. 2007 Jun 12;35(12):4055–4063. doi: 10.1093/nar/gkm421

Table 3.

Effects of mismatches on thermodynamic parameters of helix formation^a

LNA-2′OMe RNA (5′–3′)	RNA (5′–3′)	−ΔG°₃₇ (kcal/mol)	T_M^b(°C)	ΔΔG°₃₇^c (kcal/mol)
A. Effects of D^M-A, D^L-A, A^M-A, and A^L-A mismatches at internal positions.
A^MC^MU^MD^MC^MC^MA^M	UGGAAGU	3.31 ± 1.60	18.4	4.78
A^MC^MU^MD^LC^MC^MA^M	UGGAAGU	5.09 ± 0.45	27.2	4.36
A^MC^MU^MA^MU^MC^MA^M	UGAAAGU	(4.64 ± 1.18)	(9.8)	(1.18)
A^MC^MU^MD^MU^MC^MA^M	UGAAAGU	4.25 ± 0.30	16.7	2.67
A^MC^MU^MA^LU^MC^MA^M	UGAAAGU	(3.95 ± 2.75)	(11.6)	(3.07)
A^MC^MU^MD^LU^MC^MA^M	UGAAAGU	2.99 ± 0.39	19.1	5.21
B. Effects of D^M-C, D^L-C, A^M-C, and A^L-C mismatches at internal positions.
A^MC^MU^MA^MC^MC^MA^M	UGGCAGU	(3.92 ± 0.27)	(20.2)	(3.21)
A^MC^MU^MD^MC^MC^MA^M	UGGCAGU	(6.52 ± 0.02)	(36.9)	(1.57)
A^MC^MU^MA^LC^MC^MA^M	UGGCAGU	5.15 ± 0.30	27.7	3.20
A^MC^MU^MD^LC^MC^MA^M	UGGCAGU	6.46 ± 0.11	36.5	2.99
A^MC^MU^MA^MU^MC^MA^M	UGACAGU	(3.38 ± 0.66)	(14.8)	(3.64)
A^MC^MU^MD^MU^MC^MA^M	UGACAGU	4.67 ± 0.15	27.0	2.25
A^MC^MU^MA^LU^MC^MA^M	UGACAGU	3.08 ± 0.14	15.9	3.94
A^MC^MU^MD^LU^MC^MA^M	UGACAGU	5.17 ± 0.03	29.6	3.03
C. Effects of D^M-G, D^L-G, A^M-G, and A^L-G mismatches at internal and terminal positions.
A^MC^MU^MD^MC^MC^MA^M	UGGGAGU	3.95 ± 0.45	21.6	4.14
A^MC^MU^MD^LC^MC^MA^M	UGGGAGU	5.21 ± 0.14	27.8	4.24
A^MC^MU^MA^MU^MC^MA^M	UGAGAGU	3.13 ± 0.54	12.1	2.69
A^MC^MU^MD^MU^MC^MA^M	UGAGAGU	3.38 ± 0.03	18.2	3.54
A^MC^MU^MA^LU^MC^MA^M	UGAGAGU	2.81 ± 1.50	16.9	4.21
A^MC^MU^MD^LU^MC^MA^M	UGAGAGU	3.10 ± 0.29	19.7	5.10
G^MA^MC^MA^MA^MA^MC^MA^MG^M	CUGUGUGUC	5.02 ± 0.05	28.9	3.28
G^MA^MC^MA^MD^MA^MC^MA^MG^M	CUGUGUGUC	(5.61 ± 0.06)	(31.7)	(3.90)
G^MA^MC^MA^MA^LA^MC^MA^MG^M	CUGUGUGUC	5.51 ± 0.15	31.5	3.83
G^MA^MC^MA^MD^LA^MC^MA^MG^M	CUGUGUGUC	5.78 ± 0.30	33.2	5.14
A^MC^MC^MA^MA^MC^MA^M	UGUGGGU	(1.32 ± 0.25)	(12.0)	(5.37)
A^MC^MC^MD^MA^MC^MA^M	UGUGGGU	4.46 ± 0.55	15.1	2.99
A^MC^MC^MA^LA^MC^MA^M	UGUGGGU	(3.19 ± 0.36)	(17.0)	(4.71)
A^MC^MC^MD^LA^MC^MA^M	UGUGGGU	4.82 ± 0.02	25.0	3.91
A^MC^MG^MA^MA^MC^MA^M	UGUGCGU	4.28 ± 0.52	21.2	2.09
A^MC^MG^MD^MA^MC^MA^M	UGUGCGU	3.03 ± 0.78	17.2	4.04
A^MC^MG^MA^LA^MC^MA^M	UGUGCGU	(4.80 ± 0.59)	(21.0)	(2.56)
A^MC^MG^MD^LA^MC^MA^M	UGUGCGU	3.54 ± 0.50	19.3	4.80
A^MC^MU^MA^MA^MC^MA^M	UGUGAGU	3.22 ± 0.53	11.8	2.01
A^MC^MU^MD^MA^MC^MA^M	UGUGAGU	3.01 ± 0.63	16.1	3.22
A^MC^MU^MA^LA^MC^MA^M	UGUGAGU	3.36 ± 0.33	16.0	3.29
A^MC^MU^MD^LA^MC^MA^M	UGUGAGU	(2.03 ± 0.78)	(13.5)	(5.74)
A^MC^MU^MA^MC^MC^MA^M	UGGUAGG	6.76 ± 0.02	38.6	0.37
D^MC^MU^MA^MC^MC^MA^M	UGGUAGG	6.87 ± 0.03	39.4	0.78
A^LC^MU^MA^MC^MC^MA^M	UGGUAGG	(7.14 ± 0.02)	(41.3)	(0.58)
D^LC^MU^MA^MC^MC^MA^M	UGGUAGG	7.17 ± 0.11	41.0	0.98
A^MC^MU^MA^MC^MC^MA^M	GGGUAGU	6.81 ± 0.02	39.1	0.32
A^MC^MU^MA^MC^MC^MD^M	GGGUAGU	6.85 ± 0.17	39.2	0.67
A^MC^MU^MA^MC^MC^MA^L	GGGUAGU	(7.95 ± 0.01)	(46.5)	(0.48)
A^MC^MU^MA^MC^MC^MD^L	GGGUAGU	8.01 ± 0.09	47.3	0.56
D. Effects of D^M-G, D^L-G, A^M-G, and A^L-G mismatches in the presence of D^M-U and D^L-U base pairs.
D^MC^MU^MD^MC^MC^MD^M	UGGGAGU	4.70±0.08	25.7	4.03
D^LC^MU^MD^LC^MC^MD^L	UGGGAGU	7.25±0.03	41.8	4.59
D^MC^MU^MA^MC^LC^MA^M	UGGUAGG	8.14±0.03	47.2	0.70
D^MC^MU^MA^MC^LC^MA^M	UGGUAGG	8.54±0.02	49.5	0.99

^aSolutions are 100 mM NaCl, 20 mM sodium cacodylate and 0.5 mM Na₂EDTA, pH 7. Values are form T_M⁻¹ vs log (C_T/4) plots. Values in parentheses are from non-two state melts.

^bCalculated for 10⁻⁴ M oligonucleotide strand concentration.

^cDifference compared with duplex formation when bold A or D is paired with U.