Download manual - Oligo Software

OLIGO calculates free energy (∆G) values according to the equation:
∆G = ∆H - T∆S
(IX)
Where H, S, and T are the enthalpy, entropy, and temperature, respectively. The
default temperature used by OLIGO is 25°C.
Table 1. Free energy values of a nearest neighbor nucleotide used by OLIGO (in
kcal/mol X (-1); from Ref. 1 and 2; adjusted to 25°).
Second Nucleotide dA
→
First Nucleotide ↓
dA or A
dC or C
dG or G
dT1 or U
Initiation2
1
2
1.9
1.9
1.6
1.0
dC
dG
dT
A
C
G
U
1.3
3.1
3.1
1.6
1.6
3.6
3.1
1.9
1.5
1.6
1.3
1.9
1.1
2.2
2.7
1.4
2.4
3.3
3.8
2.6
1.9
2.2
3.3
2.2
1.1
1.9
2.4
1.1
-3
-5
Not listed nucleotides are treated as dT.
Initiation ∆G value is not included OLIGO ∆G calculations.
Although Oligo does not calculate Tms of PNA, you may find important
guidelines in (7, 21).
For example, pentamer d(AACTG) ∆G is:
∆GAACTG = ∆G(AA) + ∆G(AC) + ∆G(CT) + ∆G(TG) = -(1.9+1.3+1.6+1.9) = -6.7
kcal/mol
For full value of ∆G, you’d need to add the initiation values (for both Gs at the
ends, and the dangling end values, if present.
Table 2. Free energy values of dangling ends (from ref. 27)
Explanation how to read the table:
171