# Structural Biochemistry/Nucleic Acid/RNA/RNA Secondary Structure

< Structural Biochemistry | Nucleic Acid | RNA

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## Basis of RNA[edit]

- -RNA bases: A,G,C,U
- -Base Pairs: A-U, G-C
- -non-canonical pairs: G-U
- -Stability: G-C > A-U > G-U
- -Single Stranded: strand folds upon it to form base pairs; can have a diverse form of secondary structure

## Secondary Structure[edit]

### Structure Rules[edit]

- Base pairing stabilize the structure
- Unpaired sections-loops destabilize the structure
- When a base in one position changes, the base it pairs to must also change to maintain the same structure-covariation

### Representations[edit]

- -Most base pairs are non-crossing base pairs: -any two pairs (i, j) and (i’, j’) -> i < i’ <j’ < j or i’ < i < j < j’

### Circular Representation[edit]

- -Base pairs of a secondary structure represented by a circle
- -Arc drawn for each base pairing in the structure

### Combinatorics[edit]

- -The number of RNA secondary structures for the sequence: (Recurrence Relation)
- S(0)=S(1)=S(2)=1
- S(n+1)=S(n)+ƩS(j-1)S(n-j), (n≥2)

- -There are approximately 1.3 billion RNA structures of length n is 27

### Types of regions[edit]

- 1) Hairpin Loop - 4 or more bases long for each loop

- 2) Bulge Loop - bases on one side cannot form base pairs

- 3) Interior Loop - bases on both sides cannot form base pairs

- 4) Multi Loop (Junctions) – 2 or more double stranded regions converge to form a closed structure

### Structure Prediction Methods[edit]

- 1) Maximize Base Pairs
- -Determine set of maximal base pairs
- -Align bases based on ability to pair up to determine the optical structure
- -Nussinov Algorithm: 4 ways to get the optimal structure between i and j
- -Find strucuter with the most base pairs: A-U and G-C

- 2) Minimize Energy
- -Determine maximum of scores for 4 structures at a particular position
- -Stacks are the dominant stabilizing force
- -Energy minimization algorithm predicts the secondary structure by minimizing the free energy
- -Require estimation of energy terms contributing to secondary structure
- -Dynamic programming approach:
- 1) Initialization
- 2) Recursion
- 3) Traceback

- -Does not require prior sequence alighnment
- -Energy associated with any position is only influenced by local sequence and structure

## References[edit]

*How Do RNA Folding Algorithms Work?*S.R. Eddy. Nature Biotechnology, 22:1457-1458, 2004.- <http://en.wikipedia.org/wiki/Biomolecular_structure>