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RNA Folding

Explore the principles, models, and algorithms behind RNA folding, from canonical base pairs to tertiary structures. Learn about important papers, algorithms, and energy landscapes in RNA folding research.

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RNA Folding

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  1. RNA Folding Xinyu Tang Bonnie Kirkpatrick

  2. Overview • Introduction to RNA • Previous Work • Problem • Hofacker’s Paper • Chen and Dill’s Paper • Modeling RNA Folding with PRM

  3. Introduction to RNA

  4. A polymer (sequence) of ribonucleoside-phosphates Ribose (sugar) Phosphoric Acid Organic bases Adenine (A) Guanine (G) Cytosine (C) Uracil (U) Composition of Ribonucleic Acid

  5. 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

  6. 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

  7. 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:

  8. M: Multi-loop I: Internal-loop B: Bulge-loop H: hairpin-loop •: W-C pairs -: GU pairs Representations of RNA

  9. Hydrogen bonds between intra-chain pairs are represented by circular arcs Representations (cont.) All representations are equivalent

  10. 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.)

  11. Previous Work

  12. Maximum Matching Problem • Watermann and Nussinnov Algorithms • Finding the conformation with the maximum possible number of intra-chain contacts • Computed using dynamic programming

  13. 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

  14. Problem

  15. 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

  16. Elements of the Problem • Model • Sampling Pattern • Node Connection Methods • Analysis Techniques

  17. Hofacker’s Paper

  18. Chen and Dill’s Paper

  19. Modeling RNA Folding with PRM

  20. 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

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