Table 2. Interaction energies, in kcal/mol, of the modified base pairs, of the corresponding unmodified base pair, and of the modification energy E_mod.

Parent Base	#	Base Pair	E (modified)	E (unmodified)	Emod
Adenine	1	m1A:A tHW	−19.74	−12.24	−7.50
	2	m1A:U tHW(w)	−31.13	−20.11	−11.02
	3	m1A:U tHW	−21.75	−15.72	−6.03
	4	m1A: m5U tHW	−22.54	−15.79	−6.35
	5	m66A:G tS(W)S(r)	−18.46	−17.24	−1.22
Guanine	6	m1G:C tHH1	−10.67	−10.38	−0.29
	7	m2G:U cWW	−15.77	−15.59	−0.18
	8	m2G:C cWW	−27.90	−27.02	−0.88
	9	m2G:C cWW1	−17.60	−27.02	9.42
	10	m22G:A cWW	−16.09	−17.19	1.10
	11	m7G:C cWW	−37.17	−27.02	−10.15
	12	m7G:G tWH	−34.55	−19.43	−15.12
Cytosine	13	m5C:G cWW	−27.68	−27.02	−0.66
	14	m5C:G tWW	−17.96	−17.49	−0.47
Uracil	4	m5U: m1A tWH	−22.54	−21.74	−0.80
	15	m5U:A tWH	−15.80	−15.72	−0.08
	16	m5U:G cWW	−16.00	−15.59	−0.41
	17	m5U:G tWH1	−9.83	−10.08	0.25
	18	s4U:A tWH	−16.11	−15.72	−0.39
	19	H2U:U tWW	−11.86	−11.84	−0.02
	20	H2U:G cHS1	−8.55	−8.29	−0.26
	21	H2U:G tWS	−13.72	−13.66	−0.06
	22	Ψ:A cWW	−14.54	−14.93	0.39
	23	Ψ:A cHW	−16.00	−9.09	−6.91
	24	Ψ:U tWW	−12.35	−12.77	0.42
	25	Ψ:G tBsW	−12.85	−13.23	0.38
	26	Ψ: G cWW	−16.82	−15.59	−1.23
	27	Ψ:C cS(r)W	−19.44	−21.03	1.59
Non-natural	1’	5BrC:G cWW	−26.59	−27.02	0.43
	2’	5BrU:A cWW	−15.35	−14.93	−0.42
	3’	5BrU:G cWW	−15.96	−15.59	−0.37
	4’	5BrU:5BrU cWW	−12.63	−12.19	−0.44
	5’	5BrU:A cWH	−16.41	−15.98	−0.43
	6’	5BrU:A cS(r)H	−17.31	−17.27	−0.04
	7’	5BrU:A cW(r)S	−17.89	−17.93	0.04
	8’	5IU:A cWW	−15.35	−14.93	−0.42
	9’	5IU:G cWW	−15.91	−15.59	−0.32a