Obesity-related known and candidate SNP markers can significantly change affinity of TATA-binding protein for human gene promoters

Table 1 EMSA-based analysis of the complex of TBP and one of oligodeoxyribonucleotides (ODNs) in vitro.

Gene probe	³²P-labeled synthetic ODN, 26 bp, double-stranded DNA	k_a, × 10³ M^-1s^-1	k_d, × 10^-4 s^-1	K^*_D, nM	t_1/2, min	-ΔG Kcal/mol
LEP WT	atcgggccgcTATAAgaggggcgggc	2.3 ± 0.6	1.8 ± 0.6	78	64 ± 13	9.7 ± 0.9
LEP -38a	atcgggccacTATAAGaggggcgggc	3.5 ± 0.5	1.5 ± 0.2	43	77 ± 16	10.0 ± 1.0
LEP -30t	atcgggccgcTATAAGtggggcgggc	11.0 ± 2.0	8.0 ± 1.0	73	14 ± 3	9.7 ± 1.0
LEP -35g	atcgggccgcTgTAAGaggggcgggc	5.6 ± 0.8	13.0 ± 2	232	9 ± 1	9.0 ± 0.9
GCG WT	agctggagagTATATAaaagcagtgc	70 ± 10	5 ± 1.0	8	23 ± 5	11.1 ± 1.0
GCG -41g	agctggagagTgTATAaaagcagtgc	30 ± 10	6 ± 1.0	18	19 ± 4	10.5 ± 0.9

Notes: For each TBP-ODN-complex, k_a is the association rate constant, k_d is the dissociation rate constant, half-life (t_1/2) equals (ln2)/k_d, and K^*_D = k_d/k_a is the apparent dissociation constant. TATA-like subsequence: uppercase letters; ΔG = -RTln(_ka/k_d) is a change in Gibbs free energy, where R = 1.38 × 10^-23 JK^-1 is Boltzmann's constant, T is temperature in degrees Kelvin; the substitution corresponding to the minor allele of each SNP is shown in boldface.

ISSN: 1471-2164