Table 2

Oligonucleotide sequences used for EMSA. For every SNP, 4 oligonucleotides (2 complimentary pairs) were synthesized, one pair for each allele. One oligonucleotide sequence from each pair had additional GG dinucleotide overhangs at the 5'end for fill-in labeling reaction. Care was taken to make sure that the additional GG-dinucleotide did not influence the predicted TF binding capability. The complementary sequences lacked the GG pairs. Only the allelic sequence predicted to bind most stably was chosen for the fill-in labeling reaction (marked *) while the gel shift assays were carried out using competitor with a perfect match versus a competitor with the allelic mismatch. The polymorphic site is underlined. Column 'Ratio' shows the difference in competition between the labeled and non-labeled oligomers at 25-fold excess, by dividing Allele2 (x25) values by Allele1 (x25).
Gene name and rs ID
 Sequence
 Allele 1(competitor oligo is a perfect match)
 Allele 2 (competitor oligo has a mismatch)
 Ratio


x5
 x10
 x15
 x20
 x25
 x5
 x10
 x15
 x20
 x25
Serotonin receptor (5-HT-1A) rs968554 ENST00000323865
 GGAAAAGAATCCA CTTGGGCCAATG *
GGAAAAGAATCCA
GTTGGGCCAATG
 1.29
 -
 1.27
 1.23
 1.00
 1.16
 -
 1.12
 1.13
 0.96
 0.96
Dopamine receptor DRD1 rs267412 ENST00000329144
 GGAATGTAAACCC
AACACAAAAG *
GGAATGTAAGCCC
AACACAAAAG
 0.72
 -
 -
 0.54
 0.56
 0.98
 -
 1.06
 1.03
 1.12
 2.05
Dopamine receptor DRD1 rs267413 ENST00000329144
 GGTATAAAAGTCA
GTGAATACAG *
GGTATAAAAGTCT
GTGAATACAG
 0.96
 -
 0.81
 0.74
 0.81
 0.97
 -
 0.98
 0.97
 1.01
 1.24
Muscarinic acetylcholine receptor M1 rs509813 ENST00000306960
 GGCTTGGGCTCCT
CCCCCCAGCCAAC *
GGCTTGGGCTCCT
CCCGCCAGCCAAC
 0.21
 0.11
 0.08
 0.05
 0.09
 0.70
 0.60
 0.46
 0.46
 0.37
 4.11
Follicle stimulating hormone receptor. rs2882225 ENST00000304421
 GGCAAGGGAGCTG
TTTTTTTT
GGCAAGGGAGCTT
TTTTTTTT *
 1.10
 1.00
 0.86
 0.71
 0.75
 1.96
 1.73
 1.67
 1.36
 1.35
 1.80
Adenosine-A3 receptor. rs1538251 ENST00000241356
 GGTGGCCACCAGA
GGGCAGCACG *
GGTGGCCACCAGA
GGGAAGCACG
 1.08
 1.11
 0.95
 0.89
 0.76
 1.49
 1.41
 1.44
 1.51
 1.40
 1.84
Bradykinin receptor B2 rs1800508 ENST00000306005
 GGGAAGTGCCCAG
GAGGC *
GGGAAGTGCTCAG
GAGGC
 1.67
 1.28
 1.17
 1.16
 1.20
 1.10
 1.06
 1.11
 1.27
 1.33
 1.03
Bradykinin receptor B2 rs945032 ENST00000306005
 GGTTCCTGGGTGC
GGG *
GGTTCCTGGGTAC
GGG
 0.88
 0.72
 0.72
 0.62
 0.55
 1.15
 1.22
 1.29
 1.22
 1.27
 2.30
Bradykinin receptor B2 rs1799722 ENST00000306005
 GGCTGGGTAGTGA
TGTCATCAGC
GGCTGGGTAATGA
TGTCATCAGC *
 0.36
 0.21
 0.16
 0.12
 0.12
 0.50
 0.29
 0.22
 0.20
 0.20
 1.66
Calcitonin receptor precursor rs2528521 ENST00000316576, ENST00000248548
 GGCTGTCCCCGGA
GTGGCGGCT
GGCTGTCCCCGGA
GTGACGGCT *
 0.54
 0.36
 0.25
 0.22
 0.21
 0.90
 0.83
 0.73
 0.60
 0.55
 2.62

Mottagui-Tabar et al. BMC Genomics 2005 6:18   doi:10.1186/1471-2164-6-18