This article is about the biological macromolecule. For other uses, seeRNA (disambiguation).
A hairpin loop from a pre-mRNA. Highlighted are thenucleobases (green) and the ribose-phosphate backbone (blue). This is a single strand of RNA that folds back upon itself.
Ribonucleic acid (RNA) is apolymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA anddeoxyribonucleic acid (DNA) arenucleic acids. The nucleic acids constitute one of the four majormacromolecules essential for all known forms oflife. RNA is assembled as a chain ofnucleotides. Cellular organisms usemessenger RNA (mRNA) to convey genetic information (using thenitrogenous bases ofguanine,uracil,adenine, andcytosine, denoted by the letters G, U, A, and C) that directs synthesis of specific proteins. Manyviruses encode their genetic information using an RNAgenome.
Some RNA molecules play an active role within cells by catalyzing biological reactions, controllinggene expression, or sensing and communicating responses to cellular signals. One of these active processes isprotein synthesis, a universal function in which RNA molecules direct the synthesis of proteins onribosomes. This process usestransfer RNA (tRNA) molecules to deliveramino acids to theribosome, whereribosomal RNA (rRNA) then links amino acids together to form coded proteins.
It has become widely accepted in science[1] that early in thehistory of life on Earth, prior to the evolution of DNA and possibly of protein-basedenzymes as well, an "RNA world" existed in which RNA served as both living organisms' storage method forgenetic information—a role fulfilled today by DNA, except in the case ofRNA viruses—and potentially performed catalytic functions in cells—a function performed today by protein enzymes, with the notable and important exception of the ribosome, which is aribozyme.
Watson-Crick base pairs in asiRNA. Hydrogen atoms are not shown.
Eachnucleotide in RNA contains aribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, in general,adenine (A),cytosine (C),guanine (G), oruracil (U). Adenine and guanine arepurines, and cytosine and uracil arepyrimidines. Aphosphate group is attached to the 3' position of one ribose and the 5' position of the next. The phosphate groups have a negative charge each, making RNA a charged molecule (polyanion). The bases formhydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil.[2] However, other interactions are possible, such as a group of adenine bases binding to each other in a bulge,[3]or the GNRAtetraloop that has a guanine–adenine base-pair.[2]
Three-dimensional representation of the50S ribosomal subunit. Ribosomal RNA is in brown, proteins in blue. The active site is a small segment of rRNA, indicated in red.
The chemical structure of RNA is very similar to that ofDNA, but differs in three primary ways:
Unlike double-stranded DNA, RNA is usually a single-stranded molecule (ssRNA)[4] in many of its biological roles and consists of much shorter chains of nucleotides.[5] However,double-stranded RNA (dsRNA) can form and (moreover) a single RNA molecule can, by complementary base pairing, form intrastrand double helixes, as intRNA.
While the sugar-phosphate "backbone" of DNA containsdeoxyribose, RNA containsribose instead.[6] Ribose has ahydroxyl group attached to the pentose ring in the2' position, whereas deoxyribose does not. The hydroxyl groups in the ribose backbone make RNA more chemicallylabile than DNA by lowering theactivation energy ofhydrolysis.
Like DNA, most biologically active RNAs, includingmRNA,tRNA,rRNA,snRNAs, and othernon-coding RNAs, contain self-complementary sequences that allow parts of the RNA to fold[8] 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 chemicalcatalysis (like enzymes).[9] For instance, determination of the structure of the ribosome—anRNA-protein complex that catalyzes the assembly of proteins—revealed that its active site is composed entirely of RNA.[10]
Structure of a fragment of an RNA, showing a guanosyl subunit
An important structural component of RNA that distinguishes it from DNA is the presence of ahydroxyl group at the 2' position of theribose sugar. The presence of this functional group causes the helix to mostly take theA-form geometry,[11] although in single strand dinucleotide contexts, RNA can rarely also adopt the B-form most commonly observed in DNA.[12] The A-form geometry results in a very deep and narrow major groove and a shallow and wide minor groove.[13] 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.[14]
The functional form of single-stranded RNA molecules, just like proteins, frequently requires a specific spatialtertiary structure. The scaffold for this structure is provided bysecondary structural elements that are hydrogen bonds within the molecule. This leads to several recognizable "domains" of secondary structure likehairpin loops, bulges, andinternal loops.[15] In order to create, i.e., design, RNA for any given secondary structure, two or three bases would not be enough, but four bases are enough.[16] This is likely why nature has "chosen" a four base alphabet: fewer than four would not allow the creation of all structures, while more than four bases are not necessary to do so. Since RNA is charged, metal ions such asMg2+ are needed to stabilise many secondary andtertiary structures.[17]
The naturally occurringenantiomer of RNA isD-RNA composed ofD-ribonucleotides. All chirality centers are located in theD-ribose. By the use ofL-ribose or ratherL-ribonucleotides,L-RNA can be synthesized.L-RNA is much more stable against degradation byRNase.[18]
Like other structuredbiopolymers such as proteins, one can define topology of a folded RNA molecule. This is often done based on arrangement of intra-chain contacts within a folded RNA, termed ascircuit topology.
RNA is transcribed with only four bases (adenine, cytosine, guanine and uracil),[19] but these bases and attached sugars can be modified in numerous ways as the RNAs mature.Pseudouridine (Ψ), in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, andribothymidine (T) are found in various places (the most notable ones being in the TΨC loop oftRNA).[20] Another notable modified base ishypoxanthine, a deaminated adenine base whosenucleoside is calledinosine (I). Inosine plays a key role in thewobble hypothesis of thegenetic code.[21]
There are more than 100 other naturally occurring modified nucleosides.[22] The greatest structural diversity of modifications can be found intRNA,[23] while pseudouridine and nucleosides with2'-O-methylribose often present in rRNA are the most common.[24] The specific roles of many of these modifications in RNA are not fully understood. However, it is notable that, in ribosomal RNA, many of the post-transcriptional modifications occur in highly functional regions, such as the peptidyl transferase center[25] and the subunit interface, implying that they are important for normal function.[26]
Messenger RNA (mRNA) is the type of RNA that carries information from DNA to theribosome, the sites of protein synthesis (translation) in the cell cytoplasm. The coding sequence of the mRNA determines theamino acid sequence in theprotein that is produced.[27] However, many RNAs do not code for protein (about 97% of the transcriptional output is non-protein-coding in eukaryotes[28][29][30][31]).
These so-callednon-coding RNAs ("ncRNA") can be encoded by their own genes (RNA genes), but can also derive from mRNAintrons.[32] The most prominent examples of non-coding RNAs aretransfer RNA (tRNA) andribosomal RNA (rRNA), both of which are involved in the process of translation.[7] There are also non-coding RNAs involved in gene regulation,RNA processing and other roles. Certain RNAs are able tocatalyse chemical reactions such as cutting andligating other RNA molecules,[33] and the catalysis ofpeptide bond formation in theribosome;[10] these are known asribozymes.
Messenger RNA (mRNA) carries information about a protein sequence to theribosomes, the protein synthesis factories in the cell. It iscoded so that every three nucleotides (acodon) corresponds to one amino acid. Ineukaryotic cells, once precursor mRNA (pre-mRNA) has been transcribed from DNA, it is processed to mature mRNA. This removes itsintrons—non-coding sections of the pre-mRNA. The mRNA is then exported from the nucleus to thecytoplasm, where it is bound to ribosomes andtranslated into its corresponding protein form with the help oftRNA. In prokaryotic cells, which do not have nucleus and cytoplasm compartments, mRNA can bind to ribosomes while it is being transcribed from DNA. After a certain amount of time, the message degrades into its component nucleotides with the assistance ofribonucleases.[27]
Transfer RNA (tRNA) is a small RNA chain of about 80nucleotides that transfers a specific amino acid to a growingpolypeptide chain at the ribosomal site of protein synthesis during translation. It has sites for amino acid attachment and ananticodon region forcodon recognition that binds to a specific sequence on the messenger RNA chain through hydrogen bonding.[32]
A diagram of how mRNA is used to create polypeptide chains
Ribosomal RNA (rRNA) is the catalytic component of the ribosomes. The rRNA is the component of the ribosome that hosts translation. Eukaryotic ribosomes contain four different rRNA molecules: 18S, 5.8S, 28S and 5S rRNA. Three of the rRNA molecules are synthesized in thenucleolus, and one is synthesized elsewhere. In the cytoplasm, ribosomal RNA and protein combine to form a nucleoprotein called a ribosome. The ribosome binds mRNA and carries out protein synthesis. Several ribosomes may be attached to a single mRNA at any time.[27] Nearly all the RNA found in a typical eukaryotic cell is rRNA.
Transfer-messenger RNA (tmRNA) is found in manybacteria andplastids. It tags proteins encoded by mRNAs that lack stop codons for degradation and prevents the ribosome from stalling.[41]
Post-transcriptional expression levels of many genes can be controlled byRNA interference, in whichmiRNAs, specific short RNA molecules, pair with mRNA regions and target them for degradation.[46] Thisantisense-based process involves steps that first process the RNA so that it canbase-pair with a region of its target mRNAs. Once the base pairing occurs, other proteins direct the mRNA to be destroyed bynucleases.[43]
Next to be linked to regulation wereXist and otherlong noncoding RNAs associated withX chromosome inactivation. Their roles, at first mysterious, were shown byJeannie T. Lee and others to be thesilencing of blocks of chromatin via recruitment ofPolycomb complex so that messenger RNA could not be transcribed from them.[47] Additional lncRNAs, currently defined as RNAs of more than 200 base pairs that do not appear to have coding potential,[48] have been found associated with regulation ofstem cellpluripotency andcell division.[48]
The third major group of regulatory RNAs is calledenhancer RNAs.[48] It is not clear at present whether they are a unique category of RNAs of various lengths or constitute a distinct subset of lncRNAs. In any case, they are transcribed fromenhancers, which are known regulatory sites in the DNA near genes they regulate.[48][49] They up-regulate the transcription of the gene(s) under control of the enhancer from which they are transcribed.[48][50]
At first, regulatory RNA was thought to be a eukaryotic phenomenon, a part of the explanation for why so much more transcription in higher organisms was seen than had been predicted. But as soon as researchers began to look for possible RNA regulators in bacteria, they turned up there as well, termed as small RNA (sRNA).[51][44] Currently, the ubiquitous nature of systems of RNA regulation of genes has been discussed as support for theRNA World theory.[43][52] There are indications that the enterobacterial sRNAs are involved in various cellular processes and seem to have significant role in stress responses such as membrane stress, starvation stress, phosphosugar stress and DNA damage. Also, it has been suggested that sRNAs have been evolved to have important role in stress responses because of their kinetic properties that allow for rapid response and stabilisation of the physiological state.[4]Bacterial small RNAs generally act viaantisense pairing with mRNA to down-regulate its translation, either by affecting stability or affecting cis-binding ability.[43]Riboswitches have also been discovered. They are cis-acting regulatory RNA sequences actingallosterically. They change shape when they bindmetabolites so that they gain or lose the ability to bind chromatin to regulate expression of genes.[53][54]
Archaea also have systems of regulatory RNA.[55] The CRISPR system, recently being used to edit DNAin situ, acts via regulatory RNAs in archaea and bacteria to provide protection against virus invaders.[43][56]
Synthesis of RNA typically occurs in the cell nucleus and is usually catalyzed by an enzyme—RNA polymerase—using DNA as a template, a process known astranscription. Initiation of transcription begins with the binding of the enzyme to apromoter sequence in the DNA (usually found "upstream" of a gene). The DNA double helix is unwound by thehelicase activity of the enzyme. The enzyme then progresses along the template strand in the 3’ to 5’ direction, synthesizing a complementary RNA molecule with elongation occurring in the 5’ to 3’ direction. The DNA sequence also dictates where termination of RNA synthesis will occur.[57]
There are also a number ofRNA-dependent RNA polymerases that use RNA as their template for synthesis of a new strand of RNA. For instance, a number ofRNA viruses (such as poliovirus) use this type of enzyme to replicate their genetic material.[58] Also, RNA-dependent RNA polymerase is part of theRNA interference pathway in many organisms.[59]
Uridine to pseudouridine is a common RNA modification.
Many RNAs are involved in modifying other RNAs.Introns arespliced out ofpre-mRNA byspliceosomes, which contain severalsmall nuclear RNAs (snRNA),[7] or the introns can be ribozymes that are spliced by themselves.[60]RNA can also be altered by having its nucleotides modified to nucleotides other thanA,C,G andU.In eukaryotes, modifications of RNA nucleotides are in general directed bysmall nucleolar RNAs (snoRNA; 60–300 nt),[32] found in thenucleolus andcajal bodies. snoRNAs associate with enzymes and guide them to a spot on an RNA by basepairing to that RNA. These enzymes then perform the nucleotide modification. rRNAs and tRNAs are extensively modified, but snRNAs and mRNAs can also be the target of base modification.[61][62] RNA can also be methylated.[63][64]
Like DNA, RNA can carry genetic information.RNA viruses havegenomes composed of RNA that encodes a number of proteins. The viral genome is replicated by some of those proteins, while other proteins protect the genome as the virus particle moves to a new host cell.Viroids are another group of pathogens, but they consist only of RNA, do not encode any protein and are replicated by a host plant cell's polymerase.[65]
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 (seecircRNA).[73] circRNAs are thought to arise via a "back-splice" reaction where thespliceosome joins a upstream 3' acceptor to a downstream 5' donor splice site. So far the function of circRNAs is largely unknown, although for few examples a microRNA sponging activity has been demonstrated.
Robert W. Holley, left, poses with his research team.
Research on RNA has led to many important biological discoveries and numerousNobel Prizes.Nucleic acids were discovered in 1868 byFriedrich Miescher, who called the material 'nuclein' since it was found in thenucleus.[74] It was later discovered thatprokaryotic cells, which do not have a nucleus, also contain nucleic acids. The role of RNA in protein synthesis was suspected already in 1939.[75]Severo Ochoa won the 1959Nobel Prize in Medicine (shared withArthur Kornberg) after he discovered an enzyme that can synthesize RNA in the laboratory.[76] However, the enzyme discovered by Ochoa (polynucleotide phosphorylase) was later shown to be responsible for RNA degradation, not RNA synthesis. In 1956 Alex Rich and David Davies hybridized two separate strands of RNA to form the first crystal of RNA whose structure could be determined by X-ray crystallography.[77]
In the early 1970s,retroviruses andreverse transcriptase were discovered, showing for the first time that enzymes could copy RNA into DNA (the opposite of the usual route for transmission of genetic information). For this work,David Baltimore,Renato Dulbecco andHoward Temin were awarded a Nobel Prize in 1975.In 1976,Walter Fiers and his team determined the first complete nucleotide sequence of an RNA virus genome, that ofbacteriophage MS2.[79]
In 1977,introns andRNA splicing were discovered in both mammalian viruses and in cellular genes, resulting in a 1993 Nobel toPhilip Sharp andRichard Roberts.Catalytic RNA molecules (ribozymes) were discovered in the early 1980s, leading to a 1989 Nobel award toThomas Cech andSidney Altman. In 1990, it was found inPetunia that introduced genes can silence similar genes of the plant's own, now known to be a result ofRNA interference.[80][81]
In 1968,Carl Woese hypothesized that RNA might be catalytic and suggested that the earliest forms of life (self-replicating molecules) could have relied on RNA both to carry genetic information and to catalyze biochemical reactions—anRNA world.[87][88] In May 2022, scientists discovered that RNA can form spontaneously on prebioticbasalt lava glass, presumed to have been abundant on theearly Earth.[89][90]
RNA, initially deemed unsuitable for therapeutics due to its short half-life, has been made useful through advances in stabilization. Therapeutic applications arise as RNA folds into complex conformations and binds proteins, nucleic acids, and small molecules to form catalytic centers.[94] RNA-based vaccines are thought to be easier to produce than traditional vaccines derived from killed or altered pathogens, because it can take months or years to grow and study a pathogen and determine which molecular parts to extract, inactivate, and use in a vaccine. Small molecules with conventional therapeutic properties can target RNA and DNA structures, thereby treating novel diseases. However, research is scarce on small molecules targeting RNA and approved drugs for human illness. Ribavirin, branaplam, and ataluren are currently available medications that stabilize double-stranded RNA structures and control splicing in a variety of disorders.[95][96]
Protein-coding mRNAs have emerged as new therapeutic candidates, with RNA replacement being particularly beneficial for brief but torrential protein expression.[97] In vitro transcribed mRNAs (IVT-mRNA) have been used to deliver proteins for bone regeneration, pluripotency, and heart function in animal models.[98][99][100][101][102] SiRNAs, short RNA molecules, play a crucial role in innate defense against viruses and chromatin structure. They can be artificially introduced to silence specific genes, making them valuable for gene function studies, therapeutic target validation, and drug development.[97]
mRNA vaccines have emerged as an important new class of vaccines, using mRNA to manufacture proteins which provoke an immune response. Their first successful large-scale application came in the form ofCOVID-19 vaccines during theCOVID-19 pandemic.
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