. Author manuscript; available in PMC: 2011 Feb 1.

Published in final edited form as: Biochemistry. 2009 May 26;48(20):4377–4387. doi: 10.1021/bi9002056

Table 5.

Predicted increments for hydrogen bonds in RNA/RNA duplexes calculated by MMPBSA and MMGBSA (in parentheses) methods^a.

Duplex	Measured^b	Predicted^c	Measured^b	Predicted^c
Duplex	ΔH° (kcal/mol)	ΔH° (kcal/mol)	ΔΔH° (kcal/mol)	ΔΔH° (kcal/mol)

5'ACUCACA	−56.3±2.3	−56.7	0	0
3'UGAGUGU	−56.3±2.3	(−48.8)	0	(0)

5'ACUCACA	−45.2±1.9	−51.8	−11.1±3.0	−4.9
3'UGAIUGU	−45.2±1.9	(−44.0)	−11.1±3.0	(−4.8)

5'ACUDACA	−51.0±0.5	−57.0	0	0
3'UGAUUGU	−51.0±0.5	(−47.8)	0	(0)

5'ACUAACA	−49.5±1.8	−52.9	−1.5±1.9	−4.1
3'UGAUUGU	−49.5±1.8	(−44.5)	−1.5±1.9	(−3.3)

MMPBSA is Molecular Mechanics Poisson Boltzman Surface Area and MMGBSA is Molecular Mechanics Generalized Born Surface Area.

Measurements are for 2'-O-methyl RNA/RNA duplexes (Table 4 and Supporting Information).

Predictions are for RNA/RNA duplexes. Standard error of mean is 0.07 kcal/mol.