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RNA

Ribonucleic acid or RNA is a nucleic acid, consisting of many nucleotides that form a polymer. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA plays several important biological roles, including many processes involving translation of genetic information from deoxyribonucleic acid (DNA) into proteins. One type of RNA acts as a messenger between DNA and the protein synthesis complexes known as ribosomes, others form vital portions of the structure of ribosomes, act as essential carrier molecules for amino acids to be used in protein synthesis. It has also been known since the 1990s that several types of RNA regulate which genes are active.

RNA is very similar to DNA, but differs in a few important structural details: in the cell RNA is usually single stranded, while DNA is usually double stranded. RNA nucleotides contain ribose while DNA contains deoxyribose (a type of ribose that lacks one oxygen atom), and RNA uses the nucleotide uracil in its composition, instead of thymine which is present in DNA. RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other enzymes. Some of these RNA processing enzymes contain their own RNAs.

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Chemical and stereochemical structure

Each nucleotide in RNA contains a ribose, whose carbons are numbered 1' through 5'. The base – often adenine, cytosine, guanine or uracil – is attached to the 1' position. 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 at physiological pH, making RNA a charged molecule. The bases often form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil.^[1] However other interactions are possible, such as a group of adenine bases binding to each other in a bulge,^[2] or the GNRA tetraloop that has a guanine–adenine base-pair.^[1]

There are also numerous modified bases and sugars found in RNA that serve many different roles. 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 (most notably in the TΨC loop of tRNA).^[3] Another notable modified base is hypoxanthine, a deaminated guanine base whose nucleoside is called inosine. Inosine plays a key role in the wobble hypothesis of the genetic code.^[4] There are nearly 100 other naturally occurring modified nucleosides,^[5] of which pseudouridine and nucleosides with 2'-O-methylribose are the most common.^[6] 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-translational modifications occur in highly functional regions, such as the peptidyl transferase center and the subunit interface, implying that they are important for normal function.^[7]

The most important structural feature 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 enforces the C3'-endo sugar conformation (as opposed to the C2'-endo conformation of the deoxyribose sugar in DNA) that causes the helix to adopt the A-form geometry rather than the B-form most commonly observed in DNA.^[8] This results in a very deep and narrow major groove and a shallow and wide minor groove.^[9] 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.^[10]

Comparison with DNA

RNA and DNA differ in three main ways. First, unlike DNA which is double-stranded, RNA is a single-stranded molecule in most of its biological roles and has a much shorter chain of nucleotides. Secondly, while DNA contains deoxyribose, RNA contains ribose, (there is no hydroxyl group attached to the pentose ring in the 2' position in DNA, whereas RNA has two hydroxyl groups). These hydroxyl groups make RNA less stable than DNA because it is more prone to hydrolysis. Thirdly, the complementary nucleotide to adenine is not thymine, as it is in DNA, but rather uracil, which is an unmethylated form of thymine.^[11]

Like DNA, most biologically active RNAs including tRNA, rRNA, snRNAs and other non-coding RNAs are extensively base paired to form double stranded helices. Structural analysis of these RNAs have revealed that they are highly structured. Unlike DNA, this structure is not long double-stranded helices but rather collections of short helices packed together into structures akin to proteins. In this fashion, RNAs can achieve chemical catalysis, like enzymes.^[12] For instance, determination of the structure of the ribosome – an enzyme that catalyzes peptide bond formation – revealed that its active site is composed entirely of RNA.^[13]

Synthesis

Synthesis of RNA is usually catalyzed by an enzyme – RNA polymerase – using DNA as a template. Initiation of synthesis 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’ -> 5’ direction, synthesizing a complementary RNA molecule with elongation occurring in the 5’ -> 3’ direction. The DNA sequence also dictates where termination of RNA synthesis will occur.^[14]

There are also a number of RNA-dependent RNA polymerases as well 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.^[15] Also, it is known that RNA-dependent RNA polymerases are required for the RNA interference pathway in many organisms.^[16]

Biological roles

Messenger RNA (mRNA)

Main article: Messenger RNA

Messenger RNA is RNA that carries information from DNA to the ribosome sites of protein synthesis in the cell. In eukaryotic cells, once mRNA has been transcribed from DNA, it is "processed" before being exported from the nucleus into 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.^[17]

Non-coding RNA

Further information: Non-coding RNA

RNA genes are genes that encode RNA which is not translated into a protein, known as non-coding RNA or small RNA. Non-coding RNAs can also derive from introns.^[18] The most prominent examples of RNA genes are transfer RNA (tRNA) and ribosomal RNA (rRNA), both of which are involved in the process of translation. Two other groups of non-coding RNA are microRNAs (miRNA) which regulate the gene expression and small nuclear RNAs (snRNA), a diverse class that includes for example the RNAs that form spliceosomes that excise introns from pre-mRNA.^[11]

Certain RNAs are able to catalyse chemical reactions such as cutting and ligating other RNA molecules,^[19] and the catalysis of peptide bond formation in the ribosome;^[13] these are known as ribozymes.

Translation

In addition to mRNA, two types of RNA are central to translation: ribosomal RNA (rRNA) and transfer RNA (tRNA).

Ribosomal RNA is the catalytic component of the ribosomes, the protein synthesis factories in the cell. 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.^[17] rRNA is extremely abundant and makes up 80% of the 10 mg/ml RNA found in a typical eukaryotic cytoplasm.^[20]

Transfer RNA 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.^[18]

Gene regulation

Several types of RNA can downregulate gene expression by being complementary to a part of a gene. MicroRNAs (miRNA; 21-22 nt) are found in eukaryotes and act through RNA interference (RNAi), where an effector complex of miRNA and enzymes can break down mRNA which the miRNA is complementary to, block the mRNA from being translated, or cause the promoter to be methylated which generally downregulates the gene.^[21] Some miRNAs upregulate genes instead (RNA activation).^[22] While small interfering RNAs (siRNA; 20-25 nt) are often produced by breakdown of viral RNA, there are also endogenous sources of siRNAs.^[23] siRNAs act through RNA interference in a fashion similar to miRNAs. Animals have Piwi-interacting RNAs (piRNA; 29-30 nt) which are active in germline cells and are thought to be a defense against transposons and play a role in gametogenesis.^[24]^[25] X chromosome inactivation in female mammals is caused by Xist, an RNA which coats one X chromosome, inactiving it.^[26] Antisense RNAs are widespread among bacteria; most downregulate a gene, but a few are activators of transcription.^[27]

RNA modification

RNA can be modified after transcription not only by splicing, but also by having its nucleotides modified to other nucleotides than A, C, G and U.

In eukaryotes, modifications of RNA nucleotides are generally directed by small nucleolar RNAs (snoRNA; 60-300 nt),^[18] 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. rRNA and tRNA are extensively modified, but snRNA and mRNA can also be the target of base modification.^[28]^[29]

Double-stranded RNA

Double-stranded RNA (dsRNA) is RNA with two complementary strands, similar to the DNA found in all cells. dsRNA forms the genetic material of some viruses called double-stranded RNA viruses. In eukaryotes, long double-stranded RNA such as viral RNA can trigger RNA interference, where short dsRNA molecules called siRNAs (small interfering RNAs) can cause enzymes to break down specific mRNAs or silence the expression of genes. siRNA can also increase the transcription of a gene, a process called RNA activation.^[30]

RNA world hypothesis

Main article: RNA world hypothesis

The RNA world hypothesis proposes that the earliest forms of life relied on RNA both to carry genetic information (like DNA does now) and to catalyze biochemical reactions like an enzyme. According to this hypothesis, descendants of these early lifeforms gradually integrated DNA and proteins into their metabolism.

Secondary structure

Further information: RNA structure

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 which are hydrogen bonds within the molecule. This leads to several recognizable "domains" of secondary structure like hairpin loops, bulges and internal loops.^[31] There has been a significant amount of research directed at the RNA structure prediction problem.

Online tools for minimum free energy structure prediction from single sequences are provided by MFOLD and RNAfold.

Comparative studies of conserved RNA structures are significantly more accurate and provide evolutionary information. Computationally reasonable and accurate online tools for alignment folding are provided by KNetFold, RNAalifold and Pfold.

A package of RNA structure prediction programs is also available for Windows: RNAstructure.

A database of RNA sequences and secondary structures is available from Rfam, analyses and links to RNA analysis tools are available from Wikiomics.

Therapeutic RNA

An RNA oligonucleotide that is complementary to an mRNA will bind to it and activate the RNA interference machinery which will degrade most of the mRNA from a gene, thereby knocking down the expression of an unwanted gene such as an oncogene or a viral gene. RNA is shortlived in the cell so the oligonucleotide has to have various chemical changes to resist degradation. Vitravene is an example of an antisense oligonucleotide drug, it inhibits a gene from cytomegalovirus. Another possible therapeutic RNA could be ribozymes that bind to specific RNAs and cleave them.^[32]

List of RNAs

Type	Abbr.	Function	Distribution	Ref.
Messenger RNA	mRNA	Codes for protein	All organisms
Ribosomal RNA	rRNA	Translation	All organisms
Transfer RNA	tRNA	Translation	All organisms
Transfer-messenger RNA	tmRNA	Rescuing stalled ribosomes	Bacteria	^[33]
Antisense RNA	aRNA	Gene regulation	All organisms	^[34]
Small interfering RNA	siRNA	Gene regulation	Most eukaryotes	^[35]
MicroRNA	miRNA	Gene regulation	Most eukaryotes	^[36]
Piwi-interacting RNA	piRNA	Gene regulation	Animals	^[24]
Small nuclear RNA	snRNA	Various	Eukaryotes and archaea	^[37]
Small nucleolar RNA	snoRNA	Nucleotide modification of RNAs	Eukaryotes and archaea	^[38]
Guide RNA	gRNA	mRNA modification	Kinetoplastid mitochondria	^[39]
Ribonuclease P	RNase P	tRNA maturation	All organisms	^[40]
Ribonuclease MRP	RNase MRP	rRNA maturation, DNA replication	Eukaryotes	^[41]
Y RNA		RNA processing, DNA replication	Animals	^[42]
Telomerase RNA		Telomere synthesis	Most eukaryotes	^[43]
Signal recognition particle RNA	SRP RNA	Protein export	All organisms	^[44]
Retrotransposon		Self-propagating	Eukaryotes and some bacteria	^[45]
Viroid		Self-propagating	Infected plants	^[46]

In addition, the genomes of many types of viruses consist of RNA, namely double-stranded RNA viruses, positive-sense RNA viruses, negative-sense RNA viruses and most satellite viruses and reverse transcribing viruses.

History

Nucleic acids were discovered in 1868 by Friedrich Miescher, who called the material 'nuclein' since it was found in the nucleus.^[47] It was later discovered that prokaryotic cells, which do not have a nucleus, also contain nucleic acids. The role of RNA in protein synthesis had been suspected since 1939, based on experiments carried out by Torbjörn Caspersson, Jean Brachet and Jack Schultz.^[48] Gerard Marbaix isolated the first messenger RNA, for rabbit hemoglobin, and found it induced the synthesis of hemoglobin after injection into oocytes.^[49] Finally, Severo Ochoa discovered how RNA is synthesized, winning Ochoa the 1959 Nobel Prize for Medicine.^[50] The sequence of the 77 nucleotides of a yeast RNA was found by Robert W. Holley in 1965,^[51] winning Holley the 1968 Nobel Prize for Medicine. In 1976, Walter Fiers and his team at the University of Ghent determined the first complete nucleotide sequence of an RNA virus genome, that of bacteriophage MS2.^[52] In the early 1990s it was found that introduced genes can silence homologous endogenous genes in plants.^[53] At about the same time, 22 nt long RNAs, now known as microRNAs, were found to have a role in the development of C. elegans.^[54]

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RNA