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Primers for DMD RNA RT-PCR

(last modified March 19, 2006)

Several sets of primers for RT-PCR amplification of DMD RNA have been published. Below primers are shown that have been used in combination with direct sequecing of the cDNA for point mutation detection. Several other sets of primer sequences, used in combination with DMD PTT-analysis, can be found here. Note that DMD transcription can be induced using myoD-induced myodifferentiation.

cDNA sequencing

ExonsLength
(in bp)		Forward / reverse primer
1 - 4408CTACAGGACTCAGATCTGGG /
GGGCATGAACTCTTGTGGAT
1 - 4385CAATTACCTTCGGAGAAAAACG /
GGGCATGAACTCTTGTGGAT
97422GGGAAGCAGCATATTGAGAA
518ATGAGAGCATTCAAAGCCAG
413517AGATTCTCCTGAGCTGGGTC
929GAGGTGGTGACATAAGCAGC
822402TTCTCAACAGATCACGGTCA
1223CCAATCAGCTTACTTCCCAA
1147349GAGGGGTACATGATGGATTTG
1521GACCCTGACTTGTTCTTGTT
1474351CAACATAAGGTGCTTCAAGA
1822CGCTTTTAAAACGGCCAGTT
1777358CAAAATGAAATGTTATCAAG
2134TCTTCTTTTGGGGAGGTGGT
2092349ATGCTCAAGAGGAACTTCCA
2440CGATCCACCGGCTGTTCAGT
2395350GATAGCATCAAACAAGCCTC
2744GTAAAGGCCACAAAGTCTGC
2701380GGACAAGGACCCATGTTCCT
3048CCGGCTAATTTCAGAGGGCG
2979 - 3348370AAGTGGGCTATACTATCTCAG /
CTTTATCTTCTGCCCACCTT
2999 - 3348350GCACCACTGTGAAAGAGATG /
CTTTATCTTCTGCCCACCTT
3279 - 3649373TTTAGTCAGTGATATTCAGAC /
GGAGTTTCACTTTCGCTTCT
3299 - 3651351CAATTCAGCCCAGTCTAAAC /
AAGGAGTTTCACTTTCGCTTC
3605348GAGCTAAAGAAGAGGCCCAA
3952CCTCTGAATGTCGCATCAAA
3906351CTCTGAGGTGCTAGATTCAC
4256CTTGTCAAATCAGATTGGAT
4210365GCTCAAAATGCCTCAGGAAGC
4574GTCTTTATCACCATTTCCAC
4532351GTCTGAGTGAAGTGAAGTCT
4882GGTGCACCTTCTGTTTCTCA
4835351CCTGGGGAAAGCTACTCAA
5185GGCGTATGTCATTCAGTTCT
5140353GAAGACGTGCTTAAGCGTTT
5492CCTCTTTGCAACAATTCTTT
5448351GAATGAAGACAATGAGGGTA
5798GCTTGCCTACGCACTGCATT
5751350GGAATTGCAGAAGAAGAAAG
6100GCTTAAAGAGATCTTCAAAG
6029 - 6416388GCCCTATTAGAAGTGGAACAAC /
GCATGTTCCCAATTCTCAGG
6054 - 6416363CAATGCTCCTGACCTCTGTG /
GCATGTTCCCAATTCTCAGG
6370350GAACAGTTTCTCAGAAAGAC
6719GGTTCAAGTGGGATACTAGC
6675350ATGGTTGGAGGAAGCAGATA
7024GCAGCAGATGATTTAACTGC
6969351TGGGCAGCTTGAAAAAAAGCT
7318GAGTAGGAGAGGCTCCAATA
7273331CCTGACCTAGCTCCTGGACT
7603GGGCAGCGGTAATGATCATC
7554351AGGATTTGGAACAGAGGCGTC
7904GTCTGCCACTGGCGGAGGTC
53 - 8205376GGAGGGTCCCTATACAGTAG /
CATCAGCTCTTTTACTCCCTT
7860 - 8205346CACAGAAACCAAGCAGTTGG /
CATCAGCTCTTTTACTCCCTT
55347GCTACCCGTAAGGAAAGGCT
8498GGTGCCTGCCGGCTTAATTC
57346CTGGTGTGGCTACAGCTGAA
8797GGGTCTCATCTATTTTTCTC
59 - 9094351GGGAAAAATTGAACCTGCAC /
CGACGGCCACCTGCAGAAGC
59/60 - 9373439AAGGCACTTCGAGGAGAAAT /
TCAAGAGATCCAAGCAAAGG
63 - 9677428GACCATCCCAAAAATGACAGA /
GTTGAACTTGCCACTTGCTT
65 - 10019477GCTGCTGAATGTTTATGATA /
CAGCTTTGGCAGATGTCATA
68 - 10423468GTCCAATCATTGGATTCAGG /
AATGCTGGATTAACAAATGT
72/73 - 75445TAGCAGGCTAGCAGAAATGG /
CTGTGACTCCAGCTGTTT
75 - 79447CAAATCCTGGAAGACCACAA /
AAACCATGCGGGAATCAG

Legend:
NOTE - in preparation, primer sequences and length not yet checked !!

Exons: exons amplified. Length: size amplified fragment in base pairs. Forward / reverse primer: forward and reverse primer for amplification (Hamed et al. 2006).

Other primers

Target F-primer Location R-primer Location Length Reference
Dp427l           Nishio
Dp427c AAACAGCTGGCATGGAGATGAAAGA Dp427c exon 1 GCAGTGCCTTGTTGACATTGTTCAG exon 4 231 Holder
Dp427m TTGGTGGGAAGAAGTAGAGGACTG Dp427m exon 1 GCAGTGCCTTGTTGACATTGTTCAG exon 4 235 Holder
Dp427p CAGCAAAAAGCTTTCCTATGAAGG Dp427p exon 1 GCAGTGCCTTGTTGACATTGTTCAG exon 4 366, 284 Holder
exon 2A CAAGGTTATGGCCTAGCTGAGAAGAG exon 2A .... .... .... Gualandi 2006
exon 2A .... .... CAGAAGGATGAATAATGTGTCTTC exon 2A .... Gualandi 2006
DpdelC CTCAGCACTCTGGAAGACCT exon 60 tgcttttgctactactcacGTTTC intron 70 1203 Tinsley
Dp140 ACACTAGCAATGGCAAAGCT Dp140 exon 1 CTTGCTCAAGCTTTTCTTTTAGTTGC exon 46 412 Lidov
Dp71 ATGTTCGTGCTGCTGCTTTAGACG Dp71 exon 1   exon 75 1393 Tinsley
Dp40 ATGAGGGAACACCTCAAAGGCCA Dp71 exon 1 tgcttttgctactactcacGTTTC intron 70 1014 Tinsley

Legend:
Target: dystrophin isoform to detect. F-primer: forward primer for amplification. Location location forward primer. R-primer: reverse primer for amplification. Location: location reverse primer. Length: size amplified fragment in basepairs. Reference: publications containing details regarding the primers.

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