Oligo/Primer Properties & Analysis Tool
Advanced Oligo Analysis: Properties, Tm, Conversions & More
Get reliable biophysical data for your DNA and RNA oligonucleotides with Westlab's enhanced properties calculator. Designed for researchers needing accurate information for PCR, qPCR, sequencing, probe design, and quantification, this tool goes beyond basic estimates.
Input your sequence (including standard IUPAC ambiguity codes) and get a comprehensive analysis:
- Accurate Physical Properties: Calculates Molecular Weight (MW) using standard formulas and GC Content (handling ambiguities).
- Nearest-Neighbor Calculations: Employs the more accurate Nearest-Neighbor method to determine Extinction Coefficient (ε₂₆₀) for precise quantification (uses Base Composition as fallback if ambiguities are present). For DNA sequences without ambiguities, it also calculates Melting Temperature (Tm) using Nearest-Neighbor thermodynamics, incorporating salt and oligo concentration for higher accuracy.
- Tm Estimates: Provides multiple Tm values:
- Nearest-Neighbor Tm: Most accurate estimate for standard DNA.
- Salt-Adjusted Tm: Empirical formula used for RNA, sequences with ambiguities, or when NN fails.
- Basic Tm: Rough estimate for very short DNA (<14bp). (Note: Tm values are estimates; experimental verification is recommended for critical applications. Mg²⁺/dNTP corrections are not included in these Tm formulas).
- Quantification Metrics: Calculates nmol/OD₂₆₀ and µg/OD₂₆₀ based on the computed MW and ε₂₆₀.
- Convenience Tools: Instantly generate the Reverse Complement sequence (handles ambiguity codes) and perform Concentration Conversions between OD₂₆₀, nmol, µg, and µM within the tool.
- Basic Sequence Analysis: Flags potential issues like GC content outside the optimal range, homopolymer runs (≥5 bases), strong 3' GC clamps, and simple potential hairpins or self-dimers.
Make informed decisions for your experiments with this powerful, all-in-one oligo analysis tool.
Oligo/Primer Properties Calculator (Enhanced + NN Tm)
Calculate key properties for DNA/RNA oligos: MW, GC%, Tm estimates (Basic, Salt-Adjusted, Nearest-Neighbor), Extinction Coefficient (Nearest-Neighbor), nmol/OD, µg/OD. Includes Reverse Complement, Concentration Conversion, and basic sequence analysis.
Input Sequence & Options
0 bases detected.
Calculated Properties
Basic Properties
Length: - bases
GC Content: - % (Weighted avg. for ambiguities)
Molecular Weight (MW): - g/mol(ssDNA/ssRNA, anhydrous)
Quantification
Extinction Coeff. (ε₂₆₀): - M⁻¹cm⁻¹
nmol / OD₂₆₀ Unit: - nmol/OD
µg / OD₂₆₀ Unit: - µg/OD
Melting Temperature (Estimates)
Tm (Basic) Formula: 2°C(A+T/U) + 4°C(G+C). Rough estimate for DNA < 14bp in ~50mM salt.: - °C
Tm (Salt Adjusted) Formula: 81.5 + 0.41(%GC) - 675/Length + 16.6*log10([Na⁺ mM]/1000). Empirical formula for DNA ≥ 14bp or RNA. Uses [Na⁺] only.: - °C ( mM Na⁺)
Tm (Nearest-Neighbor) Thermodynamic calculation (SantaLucia 1998 parameters). Most accurate for DNA without ambiguities. Uses [Na⁺] and [Oligo]. See note below.: - °C ( mM Na⁺, nM Oligo)
Sequence Analysis Notes
- Run calculation to see analysis.
MW uses standard monophosphate weights. **Tm values are ESTIMATES.** NN Tm is generally most accurate for standard DNA. Salt-Adjusted Tm is empirical. Basic Tm is rough for short DNA. Accuracy affected by ambiguity codes. **Mg²⁺ and dNTP concentrations are NOT factored into these Tm calculations.** Experimental validation recommended for critical applications.
Concentration Conversions
Enter a value in any ONE field (and Volume if using Conc.) to calculate the others based on MW and ε₂₆₀. Assumes 1 cm path length.