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2 STRUCTURE
Structure
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 mostly adopt the Aform geometry,[10] although in single strand dinucleotide
contexts, RNA can rarely also adopt the B-form most
commonly observed in DNA.[11] The A-form geometry
results in a very deep and narrow major groove and a shallow and wide minor groove.[12] A second consequence of
the presence of the 2'-hydroxyl group is that in conformationally exible 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.[13]
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, 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 RNA is transcribed with only four bases (adenine, cyand uracil.[8] However, other interactions are possible, tosine, guanine and uracil),[14] but these bases and atsuch as a group of adenine bases binding to each other tached sugars can be modied in numerous ways as the
3
structure. The scaold 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.[21] Since RNA is charged,
metal ions such as Mg2+ are needed to stabilise many secondary and tertiary structures.[22]
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.[23]
Like other structured biopolymers such as proteins, one
can dene 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.
Chemical structure of RNA
3 Synthesis
Synthesis of RNA is usually catalyzed by an enzyme
RNA polymeraseusing 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.[24]
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.[25] Also, RNA-dependent
RNA polymerase is part of the RNA interference pathway in many organisms.[26]
There are more than 100 other naturally occurring modied nucleosides,[17] The greatest structural diversity of
modications can be found in tRNA,[18] while pseudouridine and nucleosides with 2'-O-methylribose often
present in rRNA are the most common.[19] The specic
roles of many of these modications in RNA are not fully
understood. However, it is notable that, in ribosomal
RNA, many of the post-transcriptional modications occur in highly functional regions, such as the peptidyl transferase center and the subunit interface, implying that they
are important for normal function.[20]
4 Types of RNA
See also: List of RNAs
4.1 Overview
Messenger RNA (mRNA) is the RNA that carries information from DNA to the ribosome, the sites of protein
The functional form of single-stranded RNA molecules, synthesis (translation) in the cell. The coding sequence
just like proteins, frequently requires a specic tertiary of the mRNA determines the amino acid sequence in the
4 TYPES OF RNA
RNA (siRNA), small nucleolar RNA (snoRNAs), Piwiinteracting RNA (piRNA), tRNA-derived small RNA
(tsRNA)[36] and small rDNA-derived RNA (srRNA).[37]
4.3 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 intronsnon-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.[27]
In length
4.6
RNA genomes
4.5
In RNA processing
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.[65][66][67][68]
REFERENCES
The discovery of gene regulatory RNAs has led to attempts to develop drugs made of RNA, such as siRNA,
to silence genes.[80]
6 Evolution
In March 2015, complex DNA and RNA organic compounds of life, including uracil, cytosine and thymine,
were reportedly formed in the laboratory under outer
space conditions, using starting chemicals, such as
pyrimidine, found in meteorites. Pyrimidine, like
polycyclic aromatic hydrocarbons (PAHs), the most
Robert W. Holley, left, poses with his research team.
carbon-rich chemical found in the Universe, may have
been formed in red giants or in interstellar dust and gas
[81]
after he discovered an enzyme that can synthesize RNA clouds, according to the scientists.
in the laboratory.[71] However, the enzyme discovered by
Ochoa (polynucleotide phosphorylase) was later shown
to be responsible for RNA degradation, not RNA syn- 7 See also
thesis. In 1956 Alex Rich and David Davies hybridized
two separate strands of RNA to form the rst crystal
Biomolecular structure
of RNA whose structure could be determined by X-ray
crystallography.[72]
DNA, RNA and proteins: The three essential
macromolecules of life
The sequence of the 77 nucleotides of a yeast tRNA was
found by Robert W. Holley in 1965,[73] winning Holley
the 1968 Nobel Prize in Medicine (shared with Har Gobind Khorana and Marshall Nirenberg). In 1967, 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.[74][75]
During the early 1970s, retroviruses and reverse transcriptase were discovered, showing for the rst 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 rst complete nucleotide sequence of an RNA virus genome, that
of bacteriophage MS2.[76]
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 plants own, now known to be a result of RNA interference.[77][78]
At about the same time, 22 nt long RNAs, now called
microRNAs, were found to have a role in the development
of C. elegans.[79] 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.
DNA
History of RNA Biology
List of RNA Biologists
8 References
[1] RNA: The Versatile Molecule. University of Utah.
2015.
[2] Nucleotides and Nucleic Acids (PDF). University of
California, Los Angeles.
[3] R.N. Shukla.
Analysis of Chromosomes.
9789384568177.
ISBN
[8] 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): 122549.
doi:10.1016/j.jmb.2004.09.072. PMID 15561141.
[9] Barciszewski J; Frederic B; Clark C (1999). RNA biochemistry and biotechnology. Springer. pp. 7387. ISBN
0-7923-5862-7. OCLC 52403776.
[10] Salazar M; Fedoro 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): 420715. doi:10.1021/bi00067a007.
PMID 7682844.
[11] Sedova A; Banavali NK (2016). RNA approaches the
B-form in stacked single strand dinucleotide contexts.
Biopolymers. 105 (2): 6582. doi:10.1002/bip.22750.
PMID 26443416.
[12] Hermann T; Patel DJ (2000). RNA bulges as architectural and recognition motifs. Structure. 8 (3): R47R54.
doi:10.1016/S0969-2126(00)00110-6. PMID 10745015.
[13] Mikkola S; Stenman E; Nurmi K; Youse-Salakdeh E;
Strmberg R; Lnnberg 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 (8): 161926. doi:10.1039/a903691a.
[15] Yu Q; Morrow CD (2001). Identication of critical elements in the tRNA acceptor stem and TC
loop necessary for human immunodeciency virus
type 1 infectivity.
J Virol.
75 (10): 4902
6.
doi:10.1128/JVI.75.10.4902-4906.2001.
PMC
114245 . PMID 11312362.
REFERENCES
[40] Liang, Kung-Hao; Yeh, Chau-Ting (2013). A gene expression restriction network mediated by sense and antisense Alu sequences located on protein-coding messenger
RNAs.. BMC Genomics. 14: 325. doi:10.1186/14712164-14-325. PMC 3655826 . PMID 23663499. Retrieved 2013-05-11.
[41] Wu L; Belasco JG (January 2008). Let me count
the ways: mechanisms of gene regulation by miRNAs and siRNAs.
Mol.
Cell.
29 (1): 17.
doi:10.1016/j.molcel.2007.12.010. PMID 18206964.
[42] Matzke MA; Matzke AJM (2004). Planting the seeds
of a new paradigm. PLoS Biology. 2 (5): e133.
doi:10.1371/journal.pbio.0020133.
PMC 406394 .
PMID 15138502.
[43] Vazquez F; Vaucheret H; Rajagopalan R; Lepers C; Gasciolli V; Mallory AC; Hilbert J; Bartel DP; Crt P (2004).
Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Molecular Cell. 16
(1): 6979. doi:10.1016/j.molcel.2004.09.028. PMID
15469823.
10
External links
RNA World website Link collection (structures, sequences, tools, journals)
Nucleic Acid Database Images of DNA, RNA and
complexes.
EXTERNAL LINKS
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