Enthalpies for RNA folding

Stacking enthalpies in kcal/mole

        Y                   Y                   Y                   Y
------------------  ------------------  ------------------  ------------------
 A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
------------------  ------------------  ------------------  ------------------
    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
       AX                  AX                  AX                  AX
       AY                  CY                  GY                  UY
    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
 .    .    .    .    .    .    .    .    .    .    .    .    .    .    .   -6.6
 .    .    .    .    .    .    .    .    .    .    .    .    .    .  -10.2  .
 .    .    .    .    .    .    .    .    .    .    .    .    .   -7.6  .   -3.6
 .    .    .    .    .    .    .    .    .    .    .    .   -5.7  .   -4.0  .
        Y                   Y                   Y                   Y
------------------  ------------------  ------------------  ------------------
 A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
------------------  ------------------  ------------------  ------------------
    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
       CX                  CX                  CX                  CX
       AY                  CY                  GY                  UY
    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
 .    .    .    .    .    .    .    .    .    .    .  -10.5  .    .    .    .
 .    .    .    .    .    .    .    .    .    .  -12.2  .    .    .    .    .
 .    .    .    .    .    .    .    .    .   -8.0  .   -1.8  .    .    .    .
 .    .    .    .    .    .    .    .   -7.6  .  -12.7  .    .    .    .    .
        Y                   Y                   Y                   Y
------------------  ------------------  ------------------  ------------------
 A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
------------------  ------------------  ------------------  ------------------
    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
       GX                  GX                  GX                  GX
       AY                  CY                  GY                  UY
    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
 .    .    .    .    .    .    .  -13.3  .    .    .    .    .    .    .   -3.6
 .    .    .    .    .    .  -14.2  .    .    .    .    .    .    .   -9.7  .
 .    .    .    .    .  -12.2  .  -5.3   .    .    .    .    .  -12.7  .   -3.6
 .    .    .    .  -10.2  .   -9.7  .    .    .    .    .   -4.0  .   -2.7  .
        Y                   Y                   Y                   Y
------------------  ------------------  ------------------  ------------------
 A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
------------------  ------------------  ------------------  ------------------
    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
       UX                  UX                  UX                  UX
       AY                  CY                  GY                  UY
    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
 .    .    .   -8.1  .    .    .    .    .    .    .   -4.0  .    .    .    .
 .    .  -13.3  .    .    .    .    .    .    .   -5.3  .    .    .    .    .
 .  -10.5  .   -4.0  .    .    .    .    .   -1.8  .   -5.3  .    .    .    .
-6.6  .   -3.6  .    .    .    .    .   -3.6  .   -3.6  .    .    .    .    .

Terminal mismatch and base pair enthalpies

        Y                   Y                   Y                   Y
------------------  ------------------  ------------------  ------------------
 A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
------------------  ------------------  ------------------  ------------------
    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
       AX                  AX                  AX                  AX
       AY                  CY                  GY                  UY
    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
 .    .    .   -4.0  .    .    .   -4.3  .    .    .   -3.8 -4.3 -6.0 -6.0 -6.0
 .    .   -5.2  .    .    .   -7.2  .    .    .   -7.1  .   -2.6 -2.4 -2.4 -2.4
 .  -10.3  .   -7.2  .   -5.2  .   -4.8  .   -9.4  .   -6.6 -3.4 -6.9 -6.9 -6.9
-4.3  .   -4.3  .   -2.6  .   -2.6  .   -3.4  .   -3.4  .   -3.3 -3.3 -3.3 -3.3
        Y                   Y                   Y                   Y
------------------  ------------------  ------------------  ------------------
 A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
------------------  ------------------  ------------------  ------------------
    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
       CX                  CX                  CX                  CX
       AY                  CY                  GY                  UY
    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
 .    .    .   -6.3  .    .    . -5.1 -10.3 -9.5 -10.3 -10.3 .    .    .   -1.4
 .    .   -8.8  .    .    .   -3.1  .   -5.2 -4.5 -5.2 -6.7  .    .   -5.0  .
 .   -9.5  .   -7.9  .   -4.5  .   -4.8 -9.4 -9.4 -9.4 -9.4  .   -7.4  .   -4.4
-6.0  .   -6.0  .   -2.4  .   -2.4  .   -8.1 -7.4 -8.1 -8.6 -3.3  .   -3.3  .
        Y                   Y                   Y                   Y
------------------  ------------------  ------------------  ------------------
 A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
------------------  ------------------  ------------------  ------------------
    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
       GX                  GX                  GX                  GX
       AY                  CY                  GY                  UY
    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
 .    .    .   -8.9 -5.2 -8.8 -5.6 -8.8  .    .    .   -8.9 -4.3 -6.0 -6.0 -6.0
 .    .   -5.6  .   -7.2 -3.1 -3.1 -3.9  .    .   -6.2  .   -2.6 -2.4 -2.4 -2.4
 .  -10.3  .   -9.6 -7.1 -7.4 -6.2 -7.4  .   -9.4  .   -9.2 -3.4 -6.9 -6.9 -6.9
-6.0  .   -6.0  .   -5.0 -5.0 -5.0 -5.7 -6.9  .   -6.9  .   -3.3 -3.3 -3.3 -3.3
        Y                   Y                   Y                   Y
------------------  ------------------  ------------------  ------------------
 A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
------------------  ------------------  ------------------  ------------------
    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
       UX                  UX                  UX                  UX
       AY                  CY                  GY                  UY
    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
-4.0 -6.3 -8.9 -5.9  .    .    .   -1.8 -7.2 -7.9 -9.6 -8.1  .    .    .    1.4
-4.3 -5.1 -2.0 -1.8  .    .   -3.9  .   -4.8 -4.8 -3.6 -4.8  .    .   -5.7  .
-3.8 -6.8 -8.9 -6.8  .   -6.7  .   -4.8 -6.6 -8.1 -9.2 -8.1  .   -8.6  .   -3.6
-2.8 -1.4 -2.8 -1.4 -2.4  .   -2.4  .   -5.5 -4.4 -5.5 -3.6 -3.3  .   -3.3  .

Single base stacking enthalpies

        X                   X                   X                   X
------------------  ------------------  ------------------  ------------------
 A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
------------------  ------------------  ------------------  ------------------
    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
       AX                  AX                  AX                  AX
       A                   C                   G                   U
    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
 .    .    .    .    .    .    .    .    .    .    .    .   -4.9 -0.9 -5.5 -2.3

        X                   X                   X                   X
------------------  ------------------  ------------------  ------------------
 A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
------------------  ------------------  ------------------  ------------------
    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
       CX                  CX                  CX                  CX
       A                   C                   G                   U
    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
 .    .    .    .    .    .    .    .   -9.0 -4.1 -8.6 -7.5  .    .    .    .

        X                   X                   X                   X
------------------  ------------------  ------------------  ------------------
 A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
------------------  ------------------  ------------------  ------------------
    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
       GX                  GX                  GX                  GX
       A                   C                   G                   U
    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
 .    .    .    .   -7.4 -2.8 -6.4 -3.6  .    .    .    .   -4.9 -0.9 -5.5 -2.3

        X                   X                   X                   X
------------------  ------------------  ------------------  ------------------
 A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
------------------  ------------------  ------------------  ------------------
    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
       UX                  UX                  UX                  UX
       A                   C                   G                   U
    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
-5.7 -0.7 -5.8 -2.2  .    .    .    .   -7.4 -2.4 -7.2 -4.9  .    .    .    .

        X                   X                   X                   X
------------------  ------------------  ------------------  ------------------
 A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
------------------  ------------------  ------------------  ------------------
    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
       A                   A                   A                   A
       AX                  CX                  GX                  UX
    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
 .    .    .    .    .    .    .    .    .    .    .    .   -0.5  6.9 -0.6 -0.6

        X                   X                   X                   X
------------------  ------------------  ------------------  ------------------
 A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
------------------  ------------------  ------------------  ------------------
    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
       C                   C                   C                   C
       AX                  CX                  GX                  UX
    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
 .    .    .    .    .    .    .    .   -1.6  0.7 -4.6 -0.4  .    .    .    .
 

        X                   X                   X                   X
------------------  ------------------  ------------------  ------------------
 A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
------------------  ------------------  ------------------  ------------------
    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
       G                   G                   G                   G
       AX                  CX                  GX                  UX
    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
 .    .    .    .   -2.4  3.3  0.8 -1.4  .    .    .    .   -1.5  5.1  0.1  1.0

        X                   X                   X                   X
------------------  ------------------  ------------------  ------------------
 A    C    G    U    A    C    G    U    A    C    G    U    A    C    G    U
------------------  ------------------  ------------------  ------------------
    5' --> 3'           5' --> 3'           5' --> 3'           5' --> 3'
       U                   U                   U                   U
       AX                  CX                  GX                  UX
    3' <-- 5'           3' <-- 5'           3' <-- 5'           3' <-- 5'
 1.6  2.2  0.7  3.1  .    .    .    .     1.6  2.2  0.7  3.1 .    .    .    .


Michael Zuker
Feb 6 2003