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. 2007 Feb 7;35(6):e40. doi: 10.1093/nar/gkm051

Table 1.

Details of conventional primers and DPO primers used for this study

Primer namea Direction Sequence (5′ – 3′)b Tm(°C)c
Ndufs2
Ndufs2/Df-00d Forward CTTCTCTCTTCGGATTGATGAGIIIIIGGAGATGC 83 (77)
Ndufs2/Lcf-00d Forward CTTCTCTCTTCGGATTGATGAGGTGGAGGAGATGC 88
Ndufs2/Df-33d Forward CTTCTCTCTTCGGATTGATGAGIIIIIGCAGTTGG 84 (77)
Ndufs2/Lcf-33d Forward CTTCTCTCTTCGGATTGATGAGGTGGAGCAGTTGG 88
Ndufs2/Df-53d Forward CTACTCTCTTGGGATTGAAGAGIIIIIGGAGATGC 83 (77)
Ndufs2/Lcf-53d Forward CTACTCTCTTGGGATTGAAGAGGTGGAGGAGATGC 88
dT18-ACP1 Reverse CTGTGAATGCTGCGACTACGATIIIIITTTTTTTTTTTTTTTTTT 82 (82)
dT15-ACP2 Reverse CTGTGAATGCTGCGACTACGATIIIIITTTTTTTTTTTTTTT 82 (82)
RV detection
INFa/Df Forward AGGCCCCCTCAAAGCCGAGAIIIIICAGAGACTTG 92 (90)
INFa/Lcf Forward AGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTG 96
INFa/Dr Reverse ATAGCCTTAGCTGTAGTGCTGGCIIIIICCATTCTGTT 91 (84)
INFa/Lcr Reverse ATAGCCTTAGCTGTAGTGCTGGCTAAAACCATTCTGTT 87
INFb/Df Forward TTGGCTATGACIGAAAGIATAACCIIIIICAGCCCAA 87 (75)
INFB/Lcf Forward TTGGCTATGACTGAAAGAATAACCAGAGACAGCCCAA 88
INFb/Dr Reverse TTACATGTTCGGTAAAAITCGTTTAIIIIITCCATACATG 80 (75)
INFB/Lcf Reverse TTACATGTTCGGTAAAAGTCGTTTATTCCTTCCATACATG 83
OC43/Df Forward TATGTTAGGCCGATAATTGAGGACTIIIIIACTCTGACGG 86 (80)
OC43/Lcf Forward TATGTTAGGCCGATAATTGAGGACTACTTTACTCTGACGG 86
OC43/Dr Reverse GTAATTACCGACTTTGGACTTAACATIIIIIGCAAAACCAC 83 (78)
OC43/Lcr Reverse GTAATTACCGACTTTGGACTTAACATAAACAGCAAAACCAC 84
RSVa/Df Forward AGAATTTTATCAATCAACATGCAGTGIIIIIAGCAAAGGCT 85 (77)
RSVa/Lcf Forward AGAATTTTATCAATCAACATGCAGTGCAGTCAGCAAAGGCT 88
RSVa/Dr Reverse ATTGTTGAGTGTATAATTCATAAACCTTGGIIIIICTCTTCTGGC 85 (78)
RSVa/Lcr Reverse ATTGTTGAGTGTATAATTCATAAACCTTGGTAGTTCTCTTCTGGC 85
RSVb/Df Forward TCAGTCTATCAAATGGGGTCAGTGIIIIIACCAGCAAAG 87 (81)
RSVb/Lcf Forward TCAGTCTATCAAATGGGGTCAGTGTTTTAACCAGCAAAG 86
RSVb/Dr Reverse ATTACACCATAGATAGGTAGCTGTACAACIIIIICAAGGACTTC 86 (80)
RSVb/Lcr Reverse ATTACACCATAGATAGGTAGCTGTACAACATATGCAAGGACTTC 85
SNP detection
CYP2C19/Df Forward GCTTTTATACTATCAAAAGCAGGIIIIIGTCTAGGAAATG 80 (75)
CYP2C19/Lcf Forward GCTTTTATACTATCAAAAGCAGGTATAAGTCTAGGAAATG 81
CYP2C19/Dr-a1e Reverse CAAGGTTTTTAAGTAATTTGTTIIIIITTCCInline graphicGGG 81 (71)
CYP2C19/Lcr-a1e Reverse CAAGGTTTTTAAGTAATTTGTTATGGGTTCCInline graphicGGG 84
CYP2C19/Df-a2e Forward TAATTTTCCCACTATCATTGAIIIIITCCCInline graphicGGA 82 (72)
CYP2C19/Lcf-a2e Forward TAATTTTCCCACTATCATTGATTATTTCCCInline graphicGGA 81
CYP2C19/Dr Reverse AAACTAGTCAATGAATCACAAATIIIIIAGCAGTCAC 81 (74)
CYP2C19/Lcr Reverse AAACTAGTCAATGAATCACAAATACGCAAGCAGTCAC 84

aLcf, Lcr, Df and Dr represent long conventional forward primer, long conventional reverse primer, DPO forward primer and DPO reverse primer, respectively.

bThe positions of deoxyinosine (I) are highlighted in bold. The positions of mismatched bases in Ndufs2-specific primers are underlined. The position of a single base variation in CYP2C19-specific primers is highlighted in gray.

cThe Tm value of the entire primer sequence. The Tm value of the 5′-end portion of the DPO is also indicated in parentheses. The Tm values of the primers were predicted using HYTHER™ which adopts the nearest neighbor model with optimized thermodynamic parameters for deoxyinosine pairs in DNA duplex (http://ozone3.chem.wayne.edu/).

d00, 33, 53 represent a perfectly matched primer, a 3 base mismatch in the 3′-end of the primer, a 3 base mismatch in the 5′-end of the primer, respectively.

ea1 and a2 represent allele 1-specific primer and allele 2-specific primer, respectively.