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RNA Folding. Xinyu Tang Bonnie Kirkpatrick. Overview. Introduction to RNA Previous Work Problem Hofacker ’ s Paper Chen and Dill ’ s Paper Modeling RNA Folding with PRM. Introduction to RNA. A polymer (sequence) of ribonucleoside-phosphates Ribose (sugar) Phosphoric Acid

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rna folding

RNA Folding

Xinyu Tang

Bonnie Kirkpatrick

overview
Overview
  • Introduction to RNA
  • Previous Work
  • Problem
  • Hofacker’s Paper
  • Chen and Dill’s Paper
  • Modeling RNA Folding with PRM
composition of ribonucleic acid
A polymer (sequence) of ribonucleoside-phosphates

Ribose (sugar)

Phosphoric Acid

Organic bases

Adenine (A)

Guanine (G)

Cytosine (C)

Uracil (U)

Composition of Ribonucleic Acid
complementary base pairs
Complementary Base Pairs
  • Canonical base pairs
    • Watson-Crick base pairs
      • C-G
      • A-U
      • Stable base pairs
      • Hydrogen bonds
    • Weaker G-U wobble pair
  • Non-canonical base pairs
    • Some of them stable
rna tertiary structure
RNA Tertiary Structure
  • A complex folding in 3-dimensions (similar to protein tertiary structure)
  • A specific folding is referred to as a conformation
  • Pseudo knots are considered a tertiary structure, rather than a secondary structure
rna secondary structure
RNA Secondary Structure
  • A secondary structure conformation is specified by a set of intra-chain contacts (base pairs) that follow certain rules
  • Given any two intra-chain contacts [i, j] with i < j and [i’, j’] with i’ < j’, then:
    • If i = i’, then j = j’
      • Each base can appear in only one contact pair
    • If i’ < j, then i < i’ < j’ < j
      • No pseudo-knots
  • Can be represented as planar graphs:
representations of rna
M: Multi-loop

I: Internal-loop

B: Bulge-loop

H: hairpin-loop

•: W-C pairs

-: GU pairs

Representations of RNA
representations cont1
Contact Map

A dot is placed in the ith row and jth column of a triangular array to represent the intra-chain contact [i, j]

Representations (cont.)
maximum matching problem
Maximum Matching Problem
  • Watermann and Nussinnov Algorithms
    • Finding the conformation with the maximum possible number of intra-chain contacts
    • Computed using dynamic programming
minimum energy problem
Minimum Energy Problem
  • Zuker and Stiegler Algorithm
    • Predicts the native structure by finding the conformation with the minimum energy
  • Modified Zuker Algorithm
    • Generates a set of conformations that lie within some energy range of the predicted native conformation
  • McCaskill Algorithm
    • Calculates the frequency of intra-chain contact occurrences in an ensemble of all possible structures
energy landscapes
Energy Landscapes
  • Native conformations of RNA can be predicted with accuracy
  • But the not much is known about the kinetics and thermodynamics of the folding
  • Energy landscapes show us what different conformations the RNA goes through as it folds
elements of the problem
Elements of the Problem
  • Model
  • Sampling Pattern
  • Node Connection Methods
  • Analysis Techniques
secodary vs tertiary structure
Secodary vs Tertiary Structure
  • Tertiary structure can only be determined for tRNA
  • Secondary structure predictions only approximate tertiary structure
    • For each set of intra-chain contacts, there is an ensemble of possible tertiary structures
  • Chen and Dill were able to use a