Leiden Muscular Dystrophy pages©

DMD amplification primers

( DMD / BMD )

(last modified December 23, 2008)

Contents

Quantitative multiplex PCR

Stockley et al. (2006) reported a quantitative multiplex PCR assay developed to detect deletions and duplications in all 79 exons of the DMD gene and the brain promoter (Dp427c). The assay consists of 10 separate multiplexes, each with 7 to 9 nons-equential exons.

Multiplex set A

Exon Sequence forward / reverse primer Length (bp) Primer conc. (uM)
34 GTAACAGAAAGAAAGCAACAGTTGGAGAA /
CTTTCCCCAGGCAACTTCAGAATCCAAA		 171 0.8
78 GGAAAGCCAATGAGAGAGGTTAGTGAGA /
CAATGAGCTGCAAGTGGAGAGGTGACTAC		 179 0.8
42 CACACTGTCCGTGAAGAAACGATGATGG /
CTTCAGAGACTCCTCTTGCTTAAAGAGAT		 195 0.2
64 TATTTCTGATGGAATAACAAATGCTC /
CCCTCTCTAAGTAAAAATGTACCC		 209 0.3
16 TCTATGCAAATGAGCAAATACACGC /
GGTATCACTAACCTGTGCTGTACTC		 290 0.2
2 AAACCAGCATCACTCATGTTTAATTC /
CGGATTTTTAAGATACACAGGTACATA		 306 0.5
53 GTCTCCTCCAGACTAGCATTTACTACTA /
TGGTATAATTTTATCAAATGTAACCAGT		 327 1.4

Multiplex set B

Exon Sequence forward / reverse primer Length (bp) Primer conc. (uM)
62 CTTTCCTGTTTGCGATGAAT /
ACAGGTTAGTCACAATAAATGCTCT		 174 0.08
70 TGGTCATTAGTTTTGAAATCATCC /
TATACATCAAACAAGAGTGTGTTCTG		 241 0.4
38 AAATGTATTTCTTTTGGTTTATGTTTC /
TTCAGTTGGAGACTTATCTAAGTTCT		 280 0.6
7 TAAAGGGTAAATGAATTACACTCAAG /
CCATACTAAAAGCAGTGGTAGTCCAG		 303 0.24
14 AGCGTACATAGGAGACTGAGATACTT /
GCAAGACATTAAAGAATTCCAAG		 313 0.2
46 GTTTGTGTCCCAGTTTGCATTA /
AAACACTTTAGCAAGGAACTATGAAT		 353 0.8
23 TCAGTTAATTTCACTAAAACTCATCAA /
AGATGCTGAAGGTCAAATGCTTA		 393 2
54 AAGTTTGTCCTGAAAGGTGGGGTTA /
AGTTTCACCACCCCATTATTA		 405 0.8

Multiplex set C

Exon Sequence forward / reverse primer Length (bp) Primer conc. (uM)
74 AAATACACTCCTGAGTCCCTAACCC /
TGCATACCAATGACAAAGCTAGAAA		 272 0.6
47 CCTCGGTCAAGTCGCTTCAT /
CATGTGACGGAAGAGATGGTTAATG		 290 0.2
3 AGGGGATAATCGTGAAAATGTAT /
CGAGGTTGCTTTACTAAGGAATAGG		 309 0.2
22 GGCAAAGTGTGAAACAATTAAGTG /
TGGGCAAACTACCATACTTGTCAGAAT		 317 1.2
13 TAGCAGAAAATTGGCTTGGAATG /
TTCAAGTTATAGTTCTTTTAAAGGACATA		 330 0.6
58 GGAGTTTCATAAACAAGTTCTGAG /
GCATCTATGTTTAATTTGAATTGATT		 356 0.24
67 TGGCTACTCTTGAGAATTGCTACTG /
CTGCCTACTGAAGAGCTAATATGAGA		 369 1
37 CACACGCATTTTCATTTTAGTCCTG /
CTTCGCAAGAGACCATTTAGCAC		 440 0.04

Multiplex set D

Exon Sequence forward / reverse primer Length (bp) Primer conc. (uM)
43 CTCAGGTCGGATTGACATTATTC /
GCAAGTATCAAGAAAAATATATGTGTTA		 180 0.6
71 GGCTGAGTTTGCGTGTGTC /
GAAATGAAGGAAGGGGAATTA		 226 0.2
11 AAAATAAAACTCAAAAACCACACCG /
TTGTTTTTCCATGCTAGCTACCC		 249 0.16
60 ACAAACATTCAAACCGTAGCATA /
TTATTTTACTGTAACAAAGGACAACAAT		 322 0.7
50 TTAAAAGAAATTCTACCCACTAAAGTT /
CTCTCTCACCCAGTCATCACTTCATA		 337 0.7
21 TTGCCTTACTGCTTTTTAATACCT /
TGTTAGTACCTTCTGGATTTCCC		 348 0.3
40 TGTACAAAAAAGATGAGGGACG /
ACAACACACAATACAAGGAAATGC		 399 0.3
30 TCATGCAGAGATCCCTGATCCTATA /
GAAGCTGATTCCCAGATGTACTT		 412 0.8
Dp427m
/ exon 1		 GCTGGAAGCACAACCTTATATGTAG /
CACAAACTAAACGTTATGCCAC		 460 0.4

Multiplex set E

Exon Sequence forward / reverse primer Length (bp) Primer conc. (uM)
61 CAGTCTTGGAGACTCAAAGTATCTTATC /
AATCAAGATGCAATAAAGTTAAGTG		 229 0.8
72 TGTGTGGTGGGTTTTTTCTCCATT /
AGTAGGAATCAGACAAGTTTGGG		 250 0.2
4 TTCATTTCTAGTAGATTGTCGG /
TCAGGCATACACGAATTACAACAT		 300 0.2
31 TAAAGGAAGCTACATGGTAGAGGTG /
AAATCCAATCTTGCCAATAATC		 318 0.2
24 ACATCCTTTAAACATGGGAATTGT /
GGGAGAGGAGAGCAAAATCCAC		 331 0.2
41 AAAGGATGACAATAAAGGGACAACA /
GTAGTTGCAAACACATACGTGGGT		 344 0.8
12 GCTTTCAAAGAGGTCATAATAGGCT /
CCTGAATTTTGGAGGGGACTTA		 392 0.8
51 GTTTGGCTCAAATTGTTACTCTTCA /
AAAGTGATTGGTGGAAAATCTTCAT		 429 1

Multiplex set F

Exon Primer Sequence forward / reverse primer Length (bp) Primer conc. (uM)
63 TTTTTCCTGTTTTCTTGACTACTCAT /
GCCATGTCCTTACCTAAAGACTG		 140 0.4
73 CATAAGTTTAATGAGCTTTTACGTT /
CCCTCAAAGCAATTTCATTGTCAG		 157 0.4
15 AAATTGGAAAAGTAAAGATTTATGTT /
GGGTTTTTATAAGACCATTGAA		 207 0.4
5 TAGGCATTTGGTCTCTTACCTTCAA /
CTATGGAGCAGGGTTTGTTATTGTTAG		 258 0.8
52 ATTATGTAAAAGGAATACACAACGC /
TATAAATGTGAGGGGGATATA		 273 0.4
32 ATAGGACCAGTTATTGTTTGAAAGG /
CTTAATGAGGAAAGTCAAGGG		 290 0.4
25 ATGCCATCAGTCCCAATTTTACATT /
AAAGCCTTAACCAAAAGTAACGGTG		 346 0.3

Multiplex set G

Exon Sequence forward / reverse primer Length (bp) Primer conc. (uM)
33 GGGATCTCTATTTATTTCTGTTCATA /
AAAGTGGAAAGAAGTGTTTGTGGTC		 281 1.2
65 AAAGGACACTGAAAGGAAGGTTTTACT /
CGGGAAATAAAAACATGCCATAC		 292 0.2
Dp427c GACTGACGTATCAGATAGTCAGAGT /
TAATCCTACCTTCCATGCCAGCTGT		 303 0.4
45 TTTGTTTTGCCTTTTTGGTATC /
TAGTGCCTTTCACCCTGCTTATA		 308 0.3
26 ATGTTTCATCACTGTCAATAATCGTGTT /
TAGAACCAGGAAAGAGCAGACTGTAT		 329 1.2
75 TTCTTTTTTACTTTTTTGATGCC /
TAGAACCAGGAAAGAGCAGACTGTAT		 347 0.2
55 AGTTCCTCCATCTTTCTCTTTTTATG /
TGTTTTGTCCCTGGCTTGTCA		 371 0.4
6 AATGAATCAGAATAGACTCCTAGCCTT /
CATACTGGGGAAAAATATGTCATC		 437 0.4
17 ACAATTTTATTTGGCTTCAATATGG /
GACATTACAGGTACCCGAGGATT		 448 0.4

Multiplex set H

Exon Sequence forward / reverse primer Length (bp) Primer conc. (uM)
44 CTTGATCCATATGCTTTTACCTGCA /
TCCATCACCCTTCAGAACCTGATCT		 268 0.2
76 CAAAATTTATGAGTCCTGAGTGTGTAT /
ACGACTCTACCTTTCTTCAGACAAC		 274 0.14
35 GCCGTTTCATAAGCATTAAATC /
TATGTATCTTTTTCTCGTGACAGA		 308 0.24
18 AGGGAAAATAGTGCTGCTATTAATACTA /
GCAGCAAAATGAGTACAGATATA		 320 0.8
66 TTTTCAAGGCTTTATTCTTAACTAGA /
GCCTGCAATTTAATGTTTGACAA		 353 1.6
27 ATTTATGGAAGAGACTGGAGTTCAT /
TGACAAAGACCAAGAAAAGCAAC		 364 0.16
56 CACATATTCTTCTTCCTGCTGTC /
TCCTCAAGTATCATCTCCATACC		 384 0.12
10 ATAATGCCAGTGGACAGTCCTA /
GAATCCCAAGCACATCATAGTAACT		 436 0.2

Multiplex set I

Exon Sequence forward / reverse primer Length (bp) Primer conc. (uM)
77 TTTTCCATTATTTGTTTTTGCTTTT /
TGCCATTCTGATACTGCGTGTT		 240 0.3
57 ACACTTCTAGATATTCTGACATGGT /
TAGTCACTGGATTACTATGTGCTT		 262 0.2
68 ATCTTGCCTTCTTTCCTTTCATC /
AGCAACTGGCACAGGAGATAAA		 317 0.6
36 ATGAAAATACCACTTAAAACTAATCTCA /
GACAAAGATGATTGAAGTAACTGGTG		 323 1.4
19 TCACAGTCCTTGTATTGAATTACTCA /
CTTCCAATGAACTCAAAGTTGAA		 332 1.4
9 CTTTCGGGTTACTTATGGTT /
AGCAGAATCACATGAGGGAATCAA		 348 0.4
28 TGCATTTTGAATTACCTGCTACA /
CTTTGGATTTGTCTTCTATTTGGTACT		 360 0.6
48 TATGCCTTGTGAATTATTTACCTTTT /
CCCTGTGCCTATTGTGGTTATCCT		 389 0.4

Multiplex set J

Exon Sequence forward / reverse primer Length (bp) Primer conc. (uM)
69 AATACATACGTGTTTGTTTTTGCTCTT /
ATTTATCCCAGGTGAACTAACTCTCA		 195 0.6
39 ACCAAAATGAAGACTGTACTTGTTGT /
AAACCACAGGCAAGGTATATTATA		 214 0.6
29 TTGCTGATAATCCAATGTATTTAGAA /
ATGCAAATTAGATTAAAGAGATTTT		 255 1.2
20 CTGTGGGTTCAGGGGATATA /
TGCCAAGAAATACCTATTGATTATG		 339 0.4
49 CTACATTTTTGTGCCCTTATG /
GCTTTGCCTCTGCTATTACAGTATG		 385 0.16
8 ACTCGTGATCTCATTGGTCTGC /
ACATCTTGAATAGTAGCTGTCCTTT		 420 0.3
59 GGTTACCCTCTTGTTCAACTGTACT /
CACTCAAGTTCAGATTAGAAGCTC		 446 0.3
79 TTTCTCTTTGTTTTCCAGGACACA /
TGTTTTGTTTTTAGGGGTTTT		 488 1.4

Legend:
NOTE: sequences were not checked.
Sequences were derived from Stockley et al. (2006). All forward primers were labeled with FAM, reverse primers were unlabeled. Migration of amplification products may vary slightly (1-3 bp) due to differences in equipment and polymers used. Exon: exon number. Sequence forward / reverse primer: sequence of the forward and reverse primer for PCR. Length (bp): length of the amplification product (in basepair). Primer conc.: concentration of the DNA primers (in uM).

| Top of page | LMDp homepage |
| Remarks / information |  Copyright©, liability |