RNA Prediction and Analysis of Structures BIOL 4300 Notes

RNA Structure Overview

  • Primary Structure

    • Defined by the sequence of nucleotides (monomers) e.g., ATGCCGTCAC

  • Secondary Structure

    • Refers to the 2D folding of RNA defined by hydrogen bonds among bases.

  • Tertiary Structure

    • The 3D conformation of the RNA molecule.

  • Quaternary Structure

    • Arrangement of multiple folded RNA molecules together.

Non-Coding RNAs (ncRNAs)

  • Definition: RNA molecules not translated into proteins.
  • Types of ncRNAs:
    • tRNA (Transfer RNA)
    • Assists in protein synthesis by carrying amino acids.
    • rRNA (Ribosomal RNA)
    • Component of ribosomes, crucial for protein synthesis.
    • snoRNA (Small Nuclear RNA)
    • Guides chemical modifications of other RNAs.
    • microRNA (miRNA)
    • Regulates gene expression.
    • siRNA (Short Interfering RNA)
    • Involved in RNA interference (RNAi) pathway, silencing gene expression.
    • piRNA (PIWI-Interacting RNA)
    • Involved in silencing transposons and regulating gene expression in germ line cells.
    • Long ncRNAs
    • Non-protein coding transcripts larger than 200 nucleotides.

Functions of Non-Coding RNAs

  • Can influence:

    • Gene transcription
    • Translation
    • Localization
    • Replication
    • Degradation

  • Specific functions:

    • Protein synthesis (rRNA and tRNA)
    • RNA processing (snoRNA)
    • Gene regulation (miRNA)
    • RNA interference (siRNA)
    • Gene silencing (piRNA)

RNA Structural Features

  • Single-Stranded:
    • RNA is mostly produced as a single-stranded molecule.
  • Folding:
    • The strand can fold upon itself to form base pairs.
  • Base Pairing:
    • Regular Watson-Crick base pairing (A-U, G-C).
    • Non-Watson-Crick base pairing (e.g., G/U wobble).

Types of RNA Secondary Structures

  • Loops:

    • Bulge Loop
    • Interior Loop
    • Hairpin Loop
    • Pseudoknot
    • Junction (Multiloop)

  • Complex Folds:

    • Pseudoknot
    • Kissing Hairpins
    • Hair-bulge interactions

Approaches to RNA Secondary Structure Prediction

  1. Energy Minimization:
    • Does not require prior sequence alignment; estimates energy contributions for structure.
  2. Comparative Sequence Analysis:
    • Uses sequence alignment to identify conserved residues and covariant base pairs.
  3. Simultaneous Folding and Alignment:
    • Involves structural alignment.

Energy Minimization Assumptions

  • Most likely structure is the energetically most stable.
  • Energy at any position is influenced only by local sequence and structure.
  • Pseudoknots may be neglected in predictions.

Energy Minimization Methods

  • Aim: Find structure with the most base pairs.
  • Consider only A-U and G-C pairs without distinction.
  • Nussinov Algorithm:
    • Simple base pair maximization method.
  • Energy Minimization Algorithm:
    • Predicts secondary structure by minimizing free energy (ΔG).
    • ΔG calculated from contributions of loops and stacking interactions.

Minimal Free Energy (MFE) Approach

  • The most common method for predicting RNA secondary structure.
  • Searches for a structure with the Minimal Free Energy.

Example of RNA Secondary Structure

  • Sequence: UUCGUAUGCUUC GUA UGC
    • 5’ to 3’ Folding:
    • Base pairing example:
      • G with C, A with U through hydrogen bonding.

Common Secondary Structures

  • Internal Loop
  • Hairpin Loop
  • Bulge
  • Dangling Ends
  • Stem