Table 3.

Relative Rank Comparison between RNA and DNA Experimental Nearest-Neighbor (NN) Free Energies and Computational E_NN Values.^a

RNA Nearest-Neighbor Energies (kcal/mol)
NN	ΔGNN,expb (Rank)	ENN,Calc-Hc (Rank)	ENN,Calc-H,Sold (Rank)	ENN,Calc-Mee (Rank)	ENN,Calc-Me,Solf (Rank)	Ref. 2a Rank
5’AU3’	−0.93	−7.68	−21.24	−19.04	−28.60	2
3’AU5’	(1)	(2)	(2)	(3)	(2.5)g
5’AU3’	−1.10	−10.59	−24.98	−18.61	−28.60	3
3’UA5’	(2)	(3)	(3)	(2)	(2.5)g
5’UA3’	−1.33	−4.78	−20.96	−11.46	−24.47	8
3’AU5’	(3)	(1)	(1)	(1)	(1)
5’CG3’	−2.08	−23.10	−31.64	−26.36	−32.56	4
3’UA5’	(4)	(6)	(7)	(4)	(5)
5’CG3’	−2.11	−21.52	−26.56	−26.57	−30.84	5
3’AU5’	(5)	(5)	(4)	(5)	(4)
5’AU3’	−2.24	−23.12	−32.13	−27.91	−39.12	6
3’CG5’	(6)	(7)	(8)	(7)	(8)
5’GC3’	−2.35	−20.19	−28.70	−27.85	−35.40	7
3’AU5’	(7)	(4)	(5)	(6)	(7)
5’CG3’	−2.36	−31.65	−30.80	−32.96	−33.72	9
3’GC5’	(8)	(8)	(6)	(9)	(6)
5’GC3’	−3.26	−32.21	−35.94	−34.02	−39.26	1
3’GC5’	(9)	(9)	(10)	(10)	(9)
5’GC3’	−3.42	−32.97	−34.50	−28.12	−45.34	10
3’CG5’	(10)	(10)	(9)	(8)	(10)
MADh	–	1.0	1.6	1.0	1.0	1.6
rsi	–	0.88	0.82	0.90	0.90	0.44
DNA Nearest-Neighbor Energies (kcal/mol)
NN	ΔGNN,expb (Rank)	ENN,Calc-Hc (Rank)	ENN,Calc-H,Sold (Rank)	ENN,Calc-Mee (Rank)	ENN,Calc-Me,Solf (Rank)	Ref. 2a Rank
5’TA3’	−0.60	−21.60	−31.96	−26.16	−36.39	7
3’AT5’	(1)	(2)	(1)	(2)	(1)
5’AT3’	−0.73	−18.58	−36.98	−22.40	−40.55	6
3’TA5’	(2)	(1)	(5)	(1)	(2)
5’AT3’	−1.02	−23.80	−36.92	−26.67	−44.76	5
3’AT5’	(3)	(3)	(4)	(3)	(10)
5’AT3’	−1.16	−27.13	−35.93	−33.82	−42.39	2
3’GC5’	(4)	(4)	(2)	(7)	(7)
5’CG3’	−1.38	−30.99	−36.59	−32.99	−41.53	3
3’AT5’	(5)	(6)	(3)	(6)	(5)
5’AT3’	−1.43	−30.97	−40.03	−30.10	−41.77	8
3’CG5’	(6)	(5)	(9)	(4)	(6)
5’GC3’	−1.46	−31.72	−38.95	−30.32	−41.51	4
3’AT5’	(7)	(7)	(7)	(5)	(4)
5’CG3’	−1.77	−34.92	−39.93	−37.77	−43.03	1
3’CG5’	(8)	(8)	(8)	(8)	(8)
5’CG3’	−2.09	−37.49	−38.01	−40.48	−40.84	9
3’GC5’	(9)	(9)	(6)	(10)	(3)
5’GC3’	−2.28	−43.35	−44.30	−39.92	−44.11	10
3’CG5’	(10)	(10)	(10)	(9)	(9)
MADh	–	0.4	1.4	1.2	2.0	2.8
rsi	–	0.98	0.78	0.87	0.37	0.24

^aThe rank for each approach is in parentheses under the E_NN values, with the least energetically favorable nearest-neighbor combination ranked 1 and the most favorable ranked 10.

^bΔG_NN,exp are the experimental nearest-neighbor energies from reference 6.

^cE_NN,Calc-H is the calculated nearest-neighbor energies where the sugar was replaced by an H atom and solvation is not considered.

^dE_{NN,Calc-H,Sol} is the calculated nearest-neighbor energies where the sugar was replaced by an H atom and solvation is considered via the PCM method.

^eE_NN,Calc-Me is the calculated nearest-neighbor energies where the sugar was replaced by a methyl group and solvation is not considered.

^fE_{NN,Calc-Me,Sol} is the calculated nearest-neighbor energies where the sugar was replaced by a methyl group and solvation is considered via the PCM method.

^gThe RNA E_{NN,Calc-Me,Sol} values are the exact same for the nearest-neighbor four nucleotide systems that would be ranked second and third, and thus they were each given a rank of 2.5.

^hMean absolute difference (MAD) is determined by taking the mean of the absolute difference between the NN four nucleotide system ranking of the calculated value and the ranking of the corresponding experimental value.

ⁱThe Spearman rank correlation coefficient (r_s) was determined as shown in Reference 15.