Table 1.

Experimental (Expt) and predicted (Pred) thermodynamics of oligonucleotides with inosine mismatches in 1 M NaCl

DNA duplex	$\Delta G_{37}^{°}$ (kcal/mol)		ΔH° (kcal/mol)		ΔS° (cal/K mol)		Tm (°C)
	Expt	Pred	Expt	Pred	Expt	Pred	Expt	Pred
I/C
CGCIGAACIGGC	−14.33	−14.31	−94.4	−89.9	−258.2	−243.7	64.9	66.4
CCGICTGTIGCG	−14.07	−13.90	−91.3	−89.5	−249.0	−243.8	64.9	64.8
CGAITCCAITCC	−12.73	−12.94	−91.5	−94.9	−254.0	−264.3	59.5	59.5
CGAITCCTIACC	−11.82	−12.11	−88.1	−87.5	−245.9	−243.1	56.8	58.1
CAAACAAAG4	−6.08	−6.12	−58.0	−62.4	−167.4	−181.5	34.6	35.0
CAAAIAAAG4	−6.51	−6.32	−66.0	−61.5	−191.8	−177.9	36.9	35.9
CGCIAATTCGCG24	−12.60	−12.77	−77.2	−84.2	−208.3	−230.3	63.5	63.7
GTGICTTCIGTC	−11.43	−11.20	−80.4	−82.7	−222.4	−230.5	57.1	55.6
GCATIATCG	−8.52	−8.01	−68.6	−62.1	−193.7	−174.4	46.3	44.6
CGGITCAGITGC	−13.91	−13.27	−97.2	−92.4	−268.5	−255.1	62.5	61.4
GAAICCTAICCG	−12.18	−12.11	−86.1	−85.3	−238.3	−236.0	58.8	58.7
GAAGIACGIAGG	−10.75	−11.25	−78.1	−81.9	−217.2	−227.8	54.7	56.0
CCAIGTGAICCG	−13.74	−13.40	−94.3	−91.1	−259.6	−250.5	62.7	62.3
CCTIGTGTICCG	−12.61	−12.37	−86.2	−84.6	−237.3	−232.9	60.5	60.0
CGTICCATIGGG	−11.82	−12.37	−81.2	−83.6	−223.7	−229.7	58.6	60.3
CCAICTGTICCG	−12.83	−13.07	−82.3	−84.4	−224.0	−230.0	62.7	63.1
CCAIGTGTIGCG	−13.07	−13.25	−88.7	−93.4	−243.8	−258.4	61.7	61.0
CGCITCACITGG	−13.97	−13.99	−92.2	−90.2	−252.2	−245.7	64.2	65.0
I/A
CGCIGAACIGGC	−12.49	−12.17	−76.2	−71.3	−205.4	−190.6	63.3	63.6
CCGICAAGICCG	−15.26	−14.93	−94.3	−92.0	−254.8	−248.5	68.6	68.2
CCGICTGTIGCG	−14.50	−13.88	−95.1	−89.3	−259.9	−243.2	65.4	64.8
CGTIACCTIACC	−8.86	−9.07	−67.8	−68.8	−190.0	−192.6	48.0	48.9
CGAITCCAITCC	−10.13	−10.02	−78.4	−77.5	−220.1	−217.6	51.9	51.6
CGAITCCTIACC	−9.48	−9.39	−77.1	−72.7	−218.0	−204.1	49.3	49.7
CAAAAAAAG4	−4.61	−4.56	−48.0	−51.8	−139.9	−152.3	25.1	25.6
CAAAIAAAG4	−5.28	−5.16	−63.0	−57.3	−186.1	−168.1	31.0	29.8
CGCIAATTAGCG24	−9.45	−9.43	−54.7	−61.0	−145.9	−166.3	54.5	54.9
GCATIATCG	−7.00	−6.75	−57.5	−56.0	−162.8	−158.8	39.6	38.2
GCACIGTCG	−9.22	−9.03	−61.8	−58.1	−169.5	−158.2	51.1	50.9
GCAGIGTCG	−9.73	−9.93	−64.3	−67.9	−175.9	−186.9	53.2	53.3
GCAAICTCG	−9.13	−9.32	−64.3	−68.5	−177.9	−190.8	50.1	50.2
GAAGIACGIAGG	−10.35	−10.59	−75.1	−76.7	−208.8	−213.2	53.6	54.3
CCAIGTGAICCG	−12.61	−12.65	−88.9	−91.2	−246.0	−253.3	59.8	59.3
CCTIGTGTICCG	−11.19	−11.42	−80.5	−80.9	−223.5	−224.0	56.1	57.0
CCAICTGTICCG	−12.47	−12.59	−86.2	−86.5	−237.7	−238.3	60.0	60.4
CCAIGTGTIGCG	−11.85	−12.03	−83.2	−87.7	−230.0	−244.0	58.2	57.8
CGCITCACITGG	−9.75	−10.05	−57.1	−58.0	−152.7	−154.6	55.5	57.0
I/T
CGCIGAACIGGC	−10.17	−9.97	−69.9	−64.3	−192.6	−175.2	54.0	54.5
CCGICAAGICCG	−11.10	−11.25	−80.9	−76.8	−225.1	−211.3	55.6	57.3
CGTIACCTIACC	−7.43	−7.69	−76.8	−74.0	−223.7	−213.8	40.7	41.9
CGAITCCAITCC	−7.55	−7.38	−66.9	−69.7	−191.4	−201.0	41.8	40.8
CGAITCCTIACC	−7.26	−7.38	−68.5	−71.4	−197.5	−206.4	40.3	40.7
CAAATAAAG4	−4.04	−4.19	−50.0	−59.8	−148.2	−179.3	22.3	25.3
CAAAIAAAG4	−3.82	−3.52	−58.0	−48.0	−174.7	−143.4	23.2	18.7
CGCIAATTTGCG24	−8.66	−8.75	−58.9	−67.2	−162.0	−188.4	48.6	49.7
CCAITTGCIACG	−8.11	−8.42	−69.0	−68.4	−196.3	−193.4	44.3	45.8
GTGICTTCIGTC	−7.96	−7.83	−55.4	−65.9	−153.0	−187.2	45.2	43.2
CCAITGGCIGCG	−9.79	−10.19	−73.5	−69.0	−205.4	−189.7	51.4	54.4
GCATIATCG	−6.30	−6.06	−61.4	−58.6	−177.7	−169.4	35.8	34.5
GCACIGTCG	−7.58	−7.93	−47.9	−54.6	−130.0	−150.5	43.9	45.2
GCAGIGTCG	−7.88	−7.70	−64.1	−56.5	−181.3	−157.3	43.7	43.6
GAAGIACGIAGG	−7.53	−7.65	−63.8	−67.1	−181.4	−191.7	41.9	42.3
CCTIGTGTICCG	−8.93	−8.91	−74.9	−76.7	−212.7	−218.6	47.3	46.9
CCAICTGTICCG	−9.89	−9.52	−74.7	−74.2	−209.0	−208.6	51.6	50.0
CCAIGTGTIGCG	−9.89	−8.18	−82.5	−67.8	−234.1	−192.3	50.2	44.7
CGAICCAAIGGG	−8.61	−8.19	−71.2	−62.2	−201.8	−174.2	46.3	45.5
CGCITCACITGG	−10.41	−10.01	−84.8	−75.0	−239.9	−209.5	51.9	52.1
I/G
CCGICAAGICCG	−11.72	−11.47	−78.4	−78.6	−215.0	−216.4	59.0	57.8
CCGICTGTIGCG	−10.44	−10.17	−87.8	−68.3	−249.4	−187.4	51.5	54.5
CGTIACCTIACC	−6.17	−6.57	−60.8	−61.2	−176.1	−176.1	35.2	37.2
CGAITCCAITCC	−8.05	−7.90	−71.8	−69.1	−205.5	−197.3	43.7	43.3
CGAITCCTIACC	−6.94	−7.08	−65.0	−64.7	−187.2	−185.8	39.0	39.7
CAAAGAAAG4	−3.83	−3.36	−52.0	−49.5	−155.3	−148.8	21.7	18.3
CAAAIAAAG4	−4.27	−4.05	−57.0	−51.6	−170.0	−153.3	25.2	22.8
CGCIAATTGGCG24	−6.47	−6.97	−40.8	−47.4	−110.7	−130.4	36.5	42.8
GTGICTTCIGTC	−7.77	−7.08	−52.9	−53.0	−145.5	−148.1	44.4	40.3
GCATIATCG	−5.58	−5.50	−54.9	−52.2	−159.0	−150.6	31.7	31.0
GCACIGTCG	−7.25	−7.07	−49.2	−40.8	−135.3	−108.8	41.6	41.2
CGGITCCGITCC	−8.30	−9.40	−58.4	−63.4	−161.5	−174.1	46.7	51.7
GAAGIACGIAGG	−7.43	−7.15	−59.0	−58.7	−166.3	−166.2	41.8	40.3
CCAIGTGAICCG	−9.44	−9.69	−69.9	−71.6	−194.9	−199.6	50.5	51.3
CCTIGTGTICCG	−7.86	−8.18	−61.9	−65.1	−174.2	−183.5	43.8	45.1
CCAICTGTICCG	−9.95	−10.21	−80.0	−81.6	−225.9	−230.2	50.8	51.6
CCAIGTGTIGCG	−7.97	−8.21	−49.2	−57.2	−132.9	−158.0	46.3	46.4
I/I
CGCIGAACIGGC	−8.81	−8.83	−61.0	−57.3	−168.3	−156.3	49.0	50.0
CCGICAAGICCG	−10.39	−10.15	−66.9	−63.2	−182.2	−171.0	56.0	55.8
CGAITCCAITCC	−7.53	−7.64	−74.3	−72.7	−215.3	−209.8	41.2	41.8
CGAITCCTIACC	−6.37	−6.79	−65.1	−65.4	−189.4	−189.0	36.2	38.2
CAAAIAAAG4	−4.04	−3.56	−47.0	−50.9	−138.5	−152.6	21.4	19.9
GTGICTTCIGTC	−7.19	−6.71	−56.4	−55.6	−158.7	−157.6	40.7	38.0
CGGICTTTIAGG	−6.32	−7.01	−51.2	−58.6	−144.7	−166.3	35.7	39.6
GCATIATCG	−5.51	−5.34	−56.9	−51.1	−165.7	−147.5	31.5	29.9
GCACIGTCG	−7.13	−7.36	−47.9	−51.1	−131.5	−141.0	40.9	42.1
GAAGIACGIAGG	−6.95	−6.91	−59.5	−59.3	−169.4	−168.9	39.2	39.0
Non-two state behavior or outliers in nearest neighbor determination
I/C
CCGICAAGICCG	−10.69	−13.65	−60.4	−84.8	−160.4	−229.4	59.7	65.8
CCAITGGCIGCG	−12.24	−15.14	−74.1	−94.5	−199.6	−255.2	62.7	68.9
GCACIGTCG	−11.84	−10.10	−79.1	−67.4	−217.0	−184.6	59.1	54.6
CGAICCAAIGGG	−11.33	−13.35	−70.2	−90.1	−189.7	−247.1	59.9	62.8
I/A
CGAICCAAIGGG	−10.95	−12.60	−73.2	−90.2	−200.7	−249.9	56.9	59.7
CGTICCATIGGG	−10.02	−11.42	−69.1	−79.9	−190.4	−220.7	53.6	57.3
I/T
CCGICTGTIGCG	−8.30	−10.59	−49.6	−77.7	−133.2	−216.2	48.4	54.3
CGTIGCCTIGCG	−7.78	−9.55	−48.7	−75.0	−131.8	−210.9	45.5	50.2
CCAIGTGAICCG	−9.11	−8.24	−92.3	−63.2	−267.7	−177.3	46.5	45.5
I/G
CGTIGCCTIGCC	−6.64	−9.97	−30.8	−60.4	−77.8	−162.7	38.4	55.5
CGAICCAAIGGG	−7.33	−9.64	−42.4	−58.8	−113.0	−163.3	43.1	45.8
CGTICCATIGGG	−6.38	−8.18	−37.8	−56.5	−101.6	−156.1	35.0	45.8
I/I
CCGICTGTIGCG	−13.60	−9.64	−86.8	−63.1	−236.0	−172.4	64.5	53.0

Underlined residues are paired with inosine. The opposing strands (not shown) are complementary except across from inosine.