siRNA Design Online Training

This internship is designed to introduce learners to the fundamentals and applications of RNA-based therapeutics, focusing on siRNA (small interfering RNA) design and RNA secondary structure prediction. Participants will learn about RNA interference (RNAi), target gene silencing, and how computational tools are used to predict RNA folding, thermodynamics, and stability.

Learning Objectives

By the end of the internship, participants will:

• Understand the principles of RNA interference and siRNA-mediated gene silencing
• Design effective siRNA sequences against target genes
• Predict RNA secondary structures and folding patterns
• Analyze RNA thermodynamic stability and hairpin loop formations
• Utilize online and open-source tools for RNA simulation and visualization

Project Structure

Introduction to RNAi and siRNA

• Mechanism of RNA interference

• siRNA vs miRNA vs shRNA

• Applications in therapeutics and gene regulation

Guidelines for siRNA Design

• siRNA structure and functional rules

• Off-target effects and GC content considerations

• Target site selection in mRNA

siRNA Design Tools

• Tools: siDirect, BLOCK-iT, DSIR, Whitehead siRNA Selection

• Hands-on: Designing siRNAs for target genes (e.g., BCL2, EGFR)

Advanced Filtering for siRNA

• Thermodynamics, target accessibility, specificity scoring

• Avoiding immune response triggers

Introduction to RNA Secondary Structures

• RNA folding, base pairing, stem-loops, hairpins

• RNA structure formats: dot-bracket, CT files

RNA Structure Prediction Tools

• Tools: RNAfold (ViennaRNA), Mfold, RNAstructure

• Hands-on: Predicting folding patterns and visualizing base-pair probabilities

Thermodynamic Analysis

• Free energy (ΔG) interpretation

• Structure ensemble generation

• Pseudoknot prediction

Tools & Resources

• siDirect, , DSIR , Genscript– siRNA design

Assignments & Capstone Project

• Design siRNA sequences for 2 real genes

• Predict and compare RNA secondary structures

• Submit a report with sequences, structure visuals, and design evaluation

Certification

Participants receive:

• Certificate of Completion

• Project Evaluation Letter for academic or research use

Target Audience

• Graduate and Postgraduate students in Bioinformatics, Molecular Biology, or Biotechnology
• PhD students and Researchers in Genetic Engineering or RNA Therapeutics
• Professionals in Bioinformatics and Computational RNA Biology interested in Gene Silencing
• Life sciences professionals aiming to advance their knowledge in RNA-based therapeutics