Primer Designing

2-Day Workshop: Primer Designing

From Practical Demonstration to Real Life Project

Organized by: SKI Plus International

Course Overview

This intensive, hands-on 2-day workshop is designed to equip students and researchers with both manual and computational skills for designing efficient, highly specific PCR primers. Moving from core theoretical foundations to practical demonstrations and a real-life project, participants will learn how to retrieve sequences, evaluate critical physicochemical properties, and optimize primer parameters using leading bioinformatics tools.

What You Will Learn

• Sequence Analysis: Retrieve and analyze genomic sequences for primer designing.

• Conserved Region Identification: Locate and analyze conserved regions across aligned sequences.

• Manual Design Criteria: Apply scientific rules to manually select forward and reverse primer pairs.

• Biochemical Property Calculation: Use OligoCalc to interpret melting temperature ($T_m$), GC content, and secondary structures.

• Automated Design Tools: Run and fine-tune Primer3 with custom, optimal parameters.

• Quality & Error Checking: Detect hairpins, self-dimers, hetero-dimers, and $T_m$ mismatches.

• Specificity & Off-Target Validation: Perform Primer-BLAST checks to avoid non-specific amplification.

• Final Selection & Reporting: Select the ideal primer pair for experimental PCR and compile a project report.

Workshop Syllabus

Day 1: Understanding & Manual Primer Designing

• NCBI & BLASTN: Gene searching, sequence retrieval, and nucleotide similarity checking.

• ClustalW & Conserved Regions: Multiple sequence alignment and identifying key conserved regions.

• Manual Primer Selection: Step-by-step selection of forward and reverse primers using standard molecular biology criteria.

• OligoCalc & Primer Properties: Calculating and analyzing thermodynamic properties, GC ratios, and primer kinetics.

Day 2: Computational Design & Validation

• Primer3: Automated primer generation and parameter optimization.

• Primer Quality & Analysis: In-depth evaluation of hairpin loops, primer dimers, GC clamp, and melting temperature compatibility.

• EMBOSS Needle: Pairwise sequence alignment and similarity analysis.

• Primer-BLAST & Specificity: Off-target screening and specificity validation across reference genomes.

• Final Practical Project: An interactive, hands-on session working through real biological examples and generating a final analysis report.

Key Details & Logistics

• Dates: September 12–13, 2026

• Platform: Google Meet (Live Online Session)

• Standard Fee: 700 PKR per person

• SKI Plus Alumni Fee: 600 PKR

• Certification: Official verifiable E-Certificate provided upon completion

• Availability: Limited seats available