17.1 Roles of RNA Molecules

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17.1 Roles of RNA Molecules

• Ref Ch. 5 Mount Bioinformatics
• Protein synthesis
• ribosomal RNA
• transfer RNA
• messenger RNA
• Catalysis
• e.g. ribozymes
• iii. Regulatory molecules

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17.2 Interactions of RNA Molecules

• Nucleic acid interactions
• complementary base pairing

• Protein interactions
• Shape
• Charge
• Hydrophobicity

iii. Regulatory molecules
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17.3 Shape of RNA Molecules
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

• Hydrophobicity

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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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17.6 Principles for Predicting RNA Secondary
Structure

• The most likely structure is the most stable
  structure
• Long regions of base pairing are more stable than
  short regions
• GC base pairs are more stable than AU base pairs
• Energies are estimated from experiments with
  synthetic RNA molecules

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• The structure does not have knots
• Loops need to contain at least 4 nucleotides

Energies are estimated from experiments with
synthetic RNA molecules
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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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17.7 Circle Plot
Sequence is drawn around circumference of
circle Arcs connect paired bases
Arcs dont cross (unless pseudoknots formed)
The stabilising effect of paired regions is
balanced against the destabilising effect of
unpaired regions
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Squiggle plot
Circle plot
(unless pseudoknots formed)
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17.8 ANGIS Programs
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
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17.9 Ribozymes
Self-cleaving RNA molecules Catalytic activity
depends on 2o structure
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17.10 Regulatory RNA - glmS
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
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Cech (2004) Nature 428263
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17.11 Regulatory RNAs csrA, csrB
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
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Romeo 1998 Mol. Microbiol. 291321-1330
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17.12 Evolutionary Relationships
RNA homologues maintain secondary structure -
covariation of paired bases
A
U
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Analysis of sequences of homologues for
covariation can be used to predict secondary
structure
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17.13 Summary
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