This page allows you to compute the off rate of an oligonucleotide hybridized to a template. You can select the oligonucleotide sequence, type, template with some mismatches and salt conditions. The software uses BiopyPthon to compute the dinucleotide free-energy.

Further question vincent.croquette (arobase) espci.fr

Select oligonucleotide configuration:
Oligo hybridized to its template Fork blocking Apex of an hairpin
Define the oligonucleotide sequence, typically in upper case. If you are specifying an RNA or LNA oligonucleotide, indicate bases of this type by upper case, use lower case for DNA base. If you want to introduce mismatches select the use template option and define the template otherwise leave template blank
Oligo sequence 5'to 3' (example ACGTGCT)- Use template Template 3'to 5' (only if Use template is checked)
5'--3' 3'--5'
Select oligonucleotide type (template is DNA in all cases):
DNA Oligo RNA/dna oligo LNA/dna oligo
Température
°C
[Na+ or K+]
(mM)
[Mg++]
(mM)
Force
(pN)
[Tris]
(mM)
[oligo]
(nM)
Select salt corection method for dinucleotide Free Energy calculation:
(1) 16.6 x log[Na+] (Schildkraut & Lifson (1965), Biopolymers 3: 195-208)
(2) 16.6 x log([Na+]/(1.0 + 0.7*[Na+])) (Wetmur (1991), Crit Rev Biochem Mol Biol 126: 227-259)
(3) 12.5 x log(Na+] (SantaLucia et al. (1996), Biochemistry 35: 3555-3562
(4) 11.7 x log[Na+] (SantaLucia (1998), Proc Natl Acad Sci USA 95: 1460-1465
(5) Correction for deltaS: 0.368 x (N-1) x ln[Na+] (SantaLucia (1998), Proc Natl Acad Sci USA 95: 1460-1465)
(6) (4.29(%GC)-3.95)x1e-5 x ln[Na+] + 9.40e-6 x ln[Na+]^2 (Owczarzy et al. (2004), Biochemistry 43: 3537-3554)
(7) Complex formula with decision tree and 7 empirical constants. Mg2+ is corrected for dNTPs binding (if present) (Owczarzy et al. (2008), Biochemistry 47: 5336-5353)
Display information: 0(default) give normal results, 1 give extra data 2 and more increasing information for debugging [0,10[





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