DNATools


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.)

Features

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.

Updates

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

Screenshots (ver 1.2.1)



References

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
ċ
DNATools_1.2.1.zip
(246k)
Shogo Hamada,
2011/06/22 1:54
ċ
DNATools_1.2.2.zip
(247k)
Shogo Hamada,
2011/09/06 8:31