Oligo Properties Calculator
Paste a DNA or RNA sequence (5'→3') to estimate basic oligonucleotide properties such as length, GC%, melting temperature, molecular weight, reverse complement, and more.
What this oligo properties calculator does
This tool gives a fast, practical snapshot of common oligonucleotide metrics used in PCR primer design, qPCR assay setup, sequencing workflows, cloning, and hybridization experiments. Rather than replacing specialized thermodynamic software, it helps you quickly screen candidate oligos before deeper analysis.
For each sequence, the calculator reports sequence length, nucleotide composition, GC content, estimated melting temperatures, molecular weight, extinction coefficient, and reverse complement. It also provides a simple GC clamp check for the 3' end.
Inputs and assumptions
1) Sequence format
Enter your oligo in the 5'→3' direction. The calculator accepts uppercase or lowercase letters and ignores whitespace/new lines. It validates characters based on selected chemistry:
- DNA mode: A, C, G, T
- RNA mode: A, C, G, U
2) Sodium concentration
If you provide Na+ concentration, the tool estimates a salt-adjusted Tm using a standard log-based correction. This is useful for rough comparisons when salt conditions vary between reactions.
How to interpret key results
Length
Oligo length affects specificity and annealing behavior. Typical PCR primers are often around 18–25 nt, while probes and adapters may differ depending on assay design.
GC content
GC-rich oligos generally bind more strongly than AT/AU-rich oligos. For many primer applications, a moderate GC range (often around 40–60%) is preferred.
Melting temperature (Tm)
The calculator shows common empirical estimates:
- Wallace rule: quick estimate from base counts
- Long-oligo estimate: empirical formula for longer sequences
- Salt-adjusted Tm: long-oligo estimate with Na+ correction
These values are best for screening and comparison. Final assay optimization should include nearest-neighbor modeling and experimental validation.
Molecular weight and extinction coefficient
Molecular weight helps when converting between mass and molar concentration for ordering and dilution plans. Extinction coefficient enables absorbance-based quantification (A260 methods) and a rough nmol/A260 conversion.
Practical primer design tips
- Keep primer pairs close in Tm (often within 1–3°C).
- Avoid long homopolymer runs (e.g., AAAA, GGGG).
- Aim for balanced GC content and avoid extreme GC-rich tails.
- Check for secondary structure, primer dimers, and off-target binding.
- Use a modest 3' GC clamp (commonly 1–3 G/C residues in the last 5 bases).
Limitations
This calculator is intentionally lightweight. It does not currently model mismatches, modified bases, Mg2+/dNTP competition, complex secondary structures, or full nearest-neighbor thermodynamics. Use this as a high-speed first pass, then validate with specialized oligo design tools and bench testing.
Bottom line
If you need a quick check of oligonucleotide properties for everyday molecular biology, this calculator gives immediate, actionable estimates. It is ideal for early candidate triage before moving to advanced in silico and experimental validation.