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RNA structure Single strand (usually) A,C,G,U (no T) Main types:
mRNA, tRNA, rRNA, snRNA
Substructures: duplex, ss, hairpins, bulges,
internal loops, junctions, tertiary base-pairing, base-triplets
Tetrahymena group I intron
RNase P
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RNA structural hierarchy
Primary structure - covalent chemical struct. Nucleotide base sequence
Secondary structure - “local” chain folding Base-pairing pattern (helix, bulged-G, tetraloops, etc.) 2D prediction (mFold)
Tertiary structure - “global” chain folding 3D interactions http://scor.lbl.gov/
Quaternary structure - associations between well-folded units
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A-minor motif
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RNA backbone angles
A form
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DNA is transcribed to mRNA
RNA polymerase
mRNA
DNA
Goodsell
Single strand. Temporary. Secondary structure
undesirable. Poly-A tail.
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mRNA is translated to protein by ribosomes
Ribosome
mRNA
Polypeptide
Goodsell
Ribosome Large subunit Small subunit
Make up 25% of the dry weight of pancreas cells (specialize in protein synthesis). 1 cell can synthesize 5 million molecules of protein per minute.
…
tRNA
~20 nm
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“The Tree of Life” - Anatomical systematics- Haeckel’s line of descent- 5 Kingdom Model- 3 Domain (Woese 1990, Pace)
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Secondary StructureExample: tRNA
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Alternative Base Pairing
Watson-Crick G-C, A-U
Wobble G-U, A-C
Hoogsteen A-U
Others: triplets, single H-bonds, pH effects.
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RNase P RNA
Rnase P enzyme is involved in tRNA processing that removes the 5' leader sequences from tRNA precursors.
Rnase P contains RNA and protein but some Rnase P RNAs are enzymatically active without protein cofactors.
Model molecule for modeling by sequence comparison.
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RNAi
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In vitro evolution of functional RNA
Start with random sequence library and select functional molecules. Repeat.
Groups: Szostak, Ellington, Bartel, Breaker, Eaton, Feldheim, etc.
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Schultes, 2000
Hepatitis delta virus & class III ligase (in vitro evolved).
“Intersection” sequence has both activities.
Neutral paths and networks.
Implications for evolution of new folds.
See also: Folded order for free from random RNA libraries.
Schultes et al (2005) Nature Struct Mol Biol 12, 1130
Science (2000) 289, 448-452
Class III ligaseHDV self-cleavingribozyme
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RNA (1997)
RNA composition space visualization.
Interesting clustering for functional RNA from biological and in vitro sources.
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RNA (1997) 3, 792-806
5S rRNA 16S rRNA 23S rRNA Introns & HDV Uniform random
Archea (red)Bacteria (blue)Eucarya (yellow)
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Self-organization vs. Selection in RNA Secondary Structure
J.Mol.Evol. (1999) 49:76-83
S
Q
P
S = mean length of helical stemsQ = uniqueness of foldP = base-pairing propensity
P
Q
SFrequency
Frequency
Frequency
Self-organization
Self-organization
Self-organization
Selection
Selection
Selection
Disorder
Order
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Central Dogma
DNA--> RNA--> Protein