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{{BioPsy}}
  
{{BioPsy}}
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[[Image:Pre-mRNA-1ysv.png-tubes.png|thumb|200px|right|A hairpin loop from a pre-mRNA. Highlighted are the bases (light green) and backbone (sky blue).]]
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'''Ribonucleic acid''' ('''RNA''') is a [[nucleic acid]] [[polymer]] consisting of [[nucleotide]] [[monomers]], that acts as a messenger between DNA and [[ribosome]]s, and that is also responsible for making proteins out of amino acids.[1] RNA polynucleotides contain [[ribose]] sugars and predominantly [[uracil]] unlike deoxyribonucleic acid ([[DNA]]), which contains [[deoxyribose]] and predominantly [[thymine]]. It is transcribed (synthesized) from DNA by [[enzymes]] called RNA polymerases and further processed by other enzymes. RNA serves as the template for translation of genes into [[protein]]s, transferring [[amino acid]]s to the [[ribosome]] to form proteins, and also translating the transcript into proteins.
  
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'''Ribonucleic acid''' ('''RNA''') is a biologically important type of molecule that consists of a long chain of [[nucleotide]] units. Each nucleotide consists of a [[nucleobase|nitrogenous base]], a [[ribose]] sugar, and a [[phosphate]]. 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 has the base [[uracil]] rather than [[thymine]] that is present in DNA.
   
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RNA is [[Transcription (genetics)|transcribed]] from DNA by [[enzyme]]s called [[RNA polymerase]]s and is generally further processed by other enzymes. RNA is central to [[protein synthesis]]. Here, a type of RNA called [[messenger RNA]] carries information from DNA to structures called [[ribosome]]s. These ribosomes are made from proteins and ribosomal RNAs, which come together to form a molecular machine that can read messenger RNAs and [[Translation (biology)|translate]] the information they carry into proteins. There are many RNAs with other roles – in particular [[Regulation of gene expression|regulating]] which [[gene]]s are expressed, but also as the [[genome]]s of most [[virus]]es.
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Nucleic acids were discovered in 1868 (some sources indicate 1869) by [[Johann Friedrich Miescher]] (1844-1895), who called the material 'nuclein' since it was found in the nucleus. 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 Oskar Caspersson|Torbjörn Caspersson]], [[Jean Brachet]] and [[Jack Schultz]]. [[Hubert Chantrenne]] elucidated the messenger role played by RNA in the synthesis of [[protein]]s in [[Ribosomes|ribosome]]. The sequence of the 77 nucleotides of a yeast RNA was found by [[Robert W. Holley]] in 1964, winning Holley the 1968 [[Nobel Prize for Medicine]]. In [[1976]], [[Walter Fiers]] and his team at the [[University of Ghent]] determined the complete nucleotide sequence of [[bacteriophage MS2]]-RNA.<ref>Fiers W et al., Complete nucleotide-sequence of bacteriophage MS2-RNA - primary and secondary structure of replicase gene, Nature, 260, 500-507, 1976</ref>
  
   
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==Structure==
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==Chemical and Stereochemical structure==
  
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[[Image:NA-comparedto-DNA_thymineAndUracilCorrected.png|thumb|290px|RNA with its nitrogenous bases to the left and [[DNA]] to the right.]]
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[[Image:Piwi-siRNA-basepairing.png|thumb|right|230px|Watson-Crick base pairs in a [[siRNA]] (hydrogen atoms are not shown)]]
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Each [[nucleotide]] in RNA contains a [[ribose]] sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, generally [[adenine]] (A), [[cytosine]] (C), [[guanine]] (G) or [[uracil]] (U). Adenine and guanine are [[purine]]s, cytosine and uracil are [[pyrimidine]]s. 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 (polyanion). The bases may form [[hydrogen bond]]s between cytosine and guanine, between adenine and uracil and between guanine and uracil.<ref name="pmid15561141"/> However other interactions are possible, such as a group of adenine bases binding to each other in a bulge,<ref>{{cite book | title=RNA biochemistry and biotechnology| author=Barciszewski J, Frederic B, Clark C| date=1999| pages=73–87| publisher=Springer| isbn=0792358627 | oclc=52403776}}</ref>
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or the GNRA [[tetraloop]] that has a guanine–adenine base-pair.<ref name="pmid15561141">{{cite journal | author = Lee JC, Gutell RR | title = Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs | journal = J. Mol. Biol. | volume = 344 | issue = 5 | pages = 1225–49 | year = 2004 | doi = 10.1016/j.jmb.2004.09.072| pmid=15561141}}</ref>
   
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[[Image:RNA chemical structure.GIF|thumb|left|Chemical structure of RNA]]
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RNA is a polymer with a ribose and [[phosphate]] backbone and four different bases: [[adenine]], [[guanine]], [[cytosine]], and [[uracil]]. The first three are the same as those found in DNA, but in RNA [[thymine]] is replaced by uracil as the base complementary to adenine. This base is also a pyrimidine and is very similar to thymine. Uracil is energetically less expensive to produce than thymine, which may account for its use in RNA. In DNA, however, uracil is readily produced by chemical degradation of cytosine, so having thymine as the normal base makes detection and repair of such incipient mutations more efficient. Thus, uracil is appropriate for RNA, where quantity is important but lifespan is not, whereas thymine is appropriate for DNA where maintaining sequence with high fidelity is more critical.
  
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An 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 causes the helix to adopt the [[A-DNA|A-form geometry]] rather than the B-form most commonly observed in DNA.<ref>{{cite journal | author=Salazar M, Fedoroff OY, Miller JM, Ribeiro NS, Reid BR| title=The DNA strand in DNAoRNA hybrid duplexes is neither B-form nor A-form in solution| journal=Biochemistry| year=1992| volume=32| issue=16| pages=4207–15| pmid=7682844| doi=10.1021/bi00067a007}}</ref> This results in a very deep and narrow major groove and a shallow and wide minor groove.<ref>{{cite journal | author=Hermann T, Patel DJ| title=RNA bulges as architectural and recognition motifs| journal=Structure| year=2000| volume=8| issue=3| pages=R47–R54| doi=10.1016/S0969-2126(00)00110-6 | pmid = 10745015 }}</ref> 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.<ref>{{cite journal | author=Mikkola S, Nurmi K, Yousefi-Salakdeh E, Strömberg R, Lönnberg H| title=The mechanism of the metal ion promoted cleavage of RNA phosphodiester bonds involves a general acid catalysis by the metal aquo ion on the departure of the leaving group| journal=Perkin transactions 2| year=1999| pages=1619–26| doi=10.1039/a903691a}}</ref>
   
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[[Image:Ciliate telomerase RNA.JPG|thumb|[[Secondary structure]] of a [[telomerase RNA]].]]
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However, there are also numerous modified bases and sugars found in RNA that serve many different roles. [[Pseudouridine]] (Ψ) and the DNA nucleoside [[thymidine]] are found in various places (most notably in the TΨC loop of every [[tRNA]]). Thus, it is not technically correct to say that uracil is found in RNA in place of thymine. Another notable modified base is hypoxanthine (a deaminated Guanine base whose nucleotide is called [[Inosine]]). Inosine plays a key role in the Wobble Hypothesis of the [[Genetic Code]]. There are nearly 100 other naturally occurring modified bases, of which pseudouridine and 2'-O-methylribose are by far the most common. 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, inferring that they are important for normal function.
  
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RNA is transcribed with only four bases (adenine, cytosine, guanine and uracil),<ref>{{cite book | title=Clinical gene analysis and manipulation: Tools, techniques and troubleshooting | author=Jankowski JAZ, Polak JM| date=1996| pages=14| publisher=Cambridge University Press| isbn=0521478960 | oclc=33838261}}</ref> but there are numerous modified bases and sugars in mature RNAs. [[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]]).<ref>{{cite journal | author=Yu Q, Morrow CD| title=Identification of critical elements in the tRNA acceptor stem and TΨC loop necessary for human immunodeficiency virus type 1 infectivity| journal=J Virol.| year=2001| volume=75| issue=10| pages=4902–6| doi=10.1128/JVI.75.10.4902-4906.2001 | pmid = 11312362 }}</ref> 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]].<ref>{{cite journal | author=Elliott MS, Trewyn RW| title=Inosine biosynthesis in transfer RNA by an enzymatic insertion of hypoxanthine| journal=J. Biol. Chem.| year=1983| volume=259| issue=4| pages=2407–10| pmid=6365911}}</ref> There are nearly 100 other naturally occurring modified nucleosides,<ref>{{cite book | title=TRNA: Structure, biosynthesis, and function | author=Söll D, RajBhandary U| date=1995| pages=165| publisher=ASM Press| isbn=155581073X | oclc=183036381 30663724}}</ref> of which pseudouridine and nucleosides with [[2'-O-methylation|2'-O-methylribose]] are the most common.<ref>{{cite journal | author=Kiss T| title=Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs| journal=The EMBO Journal | year=2001| volume=20| pages=3617–22| doi=10.1093/emboj/20.14.3617 | pmid = 11447102 }}</ref> 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 and the subunit interface, implying that they are important for normal function.<ref>{{cite journal | author=King TH, Liu B, McCully RR, Fournier MJ| title=Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center | journal=Molecular Cell| year=2002| volume=11| issue=2| pages=425–35| doi=10.1016/S1097-2765(03)00040-6 | pmid = 12620230}}</ref>
   
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The functional form of single stranded RNA molecules, just like proteins, frequently requires a specific [[RNA Tertiary Structure|tertiary structure]]. The scaffold for this structure is provided by [[secondary structure|secondary structural]] elements which are hydrogen bonds within the molecule. This leads to several recognizable "domains" of secondary structure like [[hairpin loop]]s, bulges and internal loops.<ref>{{cite journal | author=Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH| title=Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure| journal=Proc. Natl. Acad. Sci. USA| year=2004| volume=101| issue=19| pages=7287–92| doi=10.1073/pnas.0401799101 | pmid = 15123812}}</ref> Since RNA is charged, metal ions such as [[Magnesium|Mg<sup>2+</sup>]] are needed to stabilise many secondary and [[RNA Tertiary Structure|tertiary structures]].<ref>{{cite journal |author=Tan ZJ, Chen SJ |title=Salt dependence of nucleic acid hairpin stability |journal=Biophys. J. |volume=95 |pages=738–52 |year=2008 |pmid=18424500 |doi=10.1529/biophysj.108.131524 |issue=2}}</ref>
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Single stranded RNA exhibits a right handed stacking pattern that is stabilized by base [[Stacking (chemistry)|stacking]].
  
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The most important structural feature of RNA, indeed the only consistent difference between the two nucleic acids, 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. This result 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.
  
   
 
==Comparison with DNA==
  
==Comparison with DNA==
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Unlike DNA, RNA is a single-stranded molecule in most of its biological roles and has a much shorter chain of nucleotides. RNA contains ribose, rather than the deoxyribose found in DNA (there is no hydroxyl group attached to the pentose ring in the [[nucleic acid nomenclature|2']] position whereas RNA has two hydroxyl groups). These hydroxyl groups make RNA less stable than DNA because it is more prone to [[hydrolysis]]. Several types of RNA (tRNA, rRNA) contain a great deal of secondary structure, which help promote stability.
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RNA and [[DNA]] are both [[nucleic acid]]s, but 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. Second, while DNA contains ''[[deoxyribose]]'', RNA contains ''[[ribose]]'' (there is no hydroxyl group attached to the pentose ring in the [[nucleic acid nomenclature|2']] position in DNA). These hydroxyl groups make RNA less stable than DNA because it is more prone to [[hydrolysis]]. Third, the complementary base to [[adenine]] is not [[thymine]], as it is in DNA, but rather [[uracil]], which is an [[methylation|unmethylated]] form of thymine.<ref name=Biochemistry/>
   
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[[Image:Ribosome 50s.png|thumb|right|The [[50S]] ribosomal subunit. RNA is in orange, protein in blue. The active site is in the middle (red).]]
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Like DNA, most biologically active RNAs including tRNA, rRNA, snRNAs and other non-coding RNAs (such as the SRP RNAs) are extensively base paired to form double stranded helices. Structural analysis of these RNAs have revealed that they are not, "single-stranded" but rather highly structured. Unlike DNA, this structure is not just limited to 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. For instance, determination of the structure of the ribosome in 2000 revealed that the active site of this enzyme that catalyzes peptide bond formation is composed entirely of RNA.
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Like DNA, most biologically active RNAs, including [[mRNA]], [[tRNA]], [[rRNA]], [[snRNA]]s and other [[non-coding RNA]]s, contain self-complementary sequences that allow parts of the RNA to fold and pair with itself to form double helices. Structural analysis of these RNAs have 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.
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In this fashion, RNAs can achieve chemical [[catalysis]], like enzymes.<ref>{{cite journal | author=Higgs PG| title=RNA secondary structure: physical and computational aspects| journal=Quarterly Reviews of Biophysics| year=2000| volume=33| pages=199–253| doi=10.1017/S0033583500003620 | pmid = 11191843 }}</ref> For instance, determination of the structure of the ribosome&mdash;an enzyme that catalyzes peptide bond formation&mdash;revealed that its active site is composed entirely of RNA.<ref name=ribosome_activity>{{cite journal | author=Nissen P, Hansen J, Ban N, Moore PB, Steitz TA | title=The structural basis of ribosome activity in peptide bond synthesis | journal=Science| year=2000| volume=289| issue=5481| pages=920–30| doi=10.1126/science.289.5481.920 | pmid = 10937990}}</ref>
   
 
==Synthesis==
  
==Synthesis==
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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.
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Synthesis of RNA is usually catalyzed by an enzyme&mdash;[[RNA polymerase]]&mdash;using DNA as a template, a process known as [[Transcription (genetics)|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.<ref>{{cite journal | author=Nudler E, Gottesman ME| title=Transcription termination and anti-termination in E. coli | journal=Genes to Cells| year=2002| volume=7| pages=755–68| doi=10.1046/j.1365-2443.2002.00563.x | pmid = 12167155 }}</ref>
   
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RNAs are often [[Post-transcriptional modification|modified]] by enzymes after transcription. For example, a [[poly(A) tail]] and a [[5' cap]] are added to eukaryotic [[pre-mRNA]] and [[intron]]s are removed by the [[spliceosome]].
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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. Also, it is known that RNA-dependent RNA polymerases are required for the RNA interference pathway in many organisms.
  
   
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There are also a number of [[RNA-dependent RNA polymerase]]s 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.<ref>{{cite journal | author=Jeffrey L Hansen, Alexander M Long, Steve C Schultz| title=Structure of the RNA-dependent RNA polymerase of poliovirus | journal=Structure| year=1997| volume=5| issue=8| pages=1109–22 | doi=10.1016/S0969-2126(97)00261-X | pmid = 9309225 }}</ref> Also, RNA-dependent RNA polymerase is part of the [[RNA interference]] pathway in many organisms.<ref>{{cite journal | author=Ahlquist P| title=RNA-Dependent RNA Polymerases, Viruses, and RNA Silencing | journal=Science| year=2002| volume=296| issue=5571| pages=1270–73| doi=10.1126/science.1069132 | pmid = 12016304 }}</ref>
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==Biological roles==
  
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===Messenger RNA (mRNA)===
  
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{{main|Messenger RNA}}
  
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Messenger RNA is RNA that carries information from [[DNA]] to the [[ribosome]] sites of protein synthesis in the cell. Once mRNA has been transcribed from DNA, it is exported from the nucleus into the cytoplasm (in [[eukaryote]]s mRNA is "processed" before being exported), where it is bound to [[ribosome]]s and translated into its corresponding protein form with the help of [[tRNA]]. After a certain amount of time the message degrades into its component nucleotides, usually with the assistance of [[RNA polymerase]]s.
  
   
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===Transfer RNA (tRNA)===
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==Types of RNA==
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{{main|Transfer RNA}}
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{{seealso|List of RNAs}}
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===Overview===
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[[Image:Full length hammerhead ribozyme.png|thumb|upright|Structure of a [[hammerhead ribozyme]], a ribozyme that cuts RNA]]
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Messenger RNA (mRNA) is the RNA that carries information from DNA to the [[ribosome]], the sites of protein synthesis ([[Translation (biology)|translation]]) in the cell. The coding sequence of the mRNA determines the [[amino acid]] sequence in the [[protein]] that is produced.<ref name=The_Cell/> Many RNAs do not code for protein however (about 97% of the transcriptial output is non-protein-coding in eukaryotes <ref>{{cite journal |author=Mattick JS, Gagen MJ |title=The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms |journal=Mol. Biol. Evol. |volume=18 |issue=9 |pages=1611–30 |date=1 September 2001|pmid=11504843 |url=http://mbe.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=11504843 }}</ref><ref>Mattick, J.S. (2001). “Noncoding RNAs: the architects of eukaryotic complexity”. ''EMBO Reports'', '''2'''(11), 986-991. [http://emboreports.npgjournals.com/cgi/content/full/2/11/986]</ref><ref>Mattick, J.S. (2003). “Challenging the dogma: The hidden layer of non-protein-coding RNAs on complex organisms” ''Bioessays''. '''25''', 930-939. [http://www.imb-jena.de/jcb/journal_club/mattick2003.pdf]</ref><ref>Mattick, J.S. (2004). “The hidden genetic program of complex organisms” ''Scientific American''. '''291'''(4), 30-37. [http://www.sciam.com/article.cfm?articleID=00045BB6-5D49-1150-902F83414B7F4945]</ref>).
   
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These so-called [[non-coding RNA]]s ("ncRNA") can be encoded by their own genes (RNA genes), but can also derive from mRNA [[intron]]s.<ref name=transcriptome/> 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.<ref name=Biochemistry>{{cite book |author=Berg JM, Tymoczko JL, Stryer L |title= Biochemistry | edition=5th |pages =118–19, 781–808 | publisher= WH Freeman and Company |year=2002 |isbn= 0-7167-4684-0 |oclc=179705944 48055706 59502128}}</ref> There are also non-coding RNAs involved in gene regulation, [[RNA processing]] and other roles.
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Transfer RNA is a small RNA chain of about 74-95 [[nucleotide]]s that transfers a specific [[amino acid]] to a growing [[polypeptide]] chain at the [[ribosome|ribosomal]] site of protein synthesis during [[translation (biology)|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. It is a type of [[non-coding RNA]].
  
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Certain RNAs are able to [[catalysis|catalyse]] chemical reactions such as cutting and [[ligase|ligating]] other RNA molecules,<ref>{{cite journal | author=Rossi JJ| title=Ribozyme diagnostics comes of age | journal=Chemistry & Biology| year=2004| volume=11| issue=7| pages=894–95 | doi=10.1016/j.chembiol.2004.07.002 | pmid=15271347 | last1=Rossi | first1=JJ}}</ref> and the catalysis of [[peptide bond]] formation in the [[ribosome]];<ref name=ribosome_activity/> these are known as [[ribozyme]]s.
   
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===Ribosomal RNA (rRNA)===
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===In translation===
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[[Messenger RNA]] (mRNA) carries information about a protein sequence to the [[ribosome]]s, the protein synthesis factories in the cell. It is [[genetic code|coded]] so that every three nucleotides (a codon) correspond 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 [[intron]]s&mdash;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 [[Translation (biology)|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 [[ribonuclease]]s.<ref name=The_Cell/>
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{{main|Ribosomal RNA}}
  
   
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[[Transfer RNA]] (tRNA) is a small RNA chain of about 80 [[nucleotide]]s 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.<ref name=transcriptome/>
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'''Ribosomal RNA''' is a component of the [[ribosomes]], the protein synthetic 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. rRNA molecules are extremely abundant and make up at least 80% of the RNA molecules found in a typical [[eukaryotic]] cell.
  
   
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[[Ribosomal RNA]] (rRNA) is the catalytic component of the ribosomes. 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.<ref name=The_Cell>{{cite book | title=The Cell: A Molecular Approach| edition=3rd| author=Cooper GC, Hausman RE| date=2004| pages=261–76, 297, 339–44| publisher=Sinauer| isbn=0-87893-214-3 | oclc=174924833 52121379 52359301 56050609}}</ref> rRNA is extremely abundant and makes up 80% of the 10&nbsp;mg/ml RNA found in a typical eukaryotic [[cytoplasm]].<ref>{{cite journal | author=Kampers T, Friedhoff P, Biernat J, Mandelkow E-M, Mandelkow E| title=RNA stimulates aggregation of microtubule-associated protein tau into Alzheimer-like paired helical filaments| journal=FEBS Letters| year=1996| volume=399 | pages = 104D| pmid=8985176 | doi = 10.1016/S0014-5793(96)01386-5 | issue=3}}</ref>
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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.
  
   
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[[tmRNA|Transfer-messenger RNA]] (tmRNA) is found in many [[bacteria]] and [[plastid]]s. It tags proteins encoded by mRNAs that lack stop codons for degradation and prevents the ribosome from stalling.<ref>{{cite journal |author=Gueneau de Novoa P, Williams KP |title=The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts |journal=Nucleic Acids Res. |volume=32 |issue=Database issue |pages=D104–8 |year=2004 |pmid=14681369 |doi=10.1093/nar/gkh102}}</ref>
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===Non-coding RNA or "RNA genes"===
  
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{{main|Non-coding RNA}}
  
   
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===Regulatory RNAs===
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RNA genes (sometimes referred to as non-coding RNA or small RNA) are genes that encode RNA that is not [[translation (biology)|translated]] into a protein. 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. However, since the late [[1990s]], many new RNA genes have been found, and thus RNA genes may play a much more significant role than previously thought.
  
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Several types of RNA can downregulate gene expression by being complementary to a part of an mRNA or a gene's DNA.
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[[MicroRNA]]s (miRNA; 21-22&nbsp;[[nucleotide|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 accelerate its degradation.<ref>{{cite journal |author=Wu L, Belasco JG |title=Let me count the ways: mechanisms of gene regulation by miRNAs and siRNAs |journal=Mol. Cell |volume=29 |issue=1 |pages=1–7 |year=2008 |month=January |pmid=18206964 |doi=10.1016/j.molcel.2007.12.010}}</ref><ref>{{cite journal | author=Matzke MA, Matzke AJM | title=Planting the seeds of a new paradigm| journal=PLoS Biology | year=2004| volume=2| issue=5| doi=10.1371/journal.pbio.0020133 | pages = e133 | pmid = 15138502 }}</ref> While [[small interfering RNA]]s (siRNA; 20-25&nbsp;nt) are often produced by breakdown of viral RNA, there are also endogenous sources of siRNAs.<ref>{{cite journal | author=Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC, Hilbert J, Bartel DP, Crété P| title=Endogenous ''trans''-acting siRNAs regulate the accumulation of ''Arabidopsis'' mRNAs | journal=Molecular Cell| year=2004| volume=16| issue=1| pages= 69–79| doi=10.1016/j.molcel.2004.09.028 | pmid = 15469823}}</ref><ref>{{cite journal |author=Watanabe T, Totoki Y, Toyoda A, ''et al.'' |title=Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes |journal=Nature |volume=453 |issue=7194 |pages=539–43 |year=2008 |month=May |pmid=18404146 |doi=10.1038/nature06908 |last12=Sakaki |first12=Y |last13=Sasaki |first13=H}}</ref> siRNAs act through RNA interference in a fashion similar to miRNAs. Some miRNAs and siRNAs can cause genes they target to be [[DNA methylation|methylated]], thereby [[RNA-induced transcriptional silencing|decreasing]] or [[RNAa|increasing]] transcription of those genes.<ref>{{cite journal |author=Sontheimer EJ, Carthew RW |title=Silence from within: endogenous siRNAs and miRNAs |journal=Cell |volume=122 |issue=1 |pages=9–12 |year=2005 |month=July |pmid=16009127 |doi=10.1016/j.cell.2005.06.030}}</ref><ref>{{cite journal | author=Doran G| title=RNAi – Is one suffix sufficient? | journal=Journal of RNAi and Gene Silencing | year=2007| volume=3| issue=1| pages=217–19 | url=http://libpubmedia.co.uk/RNAiJ-Issues/Issue-5/Doran.htm}}</ref><ref>{{cite journal |author=Pushparaj PN, Aarthi JJ, Kumar SD, Manikandan J |title=RNAi and RNAa - The Yin and Yang of RNAome |journal=Bioinformation |volume=2 |issue=6 |pages=235–7 |year=2008 |pmid=18317570 |pmc=2258431}}</ref> Animals have [[Piwi-interacting RNA]]s (piRNA; 29-30&nbsp;nt) which are active in [[germline]] cells and are thought to be a defense against [[transposon]]s and play a role in [[gametogenesis]].<ref name=fruitfly_piRNA>{{cite journal | author=Horwich MD, Li C Matranga C, Vagin V, Farley G, Wang P, Zamore PD| title=The ''Drosophila'' RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC| journal=Current Biology| year=2007| volume=17| pages=1265–72| doi=10.1016/j.cub.2007.06.030 | pmid = 17604629 }}</ref><ref>{{cite journal | author=Girard A, Sachidanandam R, Hannon GJ, Carmell MA| title=A germline-specific class of small RNAs binds mammalian Piwi proteins| journal=Nature| year=2006| volume=442| pages=199–202| doi=10.1038/nature04917 | pmid = 16751776}}</ref> All prokaryotes have [[CRISPR]] RNAs, a regulatory system analogous to RNA interference.<ref>{{cite journal |author=Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV |title=A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action |journal=Biol. Direct |volume=1 |pages=7 |year=2006 |pmid=16545108 |doi=10.1186/1745-6150-1-7 |url=http://www.biology-direct.com/content/1/1/7}}</ref> [[Antisense RNA]]s are widespread; most downregulate a gene, but a few are activators of transcription.<ref>{{cite journal | author=Wagner EG, Altuvia S, Romby P| title=Antisense RNAs in bacteria and their genetic elements| journal=Adv Genet.| year=2002| volume=46| pages=361–98| pmid=11931231| doi=10.1016/S0065-2660(02)46013-0}}</ref> One way antisense RNA can act is by binding to an mRNA, forming double-stranded RNA that is enzymatically degraded.<ref>{{cite book | author=Gilbert SF |title=Developmental Biology | edition=7th |publisher=Sinauer | isbn=0878932585 | pages=101–3 | year=2003 | oclc=154656422 154663147 174530692 177000492 177316159 51544170 54743254 59197768 61404850 66754122}}</ref> There are many [[long noncoding RNA]]s that regulate genes in eukaryotes,<ref>{{cite journal |author=Amaral PP, Mattick JS |title=Noncoding RNA in development |journal=Mammalian genome : official journal of the International Mammalian Genome Society |volume= 19|issue= 7-8|pages= 454|year=2008 |month=October |pmid=18839252 |doi=10.1007/s00335-008-9136-7 |url=}}</ref> one such RNA is [[Xist]] which coats one X chromosome in female mammals and [[X-inactivation|inactivates]] it.<ref>{{cite journal | author=Heard E, Mongelard F, Arnaud D, Chureau C, Vourc'h C, Avner P| title=Human ''XIST'' yeast artificial chromosome transgenes show partial X inactivation center function in mouse embryonic stem cells | journal=Proc. Natl. Acad. Sci. USA| year=1999| volume=96| issue=12| pages=6841–46| pmid=10359800 | doi = 10.1073/pnas.96.12.6841}}</ref>
   
  +
An mRNA may contain regulatory elements itself, such as [[riboswitch]]es, in the [[Five prime untranslated region|5' untranslated region]] or [[Three prime untranslated region|3' untranslated region]]; these [[cis-regulatory element]]s regulate the activity of that mRNA.<ref>{{cite journal |author=Batey RT |title=Structures of regulatory elements in mRNAs |journal=Curr. Opin. Struct. Biol. |volume=16 |issue=3 |pages=299–306 |year=2006 |pmid=16707260 |doi=10.1016/j.sbi.2006.05.001}}</ref> The untranslated regions can also contain elements that regulate other genes.<ref>{{cite journal |author=Scotto L, Assoian RK |title=A GC-rich domain with bifunctional effects on mRNA and protein levels: implications for control of transforming growth factor beta 1 expression |journal=Mol. Cell. Biol. |volume=13 |issue=6 |pages=3588–97 |year=1993 |month=June |pmid=8497272 |pmc=359828 |doi= |url=http://mcb.asm.org/cgi/pmidlookup?view=long&pmid=8497272}}</ref>
−
In the late 1990s and early 2000, there has been persistent evidence of more complex transcription occurring in [[mammal]]ian cells (and possibly others). This could point towards a more widespread use of RNA in biology, particularly in [[gene regulation]]. A particular class of non-coding RNA, [[micro RNA]], has been found in many metazoans (from ''[[Caenorhabditis elegans]]'' to ''[[Homo sapiens]]'') and clearly plays an important role in regulating other genes.
  
   
  +
===In RNA processing===
−
First proposed in 2004 by Rassoulzadegan and published in Nature 2006,<ref>Rassoulzadegan M., et al. Nature, doi:10.1038/nature04674 , 2006</ref> RNA is implicated as being part of the [[germline]]. If confirmed, this result would significantly alter the present understanding of genetics and lead to many question on DNA-RNA roles and interactions.
  
  +
[[Image:Uridine to pseudouridine.GIF|thumb|Uridine to pseudouridine is a common RNA modification.]]
  +
Many RNAs are involved in modifying other RNAs.
  +
[[Intron]]s are [[Splicing (genetics)|spliced]] out of [[pre-mRNA]] by [[spliceosome]]s, which contain several [[small nuclear RNA]]s (snRNA),<ref name=Biochemistry/> or the introns can be ribozymes that are spliced by themselves.<ref>{{cite journal |author=Steitz TA, Steitz JA |title=A general two-metal-ion mechanism for catalytic RNA |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=90 |issue=14 |pages=6498–502 |year=1993 |pmid=8341661 | doi = 10.1073/pnas.90.14.6498}}</ref>
  +
RNA can also be altered by having its nucleotides modified to other nucleotides than [[adenosine|A]], [[cytidine|C]], [[guanosine|G]] and [[uridine|U]].
  +
In eukaryotes, modifications of RNA nucleotides are generally directed by [[small nucleolar RNA]]s (snoRNA; 60-300&nbsp;nt),<ref name=transcriptome>{{cite book | title=Mining the transcriptome – methods and applications| url=http://www.diva-portal.org/diva/getDocument?urn_nbn_se_kth_diva-4115-3__fulltext.pdf| author=Wirta W| date=2006| isbn=91-7178-436-5 | publisher=School of Biotechnology, Royal Institute of Technology | location=Stockholm | oclc=185406288}}</ref> found in the [[nucleolus]] and [[Cajal body|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.<ref>{{cite journal |author=Xie J, Zhang M, Zhou T, Hua X, Tang L, Wu W |title=Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs |journal=Nucleic Acids Res. |volume=35 |pages=D183–7 |year=2007 |pmid=17099227 |doi=10.1093/nar/gkl873 |issue=Database issue}}</ref><ref>{{cite journal | author=Omer AD, Ziesche S, Decatur WA, Fournier MJ, Dennis PP| title=RNA-modifying machines in archaea| journal=Molecular Microbiology| year=2003| volume=48| issue=3| pages=617–29| doi=10.1046/j.1365-2958.2003.03483.x | pmid = 12694609}}</ref>
   
−
===Catalytic RNA===
 +
=== RNA genomes ===
  +
Like DNA, RNA can carry genetic information. [[RNA virus]]es have [[genome]]s composed of RNA, and a variety of proteins encoded by that genome. 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. [[Viroid]]s 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.<ref>{{cite journal |author=Daròs JA, Elena SF, Flores R |title=Viroids: an Ariadne's thread into the RNA labyrinth |journal=EMBO Rep. |volume=7 |issue=6 |pages=593–8 |year=2006 |pmid=16741503 |doi=10.1038/sj.embor.7400706}}</ref>
−
{{main|Ribozyme}}
  
   
  +
=== In reverse transcription===
−
Although RNA contains only four bases, in comparison to the twenty amino acids commonly found in proteins, some RNAs are still able to catalyse chemical reactions. These include cutting and [[ligase|ligating]] other RNA molecules and also the catalysis of [[peptide bond]] formation in the [[ribosome]].
  
  +
[[Reverse transcribing virus]]es replicate their genomes by [[Reverse transcription|reverse transcribing]] DNA copies from their RNA; these DNA copies are then transcribed to new RNA. [[Retrotransposon]]s also spread by copying DNA and RNA from one another,<ref>{{cite journal |author=Kalendar R, Vicient CM, Peleg O, Anamthawat-Jonsson K, Bolshoy A, Schulman AH |title=Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes |journal=Genetics |volume=166 |issue=3 | pages = D339 |year=2004 |pmid=15082561 | doi = 10.1534/genetics.166.3.1437}}</ref> and [[telomerase]] contains an RNA that is used as template for building the ends of eukaryotic chromosomes.<ref>{{cite journal |author=Podlevsky JD, Bley CJ, Omana RV, Qi X, Chen JJ |title=The telomerase database |journal=Nucleic Acids Res. |volume=36 |issue=Database issue |pages=D339–43 |year=2008 |pmid=18073191 |doi=10.1093/nar/gkm700}}</ref>
   
 
===Double-stranded RNA===
  
===Double-stranded RNA===
−
Double-stranded RNA (or dsRNA) is RNA with two complementary strands, similar to the DNA found in all "higher" cells. dsRNA forms the genetic material of some [[virus]]es. In eukaryotes, it acts as a trigger to initiate the process of [[RNA interference]] and is present as an intermediate step in the formation of [[siRNA]]s (small interfering RNAs). [[siRNA]]s are often confused with [[miRNA]]s; [[siRNA]]s are double-stranded, whereas [[miRNA]]s are single-stranded. Although initially single stranded there are regions of intra-molecular association causing hairpin structures in pre-miRNAs; immature miRNAs. Very recently, dsRNA has been found to induce gene expression at transcriptional level, a phenomenon named "small RNA induced gene activation [[RNAa]]". Such dsRNA is called "small activating RNA (saRNA)".
  
   
  +
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 [[virus]]es ([[double-stranded RNA viruses]]). Double-stranded RNA such as viral RNA or [[siRNA]] can trigger [[RNA interference]] in [[eukaryote]]s, as well as [[interferon]] response in [[vertebrate]]s.<ref>{{cite journal | title=Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing| author=Blevins T ''et al.''| journal=Nucleic Acids Res| year=2006| volume=34| issue=21| pages=6233–46| pmid=17090584 | doi = 10.1093/nar/gkl886}}</ref><ref>{{cite journal |author=Jana S, Chakraborty C, Nandi S, Deb JK |title=RNA interference: potential therapeutic targets |journal=Appl. Microbiol. Biotechnol. |volume=65 |issue=6 |pages=649–57 |year=2004 |pmid=15372214 |doi=10.1007/s00253-004-1732-1}}</ref><ref>{{cite journal |author=Schultz U, Kaspers B, Staeheli P |title=The interferon system of non-mammalian vertebrates |journal=Dev. Comp. Immunol. |volume=28 |issue=5 |pages=499–508 |year=2004 |pmid=15062646 |doi=10.1016/j.dci.2003.09.009}}</ref>
   
  +
==Discovery==
−
==RNA secondary structures==
  
  +
[[Nucleic acid]]s were discovered in 1868 by [[Friedrich Miescher]], who called the material 'nuclein' since it was found in the [[Cell nucleus|nucleus]].<ref>{{cite journal | author=Dahm R| title=Friedrich Miescher and the discovery of DNA | journal=Developmental Biology | year=2005| volume=278| issue=2| pages=274–88 | pmid=15680349 | doi = 10.1016/j.ydbio.2004.11.028}}</ref> 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.<ref>{{cite journal | journal=Nature | author=Caspersson T, Schultz J | title=Pentose nucleotides in the cytoplasm of growing tissues | year=1939 | volume=143 | doi=10.1038/143602c0 | pages=602–3}}</ref> [[Severo Ochoa]] won the 1959 [[Nobel Prize in Medicine]] after he discovered how RNA is synthesized.<ref>{{cite web | author=Ochoa S| title=Enzymatic synthesis of ribonucleic acid| work=Nobel Lecture |year=1959| url=http://nobelprize.org/nobel_prizes/medicine/laureates/1959/ochoa-lecture.pdf}}</ref> The sequence of the 77 nucleotides of a yeast tRNA was found by [[Robert W. Holley]] in 1965,<ref>{{cite journal | author=Holley RW ''et al.''| title=Structure of a ribonucleic acid | journal=Science| year=1965| volume=147| issue=1664| pages=1462–65| doi=10.1126/science.147.3664.1462 | pmid = 14263761 }}</ref> winning Holley the 1968 Nobel Prize in Medicine.
−
The functional form of single stranded RNA molecules (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. The secondary structure of RNA molecules can be predicted computationally by calculating the minimum free energies (MFE) structure for all different combinations of hydrogen bondings and domains. There has been a significant amount of research directed at the [[RNA structure]] prediction problem.
  
  +
In 1967, [[Carl Woese]] realized RNA can be catalytic and proposed that the earliest forms of life relied on RNA both to carry genetic information and to catalyze biochemical reactions&mdash;an [[RNA world hypothesis|RNA world]].<ref>{{cite web | title=Common sequence structure properties and stable regions in RNA secondary structures| author=Siebert S| year=2006| pages=1| url=http://deposit.ddb.de/cgi-bin/dokserv?idn=982323891&dok_var=d1&dok_ext=pdf&filename=982323891.pdf| work=Dissertation, Albert-Ludwigs-Universität, Freiburg im Breisgau}}</ref><ref>{{cite journal | title=The origin of the genetic code: amino acids as cofactors in an RNA world| author=Szathmáry E| journal=Trends Genet.| year=1999| volume=15| issue=6| pages=223–9| doi=10.1016/S0168-9525(99)01730-8 | pmid = 10354582 }}</ref>
−  
  +
In 1976, [[Walter Fiers]] and his team determined the first complete nucleotide sequence of an RNA virus genome, that of [[bacteriophage MS2]].<ref>{{cite journal | author=Fiers W ''et al.''| title=Complete nucleotide-sequence of bacteriophage MS2-RNA: primary and secondary structure of replicase gene| journal=Nature| year=1976| volume=260| pages=500–7| pmid=1264203 | doi = 10.1038/260500a0 | last12=Ysebaert | first12=M | issue=5551}}</ref>
−
Online tools for MFE structure prediction from single sequences are provided by [http://www.bioinfo.rpi.edu/applications/mfold/ MFOLD] and [http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi RNAfold].
  
  +
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]].<ref>{{cite journal | author=Napoli C, Lemieux C, Jorgensen R| title=Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans| journal=Plant Cell| year=1990| volume=2| issue=4| pages=279–89| pmid=12354959 | doi = 10.1105/tpc.2.4.279}}</ref><ref>{{cite journal |author=Dafny-Yelin M, Chung SM, Frankman EL, Tzfira T |title=pSAT RNA interference vectors: a modular series for multiple gene down-regulation in plants |journal=Plant Physiol. |volume=145 |issue=4 |pages=1272–81 |year=2007 |month=December |pmid=17766396 |pmc=2151715 |doi=10.1104/pp.107.106062}}</ref> At about the same time, 22 nt long RNAs, now called [[microRNA]]s, were found to have a role in the [[developmental biology|development]] of ''[[Caenorhabditis elegans|C. elegans]]''.<ref>{{cite journal | author=Ruvkun G| title=Glimpses of a tiny RNA world| journal=Science| year=2001| volume=294| issue=5543| pages=797–99| doi=10.1126/science.1066315 | pmid = 11679654}}</ref>
−  
  +
The discovery of gene regulatory RNAs has led to attempts to develop drugs made of RNA, such as [[siRNA]], to silence genes.<ref>{{cite journal | author=Fichou Y, Férec C| title=The potential of oligonucleotides for therapeutic applications| journal=Trends in Biotechnology| year=2006| volume=24| issue=12| pages=563–70| doi=10.1016/j.tibtech.2006.10.003 | pmid = 17045686}}</ref>
−
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 [http://knetfold.abcc.ncifcrf.gov KNetFold], [http://rna.tbi.univie.ac.at/cgi-bin/alifold.cgi RNAalifold] and [http://www.daimi.au.dk/~compbio/rnafold/ Pfold].
  
−  
−
A package of RNA structure prediction programs is also available for Windows: [http://rna.urmc.rochester.edu/rnastructure.html RNAstructure].
  
−  
−
A database of RNA sequences and secondary structures is available from [http://www.sanger.ac.uk/Software/Rfam/index.shtml Rfam], analyses and links to RNA analysis tools are available from [http://wikiomics.org/wiki/List_of_articles#RNA Wikiomics].
  
   
 
== See also==
  
== See also==
  +
{{MolBioGeneExp}}
⚫
* [[Antisense mRNA]]
  
  +
{{col-begin}}{{col-break}}
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* [[Dot plot (bioinformatics)]]
  
 
* [[Genetics]]
  
* [[Genetics]]
 
* [[Molecular biology]]
  
* [[Molecular biology]]
  +
* [[Oligonucleotide synthesis]]
⚫
* [[RNAi]]
  
  ⚫
* [[Quantification of nucleic acids]]
−
* [[RNAa]]
  
−
* [[RNA interference]]
  
 
* [[RNA Ontology Consortium]]
  
* [[RNA Ontology Consortium]]
−
* [[Severo Ochoa]]
  
 
* [[Sequence profiling tool]]
  
* [[Sequence profiling tool]]
−
* [[Phosphoramidite]]
 +
* [[RNA extraction]]
  +
* [[RNA structure|RNA structure prediction]]
⚫
* [[Quantification of nucleic acids]]
  
  +
{{col-break}}
−  
  ⚫
* [[Antisense RNA]]
  +
* [[Long noncoding RNA]]
  ⚫
* [[MicroRNA]]
  +
* [[SiRNA|small interfering RNA (siRNA)]]
  +
* [[Small nucleolar RNA| Small nucleolar RNA (snoRNA)]]
  +
* [[Piwi-interacting RNA|(piRNA)]]
  +
{{col-break}}
  ⚫
* [[Guide RNA]]
  +
* [[Small nuclear RNA]]
  +
* [[Transfer RNA]]
  ⚫
* [[Ribosomal RNA]]
  +
* [[Riboswitch]]
  +
* [[RNA Tertiary Structure]]
  +
{{col-end}}
   
 
==References==
  
==References==
  +
{{Reflist|2}}
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<references/>
  
−  
   
 
==External links==
  
==External links==
  ⚫
{{Commonscat|RNA}}
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* [http://miracle.igib.res.in/ RNA@IGIB]group at the Institute of Genomics and Integrative Biology working on RNA biology
  
−
* [http://www.imb-jena.de/RNA.html] RNA World website
 +
* [http://www.imb-jena.de/RNA.html RNA World website] Link collection (structures, sequences, tools, journals)
−
* [http://ndbserver.rutgers.edu/atlas/xray/index.html] Images of DNA, RNA (eg tRNA) and complexes.
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* [http://ndbserver.rutgers.edu/atlas/xray/ Nucleic Acid Database] Images of DNA, RNA and complexes.
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{{Genetics|state=uncollapsed}}
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Latest revision as of 08:00, 31 December 2009

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File:Pre-mRNA-1ysv.png-tubes.png

A hairpin loop from a pre-mRNA. Highlighted are the bases (light green) and backbone (sky blue).

Ribonucleic acid (RNA) is a biologically important type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. 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 has the base uracil rather than thymine that is present in DNA.

RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other enzymes. RNA is central to protein synthesis. Here, a type of RNA called messenger RNA carries information from DNA to structures called ribosomes. These ribosomes are made from proteins and ribosomal RNAs, which come together to form a molecular machine that can read messenger RNAs and translate the information they carry into proteins. There are many RNAs with other roles – in particular regulating which genes are expressed, but also as the genomes of most viruses.

Structure

File:Piwi-siRNA-basepairing.png

Watson-Crick base pairs in a siRNA (hydrogen atoms are not shown)

Each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, generally adenine (A), cytosine (C), guanine (G) or uracil (U). Adenine and guanine are purines, 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 at physiological pH, making RNA a charged molecule (polyanion). The bases may 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]

File:RNA chemical structure.GIF

Chemical structure of RNA

An 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 causes the helix to adopt the A-form geometry rather than the B-form most commonly observed in DNA.[3] This results in a very deep and narrow major groove and a shallow and wide minor groove.[4] 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.[5]

File:Ciliate telomerase RNA.JPG

Secondary structure of a telomerase RNA.

RNA is transcribed with only four bases (adenine, cytosine, guanine and uracil),[6] but there are numerous modified bases and sugars in mature RNAs. 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).[7] 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.[8] There are nearly 100 other naturally occurring modified nucleosides,[9] of which pseudouridine and nucleosides with 2'-O-methylribose are the most common.[10] 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 and the subunit interface, implying that they are important for normal function.[11]

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.[12] Since RNA is charged, metal ions such as Mg2+ are needed to stabilise many secondary and tertiary structures.[13]

Comparison with DNA

RNA and DNA are both nucleic acids, but 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. Second, while DNA contains deoxyribose, RNA contains ribose (there is no hydroxyl group attached to the pentose ring in the 2' position in DNA). These hydroxyl groups make RNA less stable than DNA because it is more prone to hydrolysis. Third, the complementary base to adenine is not thymine, as it is in DNA, but rather uracil, which is an unmethylated form of thymine.[14]

Ribosome 50s

The 50S ribosomal subunit. RNA is in orange, protein in blue. The active site is in the middle (red).

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. Structural analysis of these RNAs have 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.[15] 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.[16]

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.[17]

RNAs are often modified by enzymes after transcription. For example, a poly(A) tail and a 5' cap are added to eukaryotic pre-mRNA and introns are removed by the spliceosome.

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.[18] Also, RNA-dependent RNA polymerase is part of the RNA interference pathway in many organisms.[19]

Types of RNA

See also: List of RNAs

Overview

File:Full length hammerhead ribozyme.png

Structure of a hammerhead ribozyme, a ribozyme that cuts RNA

Messenger RNA (mRNA) is the RNA that carries information from DNA to the ribosome, the sites of protein synthesis (translation) in the cell. The coding sequence of the mRNA determines the amino acid sequence in the protein that is produced.[20] Many RNAs do not code for protein however (about 97% of the transcriptial output is non-protein-coding in eukaryotes [21][22][23][24]).

These so-called non-coding RNAs ("ncRNA") can be encoded by their own genes (RNA genes), but can also derive from mRNA introns.[25] 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.[14] 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,[26] and the catalysis of peptide bond formation in the ribosome;[16] these are known as ribozymes.

In translation

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) correspond 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.[20]

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.[25]

Ribosomal RNA (rRNA) is the catalytic component of the ribosomes. 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.[20] rRNA is extremely abundant and makes up 80% of the 10 mg/ml RNA found in a typical eukaryotic cytoplasm.[27]

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.[28]

Regulatory RNAs

Several types of RNA can downregulate gene expression by being complementary to a part of an mRNA or a gene's DNA. 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 accelerate its degradation.[29][30] While small interfering RNAs (siRNA; 20-25 nt) are often produced by breakdown of viral RNA, there are also endogenous sources of siRNAs.[31][32] siRNAs act through RNA interference in a fashion similar to miRNAs. Some miRNAs and siRNAs can cause genes they target to be methylated, thereby decreasing or increasing transcription of those genes.[33][34][35] 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.[36][37] All prokaryotes have CRISPR RNAs, a regulatory system analogous to RNA interference.[38] Antisense RNAs are widespread; most downregulate a gene, but a few are activators of transcription.[39] One way antisense RNA can act is by binding to an mRNA, forming double-stranded RNA that is enzymatically degraded.[40] There are many long noncoding RNAs that regulate genes in eukaryotes,[41] one such RNA is Xist which coats one X chromosome in female mammals and inactivates it.[42]

An mRNA may contain regulatory elements itself, such as riboswitches, in the 5' untranslated region or 3' untranslated region; these cis-regulatory elements regulate the activity of that mRNA.[43] The untranslated regions can also contain elements that regulate other genes.[44]

In RNA processing

File:Uridine to pseudouridine.GIF

Uridine to pseudouridine is a common RNA modification.

Many RNAs are involved in modifying other RNAs. Introns are spliced out of pre-mRNA by spliceosomes, which contain several small nuclear RNAs (snRNA),[14] or the introns can be ribozymes that are spliced by themselves.[45] RNA can also be altered 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),[25] 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.[46][47]

RNA genomes

Like DNA, RNA can carry genetic information. RNA viruses have genomes composed of RNA, and a variety of proteins encoded by that genome. 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.[48]

In reverse transcription

Reverse transcribing viruses replicate their genomes by reverse transcribing DNA copies from their RNA; these DNA copies are then transcribed to new RNA. Retrotransposons also spread by copying DNA and RNA from one another,[49] and telomerase contains an RNA that is used as template for building the ends of eukaryotic chromosomes.[50]

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 (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.[51][52][53]

Discovery

Nucleic acids were discovered in 1868 by Friedrich Miescher, who called the material 'nuclein' since it was found in the nucleus.[54] 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.[55] Severo Ochoa won the 1959 Nobel Prize in Medicine after he discovered how RNA is synthesized.[56] The sequence of the 77 nucleotides of a yeast tRNA was found by Robert W. Holley in 1965,[57] winning Holley the 1968 Nobel Prize in Medicine. In 1967, Carl Woese realized RNA can be catalytic and proposed that the earliest forms of life relied on RNA both to carry genetic information and to catalyze biochemical reactions—an RNA world.[58][59] In 1976, Walter Fiers and his team determined the first complete nucleotide sequence of an RNA virus genome, that of bacteriophage MS2.[60] 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.[61][62] At about the same time, 22 nt long RNAs, now called microRNAs, were found to have a role in the development of C. elegans.[63] The discovery of gene regulatory RNAs has led to attempts to develop drugs made of RNA, such as siRNA, to silence genes.[64]

See also

Template:MolBioGeneExp

  • Genetics
  • Molecular biology
  • Oligonucleotide synthesis
  • Quantification of nucleic acids
  • RNA Ontology Consortium
  • Sequence profiling tool
  • RNA extraction
  • RNA structure prediction

References

  1. ↑ 1.0 1.1 Lee JC, Gutell RR (2004). Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs. J. Mol. Biol. 344 (5): 1225–49.
  2. ↑ Barciszewski J, Frederic B, Clark C (1999). RNA biochemistry and biotechnology, 73–87, Springer.
  3. ↑ Salazar M, Fedoroff OY, Miller JM, Ribeiro NS, Reid BR (1992). The DNA strand in DNAoRNA hybrid duplexes is neither B-form nor A-form in solution. Biochemistry 32 (16): 4207–15.
  4. ↑ Hermann T, Patel DJ (2000). RNA bulges as architectural and recognition motifs. Structure 8 (3): R47–R54.
  5. ↑ Mikkola S, Nurmi K, Yousefi-Salakdeh E, Strömberg R, Lönnberg H (1999). The mechanism of the metal ion promoted cleavage of RNA phosphodiester bonds involves a general acid catalysis by the metal aquo ion on the departure of the leaving group. Perkin transactions 2: 1619–26.
  6. ↑ Jankowski JAZ, Polak JM (1996). Clinical gene analysis and manipulation: Tools, techniques and troubleshooting, 14, Cambridge University Press.
  7. ↑ Yu Q, Morrow CD (2001). Identification of critical elements in the tRNA acceptor stem and TΨC loop necessary for human immunodeficiency virus type 1 infectivity. J Virol. 75 (10): 4902–6.
  8. ↑ Elliott MS, Trewyn RW (1983). Inosine biosynthesis in transfer RNA by an enzymatic insertion of hypoxanthine. J. Biol. Chem. 259 (4): 2407–10.
  9. ↑ Söll D, RajBhandary U (1995). TRNA: Structure, biosynthesis, and function, 165, ASM Press.
  10. ↑ Kiss T (2001). Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. The EMBO Journal 20: 3617–22.
  11. ↑ King TH, Liu B, McCully RR, Fournier MJ (2002). Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center. Molecular Cell 11 (2): 425–35.
  12. ↑ Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH (2004). Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. USA 101 (19): 7287–92.
  13. ↑ Tan ZJ, Chen SJ (2008). Salt dependence of nucleic acid hairpin stability. Biophys. J. 95 (2): 738–52.
  14. ↑ 14.0 14.1 14.2 Berg JM, Tymoczko JL, Stryer L (2002). Biochemistry, 5th, 118–19, 781–808, WH Freeman and Company.
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  16. ↑ 16.0 16.1 Nissen P, Hansen J, Ban N, Moore PB, Steitz TA (2000). The structural basis of ribosome activity in peptide bond synthesis. Science 289 (5481): 920–30.
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  18. ↑ Jeffrey L Hansen, Alexander M Long, Steve C Schultz (1997). Structure of the RNA-dependent RNA polymerase of poliovirus. Structure 5 (8): 1109–22.
  19. ↑ Ahlquist P (2002). RNA-Dependent RNA Polymerases, Viruses, and RNA Silencing. Science 296 (5571): 1270–73.
  20. ↑ 20.0 20.1 20.2 Cooper GC, Hausman RE (2004). The Cell: A Molecular Approach, 3rd, 261–76, 297, 339–44, Sinauer.
  21. ↑ Mattick JS, Gagen MJ (1 September 2001). The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms. Mol. Biol. Evol. 18 (9): 1611–30.
  22. ↑ Mattick, J.S. (2001). “Noncoding RNAs: the architects of eukaryotic complexity”. EMBO Reports, 2(11), 986-991. [1]
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  32. ↑ Watanabe T, Totoki Y, Toyoda A, et al. (May 2008). Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 453 (7194): 539–43.
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  45. ↑ Steitz TA, Steitz JA (1993). A general two-metal-ion mechanism for catalytic RNA. Proc. Natl. Acad. Sci. U.S.A. 90 (14): 6498–502.
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  58. ↑ Siebert S (2006). Common sequence structure properties and stable regions in RNA secondary structures. Dissertation, Albert-Ludwigs-Universität, Freiburg im Breisgau.
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  60. ↑ Fiers W et al. (1976). Complete nucleotide-sequence of bacteriophage MS2-RNA: primary and secondary structure of replicase gene. Nature 260 (5551): 500–7.
  61. ↑ Napoli C, Lemieux C, Jorgensen R (1990). Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 2 (4): 279–89.
  62. ↑ Dafny-Yelin M, Chung SM, Frankman EL, Tzfira T (December 2007). pSAT RNA interference vectors: a modular series for multiple gene down-regulation in plants. Plant Physiol. 145 (4): 1272–81.
  63. ↑ Ruvkun G (2001). Glimpses of a tiny RNA world. Science 294 (5543): 797–99.
  64. ↑ Fichou Y, Férec C (2006). The potential of oligonucleotides for therapeutic applications. Trends in Biotechnology 24 (12): 563–70.

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