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

    C
TTGGGCCAATG *

GGAAAAGAATCCA

    G
TTGGGCCAATG

1.29

-

1.27

1.23

1.00

1.16

-

1.12

1.13

0.96

0.96

Dopamine receptor DRD1 rs267412 ENST00000329144

GGAATGTAA

    A
CCC

AACACAAAAG *

GGAATGTAA

    G
CCC

AACACAAAAG

0.72

-

-

0.54

0.56

0.98

-

1.06

1.03

1.12

2.05

Dopamine receptor DRD1 rs267413 ENST00000329144

GGTATAAAAGTC

    A

GTGAATACAG *

GGTATAAAAGTC

    T

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

CCC

    C
CCAGCCAAC *

GGCTTGGGCTCCT

CCC

    G
CCAGCCAAC

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

GGCAAGGGAGCT

    G

TTTTTTTT

GGCAAGGGAGCT

    T

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

GGG

    C
AGCACG *

GGTGGCCACCAGA

GGG

    A
AGCACG

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

GGGAAGTGC

    C
CAG

GAGGC *

GGGAAGTGC

    T
CAG

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

GGTTCCTGGGT

    G
C

GGG *

GGTTCCTGGGT

    A
C

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

GGCTGGGTA

    G
TGA

TGTCATCAGC

GGCTGGGTA

    A
TGA

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

GTG

    G
CGGCT

GGCTGTCCCCGGA

GTG

    A
CGGCT *

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

Open Data