Table 1

The sequence specific oligonucleotide probes (SSOPs) targeting SNPs/haplotypes in c57, 58, 61 and 117 of the Pvdhfr gene and c383, 553 and 585 in the Pvdhps gene and artificial positive controls.

SSOP

SSOP sequence †

Washing temperature §

Incubation time ¶

Pvdhfr

(C°)

Min.

57/58/61 FST

AC TTC AGC TCG GTG ACG A

60

12

57/58/61 FR₁T

AC TTC AGA TCG GTG ACG A

60

10

57/58/61 FR₂T

AC TTC AGG TCG GTG ACG A

60

10

57/58/61 L₁R₂M

ACCTC AGG TCG GTG ATG A

62

10

57/58/61 L₂ST

AC TTG AGC TCG GTG ACG A

60

10

57/58/61 L₂R₁T

AC TTG AGA TCG GTGACG A

64

10

57/58/61 L₃R₂T

AC TTA AGG TCG GTG ACG A

62

10

117 S

G AGA AGC AGC TGG GAG AG

60

12

117 N

G AGA AGC AAC TGG GAG AG

60

10

117 T

G AGA AGC ACC TGG GAG AG

60

10

Pvdhps

383A

A TCG TCC GCC CCT TAT GT

64

10

c383 G

A TCG TCC GGC CCT TAT GT

64

10

c553A

TC GGC CTG GGG TTTGCC A

64

10

c553G

TC GGC CTG GGG TTTGGC A

64

10

c585V

C TTT ATT GTC CAC TGC AT

64

10

Positive controls*

Pvdhfr

Sequence

PcL₃R₂T

TCCGTCGATATGAAGTACTTAAGGTCGGTGACGACCTACGTGGATGAGTC

Pvdhps

Pc383G

GATTGACATCGGGGGGGAATCGTCCGGCCCTTATGTGGTCCCCAATCCGA

Pc553G

CTTTGATGTCGGCCTGGGGTTTGGCAAAAAGCACGACCAGTCTATTAAGC

† Sequences in bold indicate the codon in which the SNP occurs.

§ Optimal TMAC-washing temperature.

¶ Optimal incubation time for TMAC-wash

* Artificial positive controls mimicking specific mutated Pvdhfr or Pvdhps sequences.

Schousboe et al. Malaria Journal 2007 6:28   doi:10.1186/1475-2875-6-28