RNA Structure and Function Notes

RNA Prediction and Analysis of Structures

Structural Conformations of RNAs

• Primary Structure: Sequence of monomers (e.g., $ext{ATGCCGTCAC}$).
• Secondary Structure: 2D-fold, defined by hydrogen bonds between bases.
• Tertiary Structure: 3D-fold leading to functional configurations.
• Quaternary Structure: Complex arrangement of multiple folded RNA molecules.

Non-coding RNAs (ncRNAs)

• Definition: RNA molecules that are not translated into proteins.
• Types of ncRNAs:
  • tRNA (transfer RNA): Aids in translating mRNA to protein.
  • rRNA (ribosomal RNA): Key component of ribosomes, facilitating protein synthesis.
  • snoRNA (small nuclear RNA): Guides chemical modifications of other RNAs.
  • miRNA (microRNA): Regulates gene expression by targeting mRNA.
  • siRNA (short interfering RNA): Involved in RNA interference (RNAi) to silence genes.
  • piRNA (Piwi-interacting RNA): Linked to transcriptional gene silencing, especially in germ line cells.
  • long ncRNA: Non-protein coding transcripts longer than 200 nucleotides.

Functions of Non-coding RNAs

• Impact multiple cellular processes:
  • Protein synthesis: rRNA and tRNA play crucial roles.
  • RNA processing: SnoRNA > modifies other RNA types.
  • Gene regulation: miRNA impacts mRNA levels.
  • RNA interference: siRNAs function in gene silencing.
  • Gene silencing: piRNAs manage gene expression at the transcriptional level.

Features of RNA

• Typically produced as a single-stranded molecule.
• RNA can fold back on itself to form base pairs, showcasing structural conservation.
• Base Pairing Types:
  • Watson-Crick Pairing: Regular base pairing.
  • Non-Watson-Crick Pairing: Example is the G/U wobble pairing.

RNA Secondary Structure

• Various structural features include:
  • Single-Stranded Structure
  • Bulge Loop: An unpaired base in a pair.
  • Stem: A stable region with base pairs.
  • Interior Loop: Loop inside paired regions.
  • Pseudoknot: A unique folding structure interacting with other loops.
  • Hairpin Loop: A loop closed by base pairing.
  • Junction (Multiloop): Intersection of multiple helical regions.

Complex Folds in RNA

• Examples of complex structures include:
  • Pseudoknot
  • Kissing Hairpins: Interactions between hairpins.
  • Hair-bulge Interaction: Compounds various loops/structures bringing complexity.

Main Approaches to RNA Secondary Structure Prediction

• Energy Minimization: Does not require sequence alignment; focuses on energetics of conformations.
• Comparative Sequence Analysis: Uses sequence alignment to identify conserved areas and covariant base pairs.
• Simultaneous Folding and Alignment: Involves structural alignment during prediction.

Assumptions in Energy Minimization Approaches

• The most likely RNA structure resembles the energetically most stable one.
• Energy states depend on local sequence and structural characteristics.
• Pseudoknots are generally neglected in basic models.

Energy Minimization Methods

• Aim to maximize the number of base pairs:
  • Only consider A-U and G-C pairs without differentiation of their influence.
  • Nussinov Algorithm: Maximizes base pair count but may lack accuracy.
  • Energy Minimization Algorithm: Predicts secondary structures by minimizing the free energy (ΔG).
  • Calculating $ext{ΔG}$ is based on contributions from:
  • Loops
  • Stacking interactions

Most Common Approach for Predicting RNA Secondary Structure

• Search for an RNA structure with a Minimal Free Energy (MFE) to guide folding predictions.

RNA Secondary Structure Example

• Example formation: $$U U C G U A A U G C$.
• Folding displays base pairing:
  • Hydrogen bonding illustrated: G-C and A-U pairs forming the backbone of structure.

Short Range Interactions in RNA Structures

• Internal interactions may lead to:
  • Internal Loops
  • Hairpin Loops
  • Bulges and Dangling Ends
• Illustrations help visualize these interactions along the RNA sequences, from 5'$to$3'$$ ends.