The genomes of these viruses consist of 10 to 12 segments of dsRNA, each generally encoding one protein. The mature virions are non-enveloped. Their capsids, formed by multiple proteins, have icosahedral symmetry and are arranged generally in concentric layers. A distinguishing feature of the dsRNA viruses, irrespective of their family association, is their ability to carry out transcription of the dsRNA segments, under appropriate conditions, within the capsid. In all these viruses, the enzymes required for endogenous transcription are thus part of the virion structure.
Double-stranded RNA viruses | Reoviridae
In addition to masking key elements within single-stranded RNA, the formation of double-stranded RNA duplexes can also provide a substrate for the generation of endogenous siRNAs (endo-siRNAs) in Drosophila and mouse oocytes. The annealing of complementary sequences, such as antisense or repetitive regions between transcripts, forms an RNA duplex that may be processed by Dicer-2 into endo-siRNAs. Also, long ncRNAs that form extended intramolecular hairpins may be processed into siRNAs, compellingly illustrated by the esi-1 and esi-2 transcripts. Endo-siRNAs generated from these transcripts seem particularly useful in suppressing the spread of mobile transposon elements within the genome in the germline.
Long non-coding RNA | In siRNA-directed gene regulation
This small group of viruses, exemplified by the Hepatitis B virus, have a double-stranded, gapped genome that is subsequently filled in to form a covalently closed circle (cccDNA) that serves as a template for production of viral mRNAs and a subgenomic RNA. The pregenome RNA serves as template for the viral reverse transcriptase and for production of the DNA genome.
Viral replication | Class 7: Double-stranded DNA viruses that replicate through a single-stranded RNA intermediate
An important aspect of these folding interactions is its folding; the order that interactions form can potentially create a situation in which one interaction blocks another, creating a knot. Because the kissing-loop interactions and dovetail interactions are a half-turn or shorter, they do not create these topological issues.
RNA origami | The double crossover (DX)
This analysis also suggests that the dsRNA viruses are not closely related to each other but instead belong to four additional classes—Birnaviridae, Cystoviridae, Partitiviridae, and Reoviridae—and one additional order (Totiviridae) of one of the classes of positive ssRNA viruses in the same subphylum as the positive-strand RNA viruses. One study has suggested that there are two large clades: One includes the families "Caliciviridae", "Flaviviridae", and "Picornaviridae" and a second that includes the families "Alphatetraviridae", "Birnaviridae", "Cystoviridae", Nodaviridae", and "Permutotretraviridae".
RNA virus | Double-stranded RNA viruses
Since cells do not produce double-stranded RNA during normal nucleic acid metabolism, natural selection has favored the evolution of enzymes that destroy dsRNA on contact. The best known class of this type of enzymes is Dicer. It is hoped that broad-spectrum anti-virals could be synthesized that take advantage of this vulnerability of double-stranded RNA viruses.
Double-stranded RNA viruses | Anti-virals
Small nucleolar RNA TBR2
Small nucleolar RNA TBR7 | See also
In the nucleus the single-stranded virus genome is converted to dsDNA by a cell DNA polymerase. The ends of the genome are double stranded as a result of base pairing, and at the 3' end the terminal nucleotides act as a primer to which the polymerase binds.
Parvoviridae | Single-stranded DNA to double-stranded DNA
Modifications can also happen in short non-coding RNAs, including small nuclear RNA (snRNA) and microRNA (miRNA). However, these modifications are less common than those in mRNA, tRNA, and rRNA.
Epitranscriptome | Short non-coding RNA (sncRNA) modifications
The smallest double-stranded DNA viruses are the hepadnaviruses such as hepatitis B, at 3.2 kb and 42 nm; parvoviruses have smaller capsids, at 18-26 nm, but larger genomes, at 5 kb. It is important to consider other self-replicating genetic elements, such as satelliviruses, viroids and ribozymes.
Smallest organisms | Viruses
The TwoAYGGAY RNA motif is a conserved RNA structure identified by bioinformatics. Its name refers to the conserved AYGGAY nucleotide sequence (Y refers to either a C or U nucleotide) found in the motif's two terminal loops (see diagram). The RNAs are found in sequences derived from DNA extracted from uncultivated bacteria present in the human gut, as well as some bacteria in the classes Clostridia and Gammaproteobacteria.
TwoAYGGAY RNA motif | Introduction
Small nucleolar RNA TBR2
Small nucleolar RNA TBR5 | See also
The precise role of double-stranded (ds)RNA is still widely investigated as a central player in the Interferon System. Groups have found that positive-strand RNA viruses and dsRNA viruses produced significant amounts of dsRNA, but the precise methods mammalian cells leverage to distinguish between self vs. non-self dsRNA have yet to be uncovered. Studies suggest that recognition must extend beyond simple identification of dsRNA structure and likely relies on other epigenetic markers.
Viral strategies for immune response evasion | Double-stranded RNA mediated immune response
When a molecule of DNA is double stranded, as DNA usually is, the two strands run in opposite directions. Therefore, one end of the molecule will have the 3' end of strand 1 and the 5' end of strand 2, and vice versa in the other end. However, the fact that the molecule is two stranded allows numerous different variations.
Sticky and blunt ends | Variations in double-stranded molecules
The "T" = 13 shell of the IBDV capsid is formed by trimers of VP2, a protein generated by removal of the C-terminal domain from its precursor, pVP2. The trimming of pVP2 is performed on immature particles as part of the maturation process. The other major structural protein, VP3, is a multifunctional component lying under the "T" = 13 shell that influences the inherent structural polymorphism of pVP2. The virus-encoded RNA-dependent RNA polymerase, VP1, is incorporated into the capsid through its association with VP3. VP3 also interacts extensively with the viral dsRNA genome.
Double-stranded RNA viruses | Infectious bursal disease virus
The members of genus "Orbivirus" within the "Reoviridae" family are arthropod borne viruses and are responsible for high morbidity and mortality in ruminants. Bluetongue virus (BTV) which causes disease in livestock (sheep, goat, cattle) has been in the forefront of molecular studies for the last three decades and now represents the best understood orbivirus at the molecular and structural levels. BTV, like other members of the family, is a complex non-enveloped virus with seven structural proteins and a RNA genome consisting of 10 variously sized dsRNA segments.
Double-stranded RNA viruses | Bluetongue virus
Double-stranded RNA-specific editase B2 is an enzyme that in humans is encoded by the "ADARB2" gene.
ADARB2 | Introduction
This helps to stabilize the Shelterin complex so that it can properly cap the ends of chromosomes and protect them from recognition by DNA damage signaling pathways.
Telomeric repeat–containing RNA | Direct Telomeric Interactions
An important structural component of RNA that distinguishes it from DNA is the presence of a hydroxyl group at the 2' position of the ribose sugar. The presence of this functional group causes the helix to mostly take the A-form geometry, although in single strand dinucleotide contexts, RNA can rarely also adopt the B-form most commonly observed in DNA. The A-form geometry results in a very deep and narrow major groove and a shallow and wide minor groove. A second consequence of the presence of the 2'-hydroxyl group is that in conformationally flexible regions of an RNA molecule (that is, not involved in formation of a double helix), it can chemically attack the adjacent phosphodiester bond to cleave the backbone.
RNA | Structure
Although it is possible to model an RT-primer template complex which would make the 2'-OH accessible for the priming reaction, further extension of the DNA strand presents a problem: as DNA synthesis progresses, the bulky RNA strand extending from the 3'-OH needs somehow to spiral down the binding cleft without being blocked by steric hindrance. To overcome this issue, the msDNA reverse transcriptase clearly would require special features not shared by other RTs.
Multicopy single-stranded DNA | Biosynthesis
Infectious bursal disease virus (IBDV) is the best-characterized member of the family "Birnaviridae". These viruses have bipartite dsRNA genomes enclosed in single layered icosahedral capsids with "T" = 13l geometry. IBDV shares functional strategies and structural features with many other icosahedral dsRNA viruses, except that it lacks the "T" = 1 (or pseudo "T" = 2) core common to the "Reoviridae", "Cystoviridae", and "Totiviridae". The IBDV capsid protein exhibits structural domains that show homology to those of the capsid proteins of some positive-sense single-stranded RNA viruses, such as the nodaviruses and tetraviruses, as well as the "T" = 13 capsid shell protein of the "Reoviridae".
Double-stranded RNA viruses | Infectious bursal disease virus
Subsequently, the passenger strand is degraded, while the guide strand is incorporated into the RNA-induced silencing complex (RISC). The most well-studied outcome of the RNAi is post-transcriptional gene silencing, which occurs when the guide strand pairs with a complementary sequence in a messenger RNA molecule and induces cleavage by Argonaute, that lies in the core of RNA-induced silencing complex. Argonaute proteins are the active part of RNA-induced silencing complex, cleaving the target mRNA strand complementary to their bound siRNA. Theoretically the dicer produces short double-stranded fragments so there should be also two functional single-stranded siRNA produced. But only one of the two single-stranded RNA here will be utilized to base pair with target mRNA.
Argonaute | RNA interference
Double-stranded RNA viruses evolved two separate times from positive-strand RNA viruses. In the Baltimore classification system, dsRNA viruses belong to Group III. Virus group members vary widely in host range (animals, plants, fungi, and bacteria), genome segment number (one to twelve), and virion organization (T-number, capsid layers, or turrets). Double-stranded RNA viruses include the rotaviruses, known globally as a common cause of gastroenteritis in young children, and bluetongue virus, an economically significant pathogen of cattle and sheep. The family "Reoviridae" is the largest and most diverse dsRNA virus family in terms of host range.
Double-stranded RNA viruses | Introduction
Like most viruses with RNA genomes, double-stranded RNA viruses do not rely on host polymerases for replication to the extent that viruses with DNA genomes do. Double-stranded RNA viruses are not as well-studied as other classes. This class includes two major families, the Reoviridae and Birnaviridae. Replication is monocistronic and includes individual, segmented genomes, meaning that each of the genes codes for only one protein, unlike other viruses, which exhibit more complex translation.
Viral replication | Class 3: Double-stranded RNA viruses
It has over 60 miR-7 binding sites, far more than any known linear miRNA sponge.
Circular RNA | CDR1as/CiRS-7 as a miR-7 sponge
RNA, U2 small nuclear 2 is a protein in humans that is encoded by the RNU2-2 pseudogene.
RNU2-2 | Introduction
RNA viruses typically do not encode that many proteins, but most positive-sense, single-stranded (+ssRNA) viruses and some double-stranded RNA (dsRNA) viruses encode a major capsid protein that has a single jelly roll fold, so named because the folded structure of the protein contains a structure that resembles a jelly roll. Many RNA viruses also encode an envelope, a type of lipid membrane that typically surrounds the capsid. In particular, the viral envelope is near-universal among negative-sense, single-stranded (-ssRNA) viruses.
Orthornavirae | Structure
The L-A dsRNA virus of the yeast "Saccharomyces cerevisiae" has a single 4.6 kb genomic segment that encodes its major coat protein, Gag (76 kDa) and a Gag-Pol fusion protein (180 kDa) formed by a -1 ribosomal frameshift. L-A can support the replication and encapsidation in separate viral particles of any of several satellite dsRNAs, called M dsRNAs, each of which encodes a secreted protein toxin (the killer toxin) and immunity to that toxin. L-A and M are transmitted from cell to cell by the cytoplasmic mixing that occurs in the process of mating. Neither is naturally released from the cell or enters cells by other mechanisms, but the high frequency of yeast mating in nature results in the wide distribution of these viruses in natural isolates.
Double-stranded RNA viruses | "Saccharomyces cerevisiae" virus L-A
The gene is located on the right arm of chromosome 3. The mRNA transcript of "dbt" is 3.2 kilo-base pairs long, and it contains four exons and three introns.
Doubletime (gene) | Gene
"Duplornaviricota" contains most dsRNA viruses, including reoviruses, which infect a diverse range of eukaryotes, and cystoviruses, which are the only dsRNA viruses known to infect prokaryotes. Apart from RdRp, viruses in "Duplornaviricota" also share icosahedral capsids that contain 60 homo- or heterodimers of the capsid protein organized on a pseudo T=2 lattice. The phylum is divided into three classes: "Chrymotiviricetes", which primarily contains fungal and protozoan viruses, "Resentoviricetes", which contains reoviruses, and "Vidaverviricetes", which contains cystoviruses.
Double-stranded RNA viruses | "Duplornaviricota"
Humans appear to have four Y RNAs, named hY1, hY3, hY4 and hY5 and also a large number of pseudogenes.
Y RNA | Humans
To produce a desired shape, the RNA origami method uses double-crossovers (DX) to arrange the RNA helices in parallel to each other to form a building block. While DNA origami requires the construction of DNA molecules from multiple strands, researchers were able to devise a method in making DX molecules from only one strand for RNA. This was done through adding hairpin motifs to the edges and kissing-loop complexes on internal helices. The addition of more DNA molecules on top of one another creates a junction known as the dovetail seam. This dovetail seam has base pairs that cross between adjacent junctions; thus, the structural seam along the junction becomes sequence-specific.
RNA origami | The double crossover (DX)
The mature miRNA is part of an active RNA-induced silencing complex (RISC) containing Dicer and many associated proteins. RISC is also known as a microRNA ribonucleoprotein complex (miRNP); A RISC with incorporated miRNA is sometimes referred to as a "miRISC." Dicer processing of the pre-miRNA is thought to be coupled with unwinding of the duplex. Generally, only one strand is incorporated into the miRISC, selected on the basis of its thermodynamic instability and weaker base-pairing on the 5' end relative to the other strand. The position of the stem-loop may also influence strand choice. The other strand, called the passenger strand due to its lower levels in the steady state, is denoted with an asterisk (*) and is normally degraded.
MicroRNA | RNA-induced silencing complex
TAS1/2 transcripts undergo an initial AGO1 mediated cleavage at the 5’ end that is guided by miR173. RDR6 then converts the transcript into a double strand RNA fragment which then gets processed by DCL4 to generate the 21-nt siRNA with 2 nucleotide 3’ overhangs that target complementary mRNAs in trans.
Trans-acting siRNA | TAS1 and TAS2
Nick translation could cause double-stranded DNA breaks, if DNA polymerase I encounters another nick on the opposite strand, resulting in two shorter fragments. This does not influence the performance of the labelled probe in in-situ hybridization.
Nick translation | Introduction
Additionally, it is ambiguous on which DNA strand DUF2693 RNAs are encoded, and it is possible that the biological functional element is the reverse complement of the published DUF2693 motif. In both orientations, there are many G-U wobble base pairs and their reverse complements A-C pairs, and both strands have too many A-C pairs to confidently establish the correct strand.
DUF2693 RNA motif | Introduction
The Transposase-2 RNA motif is a conserved RNA structure that was discovered by bioinformatics. These RNAs are usually located nearby to genes that encode transposases, which are the main component of transposons. Many kinds of transposon are found adjacent to inverted repeats, which could be mistaken for simple RNA secondary structures. Therefore Transposase-2 RNAs could reflect this side effect of transposon replication, and not encode a separate RNA. However, the consistency of the RNA's alignment (e.g., all RNAs have the complete secondary structure, with no truncations) is not typical of transposon-associated repeats. Assuming that Transposase-2 RNAs do function as RNAs, they might function as cis-regulatory elements to regulate the transposase genes, or they might operate in "trans" as small RNAs that participate in the transposon's biology in some other way.
Transposase-2 RNA motif | Introduction
Most double-stranded DNA viruses require the host cell's DNA-dependent RNA polymerase to perform transcription. These host DNA are found in the nucleus, and therefore most double-stranded DNA viruses carry out a part of their infection cycle within the host cell's nucleus.
Poxviridae | Replication
Various factors can cause double-stranded DNA to break; thus, reorder genes or cause cell death.
Coding strand | Strands in transcription bubble
U11 snRNA has a stem-loop structure with a 5' end as splice site sequence (5' ss) and contains four stem loops structures (I-IV). A structural comparison of U11 snRNA between plants, vertebrates and insects shows that it is folded into a structure with a four-way junction at the 5' site and in a stem loop structure at the 3' site.
U11 spliceosomal RNA | Secondary structure
DNA may therefore be a dynamic participant in the transcription of the c-myc gene.
Triple-stranded DNA | Function
As yet, the function of PAGEV RNAs is unknown. Although the PAGEV motif was published as an RNA candidate, its potential relationship to plasmid replication leaves open the possibility that it functions as a single-stranded DNA. In terms of secondary structure, RNA and DNA are difficult to distinguish when only sequence information is available. Single-stranded DNA can occur during plasmid replication.
PAGEV RNA motif | Introduction
Twin helical strands form the DNA backbone. Another double helix may be found by tracing the spaces, or grooves, between the strands. These voids are adjacent to the base pairs and may provide a binding site. As the strands are not directly opposite each other, the grooves are unequally sized. One groove, the major groove, is 22 Å wide and the other, the minor groove, is 12 Å wide. The narrowness of the minor groove means that the edges of the bases are more accessible in the major groove. As a result, proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove.
Nucleic acid double helix | Grooves
RNA, Ro-associated Y4 pseudogene 2 is a protein that in humans is encoded by the RNY4P2 gene.
Rna, ro-associated y4 pseudogene 2 | Introduction
At the end of transcription, RdRp synthesizes a polyadynelated tail (polyA tail) consisting of hundreds of adenines in the mRNA's 3-end, which may be done by stuttering on a sequence of uracils. After the polyA tail is constructed, the mRNA is released by RdRp. In genomes that encode more than one transcribable portion, RdRp can continue scanning to the next start codon to continue with transcription.
Negative-strand RNA virus | Replication and transcription
Small nucleolar RNA TBR2
Small nucleolar RNA TBR17 | See also
Most RNA molecules are linear, single-stranded molecules, but both circular and branched molecules can result from RNA splicing reactions. The total amount of pyrimidines is equal to the total amount of purines. The diameter of the helix is about 20Å.
Nucleic acid | Topology
The secondary structure of 5S rRNA consists of five helices (denoted I-V in roman numerals), four loops (B-E), and one hinge (A), which form together a Y-like structure. Loops C and D are terminal hairpins and loops B and E are internal. According to phylogenetic studies, helices I and III are likely ancestral. Helix III includes two highly conserved adenosines. Helix V, with its hairpin structure, is thought to interact with TFIIIA.
5S ribosomal RNA | Structure