Methods and citations

The models behind every verdict: SantaLucia 1998 nearest-neighbor Tm with Mg²⁺/dNTP correction (von Ahsen 2001), a nearest-neighbor hairpin and dimer fold, cited design thresholds, and how results compare with Primer3.

OligoDesign — Oligo Design Evaluator — OligoDesign evaluates primers, probes, and molecular beacons and returns a verdict, risk drivers, recommended actions, and explicit assumptions, computed with published nearest-neighbor thermodynamics.
Single Oligo Judge — Evaluate one primer or probe sequence: role-aware oligo design evaluation covering Tm, GC content, hairpins, self-dimers, and 3′ clamp quality, with a structured verdict.
Primer Pair Judge — Evaluate a forward/reverse primer pair against a template: Tm balance, clamp quality, primer-dimer ΔG, self-priming and amplicon check in one structured verdict.
Molecular Beacon Judge — Evaluate molecular beacon designs: stem complementarity, loop length and Tm, loop-target fit, and whether the predicted fold matches the designed stem.
Tm Mismatch Check — Evaluate oligo binding across mismatched or variant targets: per-target heteroduplex Tm, ΔG and melt-curve shifts for inclusivity and specificity.
Pool Compatibility Check — Screen multiplex oligo pools for cross-dimer risk using pairwise thermodynamic free energy, not heuristic base-counting.
ePCR Mapper — In-silico primer mapping across sequence databases to evaluate on-target and off-target amplicons with a confidence score.
Primer Pair Designer — Design PCR primer pairs from a template and rank them by Tm, GC, hairpin ΔG, 3′ stability and dimer risk.
Probe Designer — Design hydrolysis probes inside an amplicon and rank them by Tm, GC balance, hairpin stability and homopolymer risk.
Learn — primer and probe design — Learn the thermodynamics and quality checks behind oligo design evaluation: melting temperature, hairpins, dimers, and design principles for primers and probes.
Training Lab — Practice oligo design judgment with constraint puzzles built on real design rules.
Community — Discuss oligo design, primer evaluation, and assay development with the OligoDesign community.
Contact — Get in touch with the OligoDesign team about oligo design evaluation tools.
What is oligo design evaluation?

Built by Dr. Lifeng Lin, a bioinformatics scientist in nucleic acid assay development for in vitro diagnostics since 2010. OligoDesign is a decision-support and educational tool; always independently verify designs before synthesis or regulated use.