Ribonucleic acid (RNA) is a
polymeric 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 and
deoxyribonucleic acid (DNA) are
nucleic acids. The nucleic acids constitute one of the four major
macromolecules essential for all known forms of
life. RNA is assembled as a chain of
nucleotides. Cellular organisms use
messenger RNA (mRNA) to convey genetic information (using the
nitrogenous bases of
guanine,
uracil,
adenine, and
cytosine, denoted by the letters G, U, A, and C) that directs synthesis of specific proteins. Many
viruses encode their genetic information using an RNA
genome.
Some RNA molecules play an active role within cells by catalyzing biological reactions, controlling
gene expression, or sensing and communicating responses to cellular signals. One of these active processes is
protein synthesis, a universal function in which RNA molecules direct the synthesis of proteins on
ribosomes. This process uses
transfer RNA (tRNA) molecules to deliver
amino acids to the
ribosome, where
ribosomal RNA (rRNA) then links amino acids together to form coded proteins.
It has become widely accepted in science[1] that early in the
history of life on Earth, prior to the evolution of DNA and possibly of protein-based
enzymes as well, an "
RNA world" existed in which RNA served as both living organisms' storage method for
genetic information—a role fulfilled today by DNA, except in the case of
RNA 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 a
ribozyme.
Comparison with DNA
The chemical structure of RNA is very similar to that of
DNA, 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 in
tRNA.
While the sugar-phosphate "backbone" of DNA contains deoxyribose, RNA contains ribose instead.[4] Ribose has a
hydroxyl group attached to the pentose ring in the
2' position, whereas deoxyribose does not. The hydroxyl groups in the ribose backbone make RNA more chemically
labile than DNA by lowering the
activation energy of
hydrolysis.
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[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 chemical
catalysis (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]
Each
nucleotide in RNA contains a
ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, in general,
adenine (A),
cytosine (C),
guanine (G), or
uracil (U). Adenine and guanine are
purines, and cytosine and uracil are
pyrimidines. A
phosphate 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 form
hydrogen bonds between 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 GNRA
tetraloop that has a guanine–adenine base-pair.[9]
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,[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]
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, and
ribothymidine (T) are found in various places (the most notable ones being in the TΨC loop of
tRNA).[16] Another notable modified base is
hypoxanthine, a deaminated adenine base whose
nucleoside is called
inosine (I). Inosine plays a key role in the
wobble hypothesis of the
genetic code.[17]
There are more than 100 other naturally occurring modified nucleosides.[18] The greatest structural diversity of modifications can be found in
tRNA,[19] while pseudouridine and nucleosides with
2'-O-methylribose often 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 specific
tertiary structure. The scaffold for this structure is provided by
secondary structural elements that are hydrogen bonds within the molecule. This leads to several recognizable "domains" of secondary structure like
hairpin loops, bulges, and
internal 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 as
Mg2+ are needed to stabilise many secondary and
tertiary structures.[25]
The naturally occurring
enantiomer of RNA is D-RNA composed of D-ribonucleotides. All chirality centers are located in the D-ribose. By the use of L-ribose or rather L-ribonucleotides, L-RNA can be synthesized. L-RNA is much more stable against degradation by
RNase.[26]
Like other structured
biopolymers 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 as
circuit topology.
Synthesis
Synthesis of RNA is usually catalyzed by an enzyme—
RNA polymerase—using DNA as a template, a process known as
transcription. Initiation of transcription begins with the binding of the enzyme to a
promoter sequence in the DNA (usually found "upstream" of a gene). The DNA double helix is unwound by the
helicase 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.[27]
There are also a number of
RNA-dependent RNA polymerases that use RNA as their template for synthesis of a new strand of RNA. For instance, a number of
RNA viruses (such as poliovirus) use this type of enzyme to replicate their genetic material.[28] Also, RNA-dependent RNA polymerase is part of the
RNA interference pathway in many organisms.[29]
Messenger RNA (mRNA) is the RNA that carries information from DNA to the
ribosome, the sites of protein synthesis (
translation) in the cell. The mRNA is a copy of DNA. The coding sequence of the mRNA determines the
amino acid sequence in the
protein that 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-called
non-coding RNAs ("ncRNA") can be encoded by their own genes (RNA genes), but can also derive from mRNA
introns.[35] The most prominent examples of non-coding RNAs are
transfer RNA (tRNA) and
ribosomal RNA (rRNA), both of which are involved in the process of translation.[5] There are also non-coding RNAs involved in gene regulation,
RNA processing and other roles. Certain RNAs are able to
catalyse chemical reactions such as cutting and
ligating other RNA molecules,[36] and the catalysis of
peptide bond formation in the
ribosome;[8] these are known as
ribozymes.
Messenger RNA (mRNA) carries information about a protein sequence to the
ribosomes, the protein synthesis factories in the cell. It is
coded so that every three nucleotides (a
codon) corresponds to one amino acid. In
eukaryotic cells, once precursor mRNA (pre-mRNA) has been transcribed from DNA, it is processed to mature mRNA. This removes its
introns—non-coding sections of the pre-mRNA. The mRNA is then exported from the nucleus to the
cytoplasm, where it is bound to ribosomes and
translated into its corresponding protein form with the help of
tRNA. 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 of
ribonucleases.[30]
Transfer RNA (tRNA) is a small RNA chain of about 80
nucleotides that transfers a specific amino acid to a growing
polypeptide chain at the ribosomal site of protein synthesis during translation. It has sites for amino acid attachment and an
anticodon region for
codon recognition that binds to a specific sequence on the messenger RNA chain through hydrogen bonding.[35]
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 the
nucleolus, 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 many
bacteria and
plastids. It tags proteins encoded by mRNAs that lack stop codons for degradation and prevents the ribosome from stalling.[44]
Post-transcriptional expression levels of many genes can be controlled by
RNA interference, in which
miRNAs, specific short RNA molecules, pair with mRNA regions and target them for degradation.[49] This
antisense-based process involves steps that first process the RNA so that it can
base-pair with a region of its target mRNAs. Once the base pairing occurs, other proteins direct the mRNA to be destroyed by
nucleases.[46]
Next to be linked to regulation were
Xist and other
long noncoding RNAs associated with
X chromosome inactivation. Their roles, at first mysterious, were shown by
Jeannie T. Lee and others to be the
silencing of blocks of chromatin via recruitment of
Polycomb complex 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 of
stem cellpluripotency and
cell division.[51]
The third major group of regulatory RNAs is called
enhancer 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 from
enhancers, 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
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 the
RNA World theory.[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 RNAs generally act via
antisense pairing with mRNA to down-regulate its translation, either by affecting stability or affecting cis-binding ability.[46]Riboswitches have also been discovered. They are cis-acting regulatory RNA sequences acting
allosterically. They change shape when they bind
metabolites so 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 DNA in situ, acts via regulatory RNAs in archaea and bacteria to provide protection against virus invaders.[46][59]
In RNA processing
Many RNAs are involved in modifying other RNAs.
Introns are
spliced out of
pre-mRNA by
spliceosomes, which contain several
small 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 than
A,
C,
G and
U.
In eukaryotes, modifications of RNA nucleotides are in general directed by
small nucleolar RNAs (snoRNA; 60–300 nt),[35] found in the
nucleolus and
cajal 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
Like DNA, RNA can carry genetic information.
RNA viruses have
genomes 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]
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 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.[68][69][70][71] In eukaryotes, double-stranded RNA (dsRNA) plays a role in the activation of the
innate immune system against viral infections.[72]
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).[73] circRNAs are thought to arise via a "back-splice" reaction where the
spliceosome 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.
Research on RNA has led to many important biological discoveries and numerous
Nobel Prizes.
Nucleic acids were discovered in 1868 by
Friedrich Miescher, who called the material 'nuclein' since it was found in the
nucleus.[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 Ochoa won the 1959
Nobel Prize in Medicine (shared with
Arthur 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 and
reverse 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 and
Howard 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 of
bacteriophage MS2.[79]
In 1977,
introns and
RNA splicing were discovered in both mammalian viruses and in cellular genes, resulting in a 1993 Nobel to
Philip Sharp and
Richard Roberts.
Catalytic RNA molecules (
ribozymes) were discovered in the early 1980s, leading to a 1989 Nobel award to
Thomas Cech and
Sidney Altman. In 1990, it was found in Petunia that introduced genes can silence similar genes of the plant's own, now known to be a result of
RNA interference.[80][81]
At about the same time, 22 nt long RNAs, now called
microRNAs, were found to have a role in the
development of C. elegans.[82]
Studies on RNA interference gleaned a Nobel Prize for
Andrew Fire and
Craig Mello in 2006, and another Nobel was awarded for studies on the transcription of RNA to
Roger Kornberg in the same year. The discovery of gene regulatory RNAs has led to attempts to develop drugs made of RNA, such as
siRNA, 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 to
Venki Ramakrishnan,
Thomas A. Steitz, and
Ada Yonath.
Relevance for prebiotic chemistry and abiogenesis
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—an
RNA world.[84][85] In May 2022, scientists reported that they discovered RNA forms spontaneously on prebiotic
basalt lava glass which is presumed to have been abundantly available on the
early Earth.[86][87]
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.[91] 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.[92][93]
Protein-coding mRNAs have emerged as new therapeutic candidates, with RNA replacement being particularly beneficial for brief but torrent-like protein expression.[94] In vitro transcribed mRNAs (IVT-mRNA) have been used to deliver proteins for bone regeneration, pluripotency, and heart function in animal models.[95][96][97][98][99] 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.[94]
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