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Oligo Calculation Tool

This tool calculates melting temperature (Tm), molecular weight (MW), Millimolar Extinction Coeff (OD/μmol, μg/OD) for oligos

Oligo Sequence:

Oligo Concentration (ng/μl): or (μM):

Salt Concentraion (M):




Calculation Methods:


Molecular Weight (Free Acid) = #A × 313.21 + #G × 329.21 + #C × 289.18 + #T × 304.2 + #M × 301.2+#R × 321.21 + #W × 308.71 + #S × 309.2 +#Y × 296.69 + #K × 316.71 + #V × 310.53 +#H × 302.2 + #D × 315.54 + #B × 307.53 + #N × 308.95 + #I × 314.19 +#U × 290.17 - 61.96

Millimolar Extinction Coefficient (OD/μmol) = ∑εnearest-neighbor − ∑εindividual

%GC=(#G + #C + #S + 0.5 × #M + 0.5 × #R + 0.5 × #Y + 0.5 × #K + 0.667 × #V + 0.333 × #H + 0.333 × #D + 0.667 × #B + 0.5 × #N) / Length

μg/OD = Molecular Weight (Free Acid) / Extinction Coefficient

Tm Calculation
 •Length ≤ 20 : Tmmin = 4 × (#G + #C + #S) + 2 × (#A + #T + #U + #I + #M + #R + #W + #Y + #K
+ #V + #H + #D + #B + #N)
Tmmax =4 × (#G + #C + #S + #M + #R + #Y + #K + #V + #H + #D + #B + #N)
+ 2 × (#A + #T + #U + #I + #W)
 •Length > 20 : Tm = 0.41 × (%GC) - 675 / Length + 81.5

*Breslauer KJ, Frank R, Blocker H, Marky LA. Proc. Natl. Acad. Sci. USA, 83:3746-3750.
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