Oligo Tm predictor

This page predicts the Tm of a short oligonucleotide for use in PCR. It uses the nearest neighbor thermodynamic parameters of Allawi et al, with the salt corrections suggested by SantaLucia. These parameters should be able to predict oligonucleotide melting behaviour with a standard error of +/- 2 degrees:

length between 6 and 20 nucleotides
between 10% and 90% GC content (not homopolymeric)
no single run of any base longer than 4
Na+ or K+ concentrations between 0.1 and 1.0 M (use 0.2M for PCR)
one oligo (primer) is in vast excess (if not, divide the concentration by 4)

References:

SantaLucia (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Nat'l Acad. Sci. USA 95:1460
Allawi et al, (1997) Thermodynamics of Internal G:T mismatches in DNA. Biochemistry 36:10581
Owczarzy et al, (1998) Predicting Sequence-Dependent Melting Stability of Short Duplex DNA Oligomers. Biopolymers 44:217
Wetmur (1991) DNA Probes: Applications of the Principles of Nucleic Acid Hybridization. Critical Reviews in Biochemistry and Molecular Biology 26:227