Version 1.2.2 (OS X 10.4.3-) Download

A Simple tool for ROUGH estimations of Tm, conc., and some info for sequence design.

(Note: This software is provided "as is", without warranty of any kind.)


Melting Temperature Prediction by three methods (Assuming the existence of complementary strand at same conc.)

  • Wallace method
  • GC fraction
  • Nearest-Neighbor method with Monovalent/Divalent cation correction (Note: I omitted the case of symmetry sequence)

Oligonucleotide concentration calc. from A260

Output Reverse / Complementary sequence

Double-clicking an output field copies the result to your clipboard.


1.2.2 Added Sugimoto's and Sigma-Aldrich's Nearest-Neighbor parameters.

1.2.1 First Release

Screenshots (ver 1.2.1)


Nearest-Neighbor Method Parameters and Tm calculation

  1. http://www.owczarzy.net/tm.htm
  2. Allawi, H.T. & SantaLucia, J. Thermodynamics and NMR of internal G.T mismatches in DNA. Biochemistry 36, 10581–10594 (1997).
  3. SantaLucia, J., Allawi, H.T. & Seneviratne, P.A. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35, 3555–3562 (1996).
  4. Sugimoto, N., Nakano, S.-I., Yoneyama, M. & Honda, K.-I. Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res. 24, 4501–4505
  5. Sigma-Aldrich Webpage

Monovalent/Divalent Cation Correction

  1. Owczarzy, R. et al. Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures. Biochemistry 43, 3537–3554 (2004).
  2. Owczarzy, R. et al. Predicting Stability of DNA Duplexes in Solutions Containing Magnesium and Monovalent Cations. Biochemistry 47, 5336–5353 (2008).