OligoCalc

OligoCalc calculates physical and thermodynamic properties of DNA and RNA oligonucleotides, including melting temperature, molecular weight, absorbance at 260 nm, and secondary-structure propensity to support experimental design.

Key Features:

• Melting Temperature Calculation: Employs three common methods, including a nearest-neighbor thermodynamic model, to calculate oligonucleotide melting temperatures under varying conditions.
• Molecular Weight and Concentration: Calculates molecular weight and solution concentration for oligonucleotides to support sample preparation and analysis.
• Absorbance Estimation: Estimates absorbance coefficients (extinction coefficients) at 260 nm for spectrophotometric quantification of nucleic acids.
• Self-Complementarity and Hairpin Loop Prediction: Assesses inter-molecular self-complementarity and predicts intra-molecular hairpin loop formations to evaluate secondary-structure risks.

Scientific Applications:

• Oligonucleotide design and PCR optimization: Provides Tm and concentration data to inform primer design and PCR condition selection.
• Hybridization assays: Supports design and optimization of hybridization-based assays through melting temperature and secondary-structure predictions.
• RNA folding studies: Aids analysis of RNA secondary structure by predicting hairpins and self-complementarity.
• Nucleic acid quantification and sample preparation: Enables estimation of extinction coefficients and concentration calculations for spectrophotometric quantification and sample setup.

Methodology:

Calculates melting temperatures using three methods, including a nearest-neighbor thermodynamic model, and applies established thermodynamic algorithms to predict physical properties and secondary-structure propensity.