Table 2.
Type of DNA targeted, primer set designation | SYBR green primer sequence |
TaqMan primer sequenceb | Sequence sourcec | Source or reference | |
---|---|---|---|---|---|
Forward | Reverse | ||||
Minicircle | |||||
kDNA 1 minicircle | GGGTAGGGGCGTTCTGC | TACACCAACCCCCAGTTTGC | M94088 | J.L.W.c | |
kDNA 2 | AACTTTTCTGGTCCTCCGGGTAG | ACCCCCAGTTTCCCGCC | EU437406 | Leish1 and -2 (20) | |
kDNA 3 minicircle | GGGTAGGGGCGTTCTGC | CCCGGCCTATTTTACACCAACC | M94088 | J.L.W. | |
kDNA 4 minicircle | GGGTGCAGAAATCCCGTTCA | CCCGGCCCTATTTTACACCA | ACCCCCAGTTTCCCGCCCCG | Conserved kDNAd | J.L.W. |
kDNA 5 minicircle | CTTTTCTGGTCCTCCGGGTAGG | CCACCCGGCCCTATTTTACACCAA | TTTTCGCAGAACGCCCCTACCCGC | L. infantum contig 1335 | TaqMan qPCR (40)e |
kDNA 7 minicircle | AATGGGTGCAGAAATCCCGTTC | CCACCACCCGGCCCTATTTTAC | CCCCAGTTTCCCGCCCCGGA | Conserved kDNAd | J.L.W. |
L. (L.) amazonensis kDNA 1 | GGTCCCGGCCCAAACTTTTC | CCGGGGTTTCGCACTCATTT | U19810 | J.L.W. | |
L. (L.) amazonensis kDNA 2 | GGTAGGGGCGTTCTGCGAAT | CCCGGCCTATTTTACACCAACC | EU370875 | J.L.W. | |
L. (L.) amazonensis kDNA 3 | GGGTAGGGGCGTTCTGC | TACACCAACCCCCAGTTTGC | M94089 | J.L.W. | |
L. (L.) amazonensis kDNA 4 | TGAGTGCAGAAACCCCGTTCATA | ACACCAACCCCCAGTTGTGA | EU370875 | J.L.W. | |
L (V.) braziliensis kDNA 1 | AATTTCGCAGAACGCCCCTAC | GTACTCCCCGACATGCCTCTG | U19807 | J.L.W. | |
L (V.) braziliensis kDNA 3 | TGCTATAAAATCGTACCACCCGACA | GAACGGGGTTTCTGTATGCCATTT | TTGCAGAACGCCCCTACCCAGAGGC | AF231100 | Adapted from PCR (56)f |
L (L.) infantum minicircle 1 | TCCGCAGGAGACTTCGTATG | CACGACTATCCACCCCATCC | CTGAGAGACCCGCCGGGGCG | AF032997 | Adapted from nested PCR (51) |
L. (L.) major minicircle 1 | ACGGGGTTTCTGCACCCATT | GTAGGGGCGTTCTGCGAAAA | LM15_BIN_Contig406 | J.L.W. | |
L. (L.) mexicana minicircle 1 | AATGCGAGTGTTGCCCTTTTG | GCCGAACAACGCCATATTAACC | AY145437 | J.L.W. | |
L. (L.) tropica minicircle 1 | GGGGGTTGGTGTAAAATAGGG | ACCACCAGCAGAAGGTCAAAG | TCCTGGCGGGGGTTTTCGCT | AF308689 | J.L.W. |
L. (L.) donovani minicircle 1 | GCGGTGGCTGGTTTTAGATG | TCCAATGAAGCCAAGCCAGT | CCCATACCACCAAACGCAGCCCA | FJ416603 | J.L.W. |
Maxicircle | |||||
Cytochrome B 1 | ATTTTAGTATGAGTGGTAGGTTTTGTT | CAATAACTGGGACGGTTGCT | CCATGTACGATGATGTCGTATTGAGGTCTAACA | AB095960 | J.L.W. |
L. (L.) amazonensis cytochrome B 1 | GCGGAGAGGAAAGAAAAGGCTTA | AAAAGTCATGCTAAACACACACCACA | AB095964 | J.L.W. | |
L. (L.) tropica cytochrome B 1 | CAGGTTGCTTACTACGTGTTTATGGTG | TCGTATTACAAACCCTAAATCAAAATCTCA | AB095960 | J.L.W. | |
L. (L.) tropica cytochrome B 2 | TCAGGTTGCTTACTACGTGTTTATGGTG | TGCTAAACAAACACCACATATGATCTGC | AB095960 | J.L.W. | |
L. (L.) tropica cytochrome B 3 | TGACACACATATTTTAGTGTGGGTGGTAGG | TCCCCAATAAGACATCATTGTACATGGTAA | EF579904 | J.L.W. | |
L. (L.) tropica cytochrome B 4 | CACATATTTTAGTGTGGGTGGTAGGTTTTG | TCCCCAATAAGACATCATTGTACATGGTAA | EF579904 | J.L.W. | |
Maxicircle 1 | GCTTGGTTGGATTATTTTTGCTG | AACAACATTTTAACTCTTGTAGGATTCG | CTTTAGGTAGGGAGTTGTACTACGTTTTTTGACCT | DQ492252 | J.L.W. |
Genomic | |||||
Alpha-tubulin 1 | GAGGTGTTTGCCCGCATC | CTCGCCCATGTCGTCG | TGAGGGCATGGAGGAGGGCG | XM_001681731 | J.L.W. |
DNA polymerase 1 | TGTCGCTTGCAGACCAGATG | GCATCGCAGGTGTGAGCA | CAGCAACAACTTCGAGCCTGGCACC | AF009147 | TaqMan qPCR (8)e |
DNA polymerase 2 | AGGAGGATGGCAAGCGGAAG | GCGACGGGTACAGGGAGTTG | TGGGGTCGAGCACCATGCCGCC | AF009136 | J.L.W. |
Miniexon 1 | CGAAACTTCCGGAACCTGTCTT | CACCACACGCACGCACAC | CGGCAAGATTTTGGAAGCGCGCA | AL389894 | J.L.W. |
Miniexon 2 | GTGTGGTGGCGGGTGTATGT | GCCCAGGTCGCTGTGAGG | LbrM02_V2.0710 | J.L.W. | |
MAG 1 (MSP-associated gene 1) | AGAGCGTGCCTTGGATTGTG | CGCTGCGTTGATTGCGTTG | TGCGCACTGCACTGTCGCCCCC | AF058760 | J.L.W. |
MAG 2 (MSP-associated gene 2) | AGTTTTGGTTGGCGCTCCTG | CCCACTCGCTTTCCTTGGTC | CGCTGAGAGCGAGGCAGGCACGC | AF058760 | J.L.W. |
SIDER repeat 1 | CGACCCTGTCACCACCACAG | GAGGCCACCCTATCGCTGAC | AM937229 | J.L.W. | |
L. (V.) braziliensis DNA polymerase 1 | TCGTTGAGGGAGGAGGTGTTTC | TCGGCTTTGAGGTTGGCTTC | XM_001563712 | J.L.W. | |
L. (V.) braziliensis DNA polymerase 2 | ACGTCGCCAACTGCTTCACC | GTGTTCGCACCGCCTTGAC | XM_001563712 | J.L.W. | |
L. major MAG 1 | GTCGTTGTCCGTGTCGCTGT | CGCTGTGTGTGTCCGTGTGT | XM_001681328 | J.L.W. | |
L (L.) amazonensis DNA polymerase 1 | GACGACGACGAGGAGGATGG | GCGACGGGTACAGGGAGTTG | AF009136 | J.L.W. | |
GPI | CCAGATGCCGACCAAAGC | CGCGCACGTGATGGATAAC | AM117195 | (66) | |
HSP70-1 | GAAGGTGCAGTCCCTCGTGT | CCTCCGTCTGCTTGCTCTTG | FN395029 | J.L.W. | |
HSP70-4 | TCGAGATCGACGCGTTGTT | CCGCACAGCTCCTCGAA | FN395037 | J.L.W. | |
SLACS | GGAGAAACTCACGGCACAGG | GCGCCTCGTAGGTCACAGTT | XM_001562078 | J.L.W. | |
Leptomonas DNA | |||||
Leptomonas miniexon 1 | TGGAGCGGGTGCATTAACTC | GGTCTCGAGGTGCCCATGAC | S78663 | J.L.W. | |
Leptomonas GAPDH 2 | AGAAGCCGGATGTGCTTGTG | GCCCTCAGCCTTCACCTTGT | AF053738 | J.L.W. | |
Human DNA | |||||
Human TNF-α 1 | GCCCTGTGAGGAGGACGAAC | AAGAGGTTGAGGGTGTCTGAAGGA | CCTTCCCAAACGCCTCCCCTGCCCC | NM_000594 | J.L.W. |
Human TNF-α 2 | GCGCTCCCCAAGAAGACAGG | TGCCACGATCAGGAAGGAGAAG | CACCGCCTGGAGCCCTGGGGC | NM_000594 | J.L.W. |
Human GAPDH 1 | GGGCTCTCCAGAACATCATCC | CCAGTGAGCTTCCCGTTCAG | NG_007073 | J.L.W. | |
Human GAPDH 2 | CATCAAGAAGGTGGTGAAGCAG | CGTCAAAGGTGGAGGAGTGG | NG_007073 | J.L.W. | |
Human GAPDH 3 | GCATGGCCTTCCGTGTCC | CGCCTGCTTCACCACCTTCT | NG_007073 | J.L.W. |
All sequences were developed for use in SYBR green and/or TaqMan assays.
The TaqMan probe used for human DNA was 5′VIC/3′TAMRA. The TaqMan probe used for all other DNA was 5′FAM/3′TAMRA.
Primers and probes were designed by one of us (J. L. Weirather [J.L.W.]) from sequences available on the World Wide Web. GenBank accession numbers are listed.
The “conserved kDNA” sequences used multiple sources aligned with CLUSTALW.
For TaqMan qPCR, the primers and probes are the exact ones used for TaqMan but not SYBR green assay reported in the literature cited.
“Adapted from” indicates that the targeted gene in the literature cited was used by J. L. Weirather to redesign primers and probes.