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Ref: Ch. 5 Mount: Bioinformatics
i. Protein synthesis:
ribosomal RNA
transfer RNA
messenger RNA
ii. Catalysis
e.g. ribozymes
iii. Regulatory molecules
17.1 Roles of RNA Molecules
2iii. Regulatory molecules
Nucleic acid interactions - complementary base pairing
Protein interactions
- Shape
- Charge
- Hydrophobicity
17.2 Interactions of RNA Molecules
3- Hydrophobicity
Self-complementary regions undergo complementary base pairing
- depends on the formation of loops
- 5’ end of one part of the molecule aligned with 3’ end of other part
17.3 Shape of RNA Molecules
5’
3’
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17.4 Types of Structures
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17.4 Types of Structures
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17.4 Types of Structures
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17.4 Types of Structures
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17.4 Types of Structures
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17.4 Types of Structures
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17.5 Complex Interactions
Pseudoknot
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17.5 Complex Interactions
Kissing hairpins
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17.5 Complex Interactions
Hairpin-bulge contact
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1. The most likely structure is the most stable structure
2. Long regions of base pairing are more stable than short regions
3. GC base pairs are more stable than AU base pairs
4. Energies are estimated from experiments with synthetic RNA molecules
17.6 Principles for Predicting RNA Secondary Structure
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Energies are estimated from experiments with synthetic RNA molecules
5. The structure does not have knots
6. Loops need to contain at least 4 nucleotides
5’
3’
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Note:
• Many structures are possible• Formation of some loops prevents
formation of other loops• The stabilising effect of paired regions
is balanced against the destabilising effect of unpaired regions
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The stabilising effect of paired regions is balanced against the destabilising effect of unpaired regions
Sequence is drawn around circumference of circle
Arcs connect paired bases
Arcs don’t cross
(unless pseudoknots formed)
17.7 Circle Plot
17(unless pseudoknots formed)
Squiggle plotCircle plot
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WAG (Web Angis GCG)
RNA secondary structure
e.g. mfold
Input file: VapHGRNA
Output: VAPHGRNA MFOLD
Use Plotfold (from WAG) to display output
Save as GIF
17.8 ANGIS Programs
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Self-cleaving RNA molecules
Catalytic activity depends on 2o structure
17.9 Ribozymes
Lehninger Principles of Biochemistry 3rd Edition Nelson & Cox
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glmS gene produces enzyme GlmS
GlmS RNA is a ribozyme – can cleave itself
Ribozyme activity is greatly increased by the product of reaction catalysed by GlmS
Product of GlmS enzyme shuts off synthesis of GlmS enzyme
17.10 Regulatory RNA - glmS
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Cech (2004) Nature 428:263
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CsrA protein binds to specific mRNAs and prevents their translation
CsrB RNA is an antagonist of CsrA
- has 18 binding sites for CsrA protein
CsrA protein binds to CsrB and is not available to bind to the specific mRNAs
17.11 Regulatory RNAs – csrA, csrB
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Romeo 1998 Mol. Microbiol. 29:1321-1330
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RNA homologues maintain secondary structure
- covariation of paired bases
17.12 Evolutionary Relationships
5’
3’
A
U
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Analysis of sequences of homologues for covariation can be used to predict secondary structure
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Types of secondary structure
Principles for prediction of secondary structure
mfold program
Circle and squiggle plots
Secondary structure of regulatory RNA molecules
Covariation of paired bases in evolution
17.13 Summary
