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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.
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Ribonucleic acid(RNA) is apolymericmolecule 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 majormacromoleculesessential for all known forms oflife.RNA is assembled as a chain ofnucleotides.Cellular organisms usemessenger RNA(mRNA) to convey genetic information (using thenitrogenous basesofguanine,uracil,adenine,andcytosine,denoted by the letters G, U, A, and C) that directs synthesis of specific proteins. Manyvirusesencode 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 acidsto 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-basedenzymesas 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.

Comparison with DNA

[edit]
Three-dimensional representation of the50Sribosomal 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)[2]in many of its biological roles and consists of much shorter chains of nucleotides.[3]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 containsriboseinstead.[4]Ribose has ahydroxylgroup attached to the pentose ring in the2'position, whereas deoxyribose does not. The hydroxyl groups in the ribose backbone make RNA more chemicallylabilethan DNA by lowering theactivation energyofhydrolysis.
  • The complementary base toadeninein DNA isthymine,whereas in RNA, it isuracil,which is anunmethylatedform of thymine.[5]

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[6]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).[7]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.[8]

Structure

[edit]
Main article:Nucleic acid structure
Watson-Crick base pairs in asiRNA.Hydrogen atoms are not shown.

Eachnucleotidein RNA contains aribosesugar, 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.Aphosphategroup 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 bondsbetween cytosine and guanine, between adenine and uracil and between guanine and uracil.[9]However, other interactions are possible, such as a group of adenine bases binding to each other in a bulge,[10] or the GNRAtetraloopthat has a guanine–adenine base-pair.[9]

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 ahydroxylgroup 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]

Secondary structureof atelomerase RNA

RNA is transcribed with only four bases (adenine, cytosine, guanine and uracil),[15]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).[16]Another notable modified base ishypoxanthine,a deaminated adenine base whosenucleosideis calledinosine(I). Inosine plays a key role in thewobble hypothesisof thegenetic code.[17]

There are more than 100 other naturally occurring modified nucleosides.[18]The greatest structural diversity of modifications can be found intRNA,[19]while pseudouridine and nucleosides with2'-O-methylriboseoften present in rRNA are the most common.[20]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[21]and the subunit interface, implying that they are important for normal function.[22]

The functional form of single-stranded RNA molecules, just like proteins, frequently requires a specifictertiary structure.The scaffold for this structure is provided bysecondary structuralelements that are hydrogen bonds within the molecule. This leads to several recognizable "domains" of secondary structure likehairpin loops,bulges, andinternal loops.[23]In order to create, i.e., design, a RNA for any given secondary structure, two or three bases would not be enough, but four bases are enough.[24]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.[25]

The naturally occurringenantiomerof 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.[26]

Like other structuredbiopolymerssuch 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.

Synthesis

[edit]

Synthesis of RNA 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 apromotersequence in the DNA (usually found "upstream" of a gene). The DNA double helix is unwound by thehelicaseactivity 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.[27]

Primary transcriptRNAs are oftenmodifiedby enzymes after transcription. For example, apoly(A) tailand a5' capare added to eukaryoticpre-mRNAandintronsare removed by thespliceosome.

There are also a number ofRNA-dependent RNA polymerasesthat 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.[28]Also, RNA-dependent RNA polymerase is part of theRNA interferencepathway in many organisms.[29]

Types of RNA

[edit]
See also:List of RNAs

Overview

[edit]
Structure of ahammerhead ribozyme,a ribozyme that cuts RNA

Messenger RNA (mRNA) is the RNA that carries information from DNA to theribosome,the sites of protein synthesis (translation) in the cell. The mRNA is a copy of DNA. The coding sequence of the mRNA determines theamino acidsequence in theproteinthat is produced.[30]However, many RNAs do not code for protein (about 97% of the transcriptional output is non-protein-coding in eukaryotes[31][32][33][34]).

These so-callednon-coding RNAs( "ncRNA" ) can be encoded by their own genes (RNA genes), but can also derive from mRNAintrons.[35]The most prominent examples of non-coding RNAs aretransfer RNA(tRNA) andribosomal RNA(rRNA), both of which are involved in the process of translation.[5]There are also non-coding RNAs involved in gene regulation,RNA processingand other roles. Certain RNAs are able tocatalysechemical reactions such as cutting andligatingother RNA molecules,[36]and the catalysis ofpeptide bondformation in theribosome;[8]these are known asribozymes.

In length

[edit]

According to the length of RNA chain, RNA includessmall RNAand long RNA.[37]Usually,small RNAsare shorter than 200ntin length, and long RNAs are greater than 200ntlong.[38]Long RNAs, also called large RNAs, mainly includelong non-coding RNA(lncRNA) andmRNA.Small RNAs mainly include 5.8Sribosomal 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)[39]and small rDNA-derived RNA (srRNA).[40] There are certain exceptions as in the case of the5S rRNAof the members of the genusHalococcus(Archaea), which have an insertion, thus increasing its size.[41][42][43]

In translation

[edit]

Messenger RNA(mRNA) carries information about a protein sequence to theribosomes,the protein synthesis factories in the cell. It iscodedso that every three nucleotides (acodon) corresponds to one amino acid. Ineukaryoticcells, 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 andtranslatedinto 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.[30]

Transfer RNA(tRNA) is a small RNA chain of about 80nucleotidesthat transfers a specific amino acid to a growingpolypeptidechain at the ribosomal site of protein synthesis during translation. It has sites for amino acid attachment and ananticodonregion forcodonrecognition that binds to a specific sequence on the messenger RNA chain through hydrogen bonding.[35]

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.[30]Nearly all the RNA found in a typical eukaryotic cell is rRNA.

Transfer-messenger RNA(tmRNA) is found in manybacteriaandplastids.It tags proteins encoded by mRNAs that lack stop codons for degradation and prevents the ribosome from stalling.[44]

Regulatory RNA

[edit]

The earliest known regulators ofgene expressionwere proteins known asrepressorsandactivators– regulators with specific short binding sites withinenhancerregions near the genes to be regulated.[45]Later studies have shown that RNAs also regulate genes. There are several kinds of RNA-dependent processes in eukaryotes regulating the expression of genes at various points, such asRNAirepressing genespost-transcriptionally,long non-coding RNAsshutting down blocks ofchromatinepigenetically,andenhancer RNAsinducing increased gene expression.[46]Bacteria and archaeahave also been shown to use regulatory RNA systems such asbacterial small RNAsandCRISPR.[47]Fire and Mello were awarded the 2006Nobel Prize in Physiology or Medicinefor discoveringmicroRNAs(miRNAs), specific short RNA molecules that can base-pair with mRNAs.[48]

RNA interference by miRNAs

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See also:RNA interference

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.[49]Thisantisense-based process involves steps that first process the RNA so that it canbase-pairwith a region of its target mRNAs. Once the base pairing occurs, other proteins direct the mRNA to be destroyed bynucleases.[46]

Long non-coding RNAs

[edit]
See also:Long Non-coding RNA

Next to be linked to regulation wereXistand otherlong noncoding RNAsassociated withX chromosome inactivation.Their roles, at first mysterious, were shown byJeannie T. Leeand others to be thesilencingof blocks of chromatin via recruitment ofPolycombcomplex so that messenger RNA could not be transcribed from them.[50]Additional lncRNAs, currently defined as RNAs of more than 200 base pairs that do not appear to have coding potential,[51]have been found associated with regulation ofstem cellpluripotencyandcell division.[51]

Enhancer RNAs

[edit]
See also:Enhancer RNA

The third major group of regulatory RNAs is calledenhancer RNAs.[51]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.[51][52]They up-regulate the transcription of the gene(s) under control of the enhancer from which they are transcribed.[51][53]

Regulatory RNA in prokaryotes

[edit]

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).[54][47]Currently, the ubiquitous nature of systems of RNA regulation of genes has been discussed as support for theRNA Worldtheory.[46][55]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.[2]Bacterial small RNAsgenerally act viaantisensepairing with mRNA to down-regulate its translation, either by affecting stability or affecting cis-binding ability.[46]Riboswitcheshave also been discovered. They are cis-acting regulatory RNA sequences actingallosterically.They change shape when they bindmetabolitesso that they gain or lose the ability to bind chromatin to regulate expression of genes.[56][57]

Archaea also have systems of regulatory RNA.[58]The CRISPR system, recently being used to edit DNAin situ,acts via regulatory RNAs in archaea and bacteria to provide protection against virus invaders.[46][59]

In RNA processing

[edit]
Uridine to pseudouridine is a common RNA modification.

Many RNAs are involved in modifying other RNAs. Intronsaresplicedout ofpre-mRNAbyspliceosomes,which contain severalsmall nuclear RNAs(snRNA),[5]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,GandU. In eukaryotes, modifications of RNA nucleotides are in general directed bysmall nucleolar RNAs(snoRNA; 60–300 nt),[35]found in thenucleolusandcajal 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]

RNA genomes

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Like DNA, RNA can carry genetic information.RNA viruseshavegenomescomposed 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.Viroidsare 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 reverse transcription

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Reverse transcribing viruses replicate their genomes byreverse transcribingDNA copies from their RNA; these DNA copies are then transcribed to new RNA.Retrotransposonsalso spread by copying DNA and RNA from one another,[66]andtelomerasecontains anRNA that is used as templatefor building the ends ofeukaryotic chromosomes.[67]

Double-stranded RNA

[edit]
Double-stranded RNA
Main article:Double-stranded RNA

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 and the adding of one oxygen atom. dsRNA forms the genetic material of someviruses(double-stranded RNA viruses). Double-stranded RNA, such as viral RNA orsiRNA,can triggerRNA interferenceineukaryotes,as well asinterferonresponse invertebrates.[68][69][70][71]In eukaryotes, double-stranded RNA (dsRNA) plays a role in the activation of theinnate immune systemagainst viral infections.[72]

Circular RNA

[edit]
Main article:Circular RNA

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 thespliceosomejoins 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.

Key discoveries in RNA biology

[edit]
Further information:History of RNA biology
Robert W. Holley, left, poses with his research team.

Research on RNA has led to many important biological discoveries and numerousNobel Prizes.Nucleic acidswere discovered in 1868 byFriedrich Miescher,who called the material 'nuclein' since it was found in thenucleus.[74]It was later discovered that prokaryotic 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 Ochoawon 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]

The sequence of the 77 nucleotides of a yeast tRNA was found byRobert W. Holleyin 1965,[78]winning Holley the1968 Nobel Prize in Medicine(shared withHar Gobind KhoranaandMarshall Nirenberg).

In the early 1970s,retrovirusesandreverse transcriptasewere 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 DulbeccoandHoward Teminwere awarded a Nobel Prize in 1975. In 1976,Walter Fiersand his team determined the first complete nucleotide sequence of an RNA virus genome, that ofbacteriophage MS2.[79]

In 1977,intronsandRNA splicingwere discovered in both mammalian viruses and in cellular genes, resulting in a 1993 Nobel toPhilip SharpandRichard Roberts. Catalytic RNA molecules (ribozymes) were discovered in the early 1980s, leading to a 1989 Nobel award toThomas CechandSidney Altman.In 1990, it was found inPetuniathat introduced genes can silence similar genes of the plant's own, now known to be a result ofRNA interference.[80][81]

At about the same time, 22 nt long RNAs, now calledmicroRNAs,were found to have a role in thedevelopmentofC. elegans.[82] Studies on RNA interference gleaned a Nobel Prize forAndrew FireandCraig Melloin 2006, and another Nobel was awarded for studies on the transcription of RNA toRoger Kornbergin the same year. The discovery of gene regulatory RNAs has led to attempts to develop drugs made of RNA, such assiRNA,to silence genes.[83]Adding to the Nobel prizes awarded for research on RNA in 2009 it was awarded for the elucidation of the atomic structure of the ribosome toVenki Ramakrishnan,Thomas A. Steitz,andAda Yonath.In 2023 theNobel Prize in Physiology or Medicinewas awarded toKatalin KarikóandDrew Weissmanfor their discoveries concerningmodified nucleosidesthat enabled the development of effective mRNA vaccines against COVID-19.[84][85][86]


Relevance for prebiotic chemistry and abiogenesis

[edit]

In 1968,Carl Woesehypothesized 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 reported that they discovered RNA forms spontaneously on prebioticbasalt lava glasswhich is presumed to have been abundantly available on theearly Earth.[89][90]

In March 2015,DNAand RNAnucleobases,includinguracil,cytosineandthymine,were reportedly formed in the laboratory underouter spaceconditions, using starter chemicals, such aspyrimidine,anorganic compoundcommonly found inmeteorites.Pyrimidine,likepolycyclic aromatic hydrocarbons(PAHs), is one of the most carbon-rich compounds found in theUniverseand may have been formed inred giantsor ininterstellar dustand gas clouds.[91]In July 2022, astronomers reported the discovery of massive amounts ofprebiotic molecules,including possible RNA precursors, in theGalactic Centerof theMilky Way Galaxy.[92][93]

Medical applications

[edit]

RNA, initially deemed unsuitable for therapeutic use due to its short half-life, has been proven to possess numerous therapeutic properties through advancements in stabilization chemistry. RNA molecules have potential therapeutic applications due to their ability to fold into complex conformations and binding proteins, nucleic acids, small molecules, and form catalytic centers.[94]RNA-based vaccines are thought to be a quicker way to obtain immunological resistance than the traditional approach of vaccines that rely on a killed or altered version of the pathogen, because it can take months or even years to grow and study a pathogen in order to 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 on small molecules targeting RNA and approved drugs for human illness therapy is scarce. 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 torrent-like 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 vaccineshave emerged as an important new class of vaccines, using mRNA to produce an immune response. Their first successful large-scale application came in the form ofCOVID-19 vaccinesduring theCOVID-19 pandemic.

See also

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References

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