Table 2.

Comparison between experimental thermodynamic parameters measured in 20% PEG 200 and predicted parameters using either the standard or derived 20% PEG 200 nearest neighbor parameters.

Duplexa	Length	FGC	Predicted Tm in H2Ob (°C)	T m in PEG (°C)	ΔTmc (°C)	Predicted ΔG°37 in H2Ob (kcal/mol)	ΔG°37 in PEG (kcal/mol)	ΔΔG°37c (kcal/mol)	PEG NN ΔG°37d (kcal/mol)	ΔΔG°37e (kcal/mol)
5′-UCAUGA-3′	6	0.33	25.5	22.9	-2.6	-4.60	-3.00	1.60	-3.26	0.26
5′-ACUGCG-3′	6	0.33	44.2	38.1	-6.1	-7.67	-6.73	0.94	-6.76	0.03
5′-AUGGAC-3′	6	0.50	36.9	33.2	-3.7	-6.52	-5.94	0.58	-5.91	-0.03
5′-GCGAUA-3′	6	0.50	33.9	30.0	-3.9	-6.02	-5.32	0.70	-5.30	-0.02
5′-GCUAUG-3′	6	0.50	31.8	30.0	-1.8	-5.95	-5.18	0.77	-5.25	0.07
5′-ACCGGU-3′	6	0.67	53.7	45.6	-8.1	-7.94	-7.12	0.82	-7.16	0.04
5′-AGCGCU-3′	6	0.67	53.5	43.6	-9.9	-7.94	-6.80	1.14	-6.74	-0.06
5′-CACGUG-3′	6	0.67	42.4	37.8	-4.6	-6.54	-5.81	0.73	-5.42	-0.39
5′-CAGCUG-3′	6	0.67	46.6	38.0	-8.6	-7.28	-5.85	1.43	-6.03	0.18
5′-CCAUGG-3′	6	0.67	46.6	41.4	-5.2	-7.32	-6.52	0.80	-6.30	-0.22
5′-CCUAGG-3′	6	0.67	48.1	44.2	-3.9	-7.49	-6.92	0.57	-6.79	-0.13
5′-CUGCAG-3′	6	0.67	46.6	40.0	-6.6	-7.28	-6.19	1.09	-6.03	-0.16
5′-GACGUC-3′	6	0.67	45.1	42.1	-3.0	-7.02	-6.56	0.46	-6.32	-0.24
5′-GAGCUC-3′	6	0.67	49.0	43.7	-5.3	-7.76	-6.90	0.86	-6.93	0.03
5′-GCAUGC-3′	6	0.67	48.3	43.3	-5.0	-7.64	-6.85	0.79	-6.52	-0.33
5′-CGCGCG-3′	6	1.0	58.5	49.7	-8.8	-9.40	-7.72	1.68	-8.14	0.42
5′-CGGCCG-3′	6	1.0	62.2	54.0	-8.2	-10.14	-8.49	1.65	-9.17	0.68
5′-GCCGGC-3′	6	1.0	66.6	60.1	-6.5	-11.20	-10.23	0.97	-10.42	0.19
5′-GCGCGC-3′	6	1.0	63.1	54.8	-8.3	-10.46	-9.03	1.43	-9.39	0.36
5′-UAUAUAUA-3′	8	0.0	25.3	21.1	-4.2	-3.20	-2.30	0.90	-2.42	0.12
5′-UAAUAUUA-3′	8	0.0	17.0	18.2	1.2	-2.63	-1.88	0.75	-1.69	-0.19
5′-AACUAGUU-3′	8	0.25	43.5	38.9	-4.6	-6.41	-6.02	0.39	-5.51	-0.51
5′-ACUAUAGU-3′	8	0.25	46.2	37.7	-8.5	-6.98	-5.82	1.16	-6.24	0.42
5′-AGAUAUCU-3′	8	0.25	45.6	37.2	-8.4	-6.97	-5.72	1.25	-6.01	0.29
5′-GAUAUAUC-3′	8	0.25	39.4	36.1	-3.3	-6.14	-5.48	0.66	-5.52	0.04
5′-GAAUAUUC-3′	8	0.25	36.6	32.6	-4.0	-5.57	-4.72	0.85	-4.79	0.07
5′-AACCGGUU-3′	8	0.50	59.8	54.1	-5.7	-9.80	-8.98	0.82	-8.92	-0.06
5′-ACUGCAGU-3′	8	0.50	63.2	52.1	-11.1	-10.86	-9.19	1.67	-9.65	0.46
5′-GCAAUUGC-3′	8	0.50	55.0	46.9	-8.1	-9.50	-8.09	1.41	-8.28	0.19
5′-GAACGUUC-3′	8	0.50	52.5	46.0	-6.5	-8.88	-7.76	1.12	-8.08	0.32
5′-AGCGCGCU-3′	8	0.75	74.2	64.7	-9.5	-13.72	-12.45	1.27	-12.37	-0.08
5′-AGCCGGCU-3′	8	0.75	77.0	69.7	-7.3	-14.46	-13.86	0.60	-13.40	-0.46
5′-GCGAUCGC-3′	8	0.75	67.1	60.0	-7.1	-12.84	-12.38	0.46	-11.80	-0.58
5′-GACCGGUC-3′	8	0.75	70.3	64.8	-5.5	-13.54	-12.93	0.61	-12.98	0.05
5′-UUAUCGAUAA-3′f	10	0.20	49.0	43.4	-5.6	-9.21	-6.94	2.27	-7.24	0.30
5′-UAUCGAUA-3′f	8	0.25	41.4	37.7	-3.7	-7.10	-5.83	1.27	-5.48	-0.35
5′-AGCGCU-3′f	6	0.67	51.6	42.6	-9.0	-7.94	-6.60	1.34	-6.74	0.14
5′-CGCGCG-3′f	6	1.0	58.5	50.9	-7.6	-9.40	-8.55	0.85	-8.14	-0.41
Average					-6.0			1.02		0.23g

^aAll listed strands are paired with their Watson–Crick complement.

^bValues were predicted using the standard nearest neighbor model (7).

^cDifference between values predicted using the standard nearest neighbor model and experimental values for duplexes in 20% PEG 200 (7).

^dΔG°₃₇ values predicted using the derived parameters for a 20% PEG 200 solution.

^eDifference between experimental ΔG°₃₇ values in 20% PEG 200 and values predicted by the derived model for 20% PEG 200.

^fThermodynamic data for these strands are from (20).

^gAverage of the absolute value of each ΔG°₃₇ value.