Individual skill
pcr-optimization
PCR assay optimization and troubleshooting — primer design, cycling conditions, and fixing failed reactions.
skills/pcr-optimization/SKILL.md
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## Overview
pcr-optimization covers designing robust PCR assays and systematically troubleshooting failures:
primer design rules, reaction chemistry, cycling parameters, and the diagnostic logic that
distinguishes primer problems from template, enzyme, and contamination issues. Most PCR failures
are primer or template problems — this skill teaches you to determine which, quickly.
## When to use
- Designing primers: length, Tm, GC content, specificity checking.
- Setting up new assays: polymerase choice, buffer, Mg²⁺, cycling conditions.
- Troubleshooting: no product, wrong-size bands, smears, primer-dimers, non-specific
amplification.
- qPCR: efficiency, standard curves, reference genes, MIQE basics.