Free energy estimation of short DNA duplex hybridizations

BMC Bioinformatics

Table 1 Summary of features for the data sets used in this study

Set	Num. duplexes	Seq. len.	T[C]	[Na]⁺ [M]	Seq. conc. [M]
Aboul-ela et al. [32]	34	16	25, 50	1	[11e-6,440e-6]
Allawi et al.-1 [37]	24	9 - 12	37	1	1e-4
Allawi et al.-2 [20]	28	9 - 14	37	1	1e-4
Allawi et al.-3 [21]	22	9 - 14	37	1	1e-4
Bommarito et al. [43]	37	8 - 9	37	1	n.r.
Breslauer et al. [26]	12	6 - 16	25	1	n.r.
Clark et al. [44]	1	24	37	0.15	2.5e-6
Doktycz et al. [19]	140	8	25	1	2e-6
Gelfand et al. [45]	4	13	25	1	5e-5
LeBlanc et al. [46]	7	10 - 11	25	1	5e-5
Leonard et al. [22]	5	12	25	1	4e-4
Lesnik et al. [39]	14	8 - 21	37	0.1	4e-6
Li et al. [23]	12	8 - 10	25	1	6.1e-6
Nakano et al. [40]	21	6 - 14	37	0.1	8e-6
Petruska et al.-1 [47]	4	9	37	n.r.	n.r.
Petruska et al.-2 [36]	2	30	37	0.17	1e-4
Peyret et al. [48]	52	9 - 12	37	1	1e-4
Pirrung et al. [49]	2	25	25	0.1	1e-6
Plum et al. [50]	2	13	25	1	6e-6
Ratmeyer et al. [51]	2	12	37	1	6e-6
SantaLucia et al.-1 [29]	23	4 - 16	37	1	4e-4
SantaLucia et al.-2 [29]	10	12	24.85	1	5e-6
Sugimoto et al.-1 [30]	50	5 - 14	37	1	5e-6
Sugimoto et al.-2 [38]	1	8	37	n.r.	1e-4
Sugimoto et al.-3 [52]	8	6 - 8	37	1	n.r.
Tanaka et al. [34]	126	12 - 25	37	1	5e-5
Tibanyenda et al. [33]	3	16	24.85	1	17.5e-6
Wilson et al. [35]	3	11	25	0.4	n.r.
Wu et al. [53]	48	5 - 11	25, 37	1	1e-4
TOTAL:	695

Each data set has the following characteristics: the number of sequence pairs (Num. duplexes), the length of the sequences (Seq. len), the experimental temperature measured in degrees Celsius for estimating free energies (T), the sodium concentration measured in molar units ([Na]⁺)and the sequence concentration (Seq. conc). The set of 695 DNA duplexes contains: (i) 143 perfect match free energies measured at a temperature of 37°C and a sodium concentration of 1 M, (ii) 197 perfect match duplexes measured at a temperature of 25°C and a sodium concentration of 1 M, (iii) 7 perfect match duplexes measured at a temperature of 50°C and a sodium concentration of 1 M, and (iv) 348 duplexes with mismatches measured at various temperatures and sodium concentrations. Note: n.r. denotes values that have not been reported in the original documents.

ISSN: 1471-2105