Table 1.

Primer sequences used


Primers

Direction

Exon

Annealing temperature, °C
5′-CAGCTCAAGGGACTCAGCCAA-3′   Sense   Exon 1   65  
5′-CAAATCCTCGGTTAGACCCTCTC-3′   Antisense   Exon 1   65  
5′-GAATGGAATATGAGGTCCTACTC-3′   Sense   Exon 2 (1st segment)   58  
5′-AGACTCTCGAAAAAGACGTTATC-3′   Antisense   Exon 2 (1st segment)   58  
5′-ACACCCGCCCTGGATAACGTCTT-3′   Sense   Exon 2 (2nd segment)   61  
5′-CGCGACTCTTTGGATCTTTGCTC-3′   Antisense   Exon 2 (2nd segment)   61  
5′-GTCCTAACCCAGGCCAACCT-3′   Sense   Exon 3 (1st segment)   61  
5′-GGCCATCTCCTCGTAGTCGC-3′   Antisense   Exon 3 (1st segment)   61  
5′-AGCTGCTGGAGGCTGTGGAC-3′   Sense   Exon 3 (2nd segment)   61  
5′-CTGACTCGCCTTCCCTAGGG-3′   Antisense   Exon 3 (2nd segment)   61  
5′-CAACAGGGACCTCCTCTCTATC-3′   Sense   Exon 4   62  
5′-CTGCACACACAGGGACAGCAG-3′   Antisense   Exon 4   62  
5′-GTACCTGGCCCTGGGGCTGCTG-3′   Sense   Exon 5   66  
5′-GATTCCCACCCCAGTGCCAGCT-3′   Antisense   Exon 5   66  
5′-CACTCACCCCTGCAGGCACCTGA-3′   Sense   Exon 6   60  
5′-GCACCGCCCAGACCCTGGCGG-3′   Antisense   Exon 6   60  
5′-CAGCATGCATCCTAGGCAGTTCA-3′   Sense   Exon 7a   65  
5′-TCTGAGAGTCACCTGCTGTGGCT-3′   Antisense   Exon 7a   65  
5′-AGGTCTCTTCCAGCCCTCAGTCT-3′   Sense   Exon 7b (1st segment)   61  
5′-CCTTTGCAGCTGGGCAGGATGTT-3′   Antisense   Exon 7b (1st segment)   61  
5′-AAGCCAGCACTCCTGCCATCACA-3′   Sense   Exon 7b (2nd segment)   61  
5′-CTGTAAGAGCATGGGCTGGAGGA-3′   Antisense   Exon 7b (2nd segment)   61  
5′-GTGTTCTGCACAGGTGCTTGC-3′   Sense   Exon 8   63  
5′-GTTGTTGGCCAGAGCTCAGAG-3′   Antisense   Exon 8   63  
5′-CACCCCAGAGCTCTCTGTGAC-3′   Sense   Exon 9 (1st segment)   65  
5′-CTCGCCAGGTAGGTCTGGGCCA-3′   Antisense   Exon 9 (1st segment)   65  
5′-ACTCAAGAACCTGGCCCAGACCT-3′   Sense   Exon 9 (2nd segment)   62  
5′-CAGGACCTGGGAATGCTGTGATG-3′   Antisense   Exon 9 (2nd segment)   62  
5′-CTGGAGGCTGTGGACGCGCGGTA-3′   Sense   M4   55  
5′-TCTTCTGGATGCTGCGGCGGAA-3′   Antisense   R7   55  
5′-AGTGTACGCCTTCTCCATCAAAG-3′   Sense   M2   55  
5′-CTTGCAGCCCTCACAGGCGCTG-3′
 
Antisense
 
RJ
 
55
 

Primers

Direction

Exon

Annealing temperature, °C
5′-CAGCTCAAGGGACTCAGCCAA-3′   Sense   Exon 1   65  
5′-CAAATCCTCGGTTAGACCCTCTC-3′   Antisense   Exon 1   65  
5′-GAATGGAATATGAGGTCCTACTC-3′   Sense   Exon 2 (1st segment)   58  
5′-AGACTCTCGAAAAAGACGTTATC-3′   Antisense   Exon 2 (1st segment)   58  
5′-ACACCCGCCCTGGATAACGTCTT-3′   Sense   Exon 2 (2nd segment)   61  
5′-CGCGACTCTTTGGATCTTTGCTC-3′   Antisense   Exon 2 (2nd segment)   61  
5′-GTCCTAACCCAGGCCAACCT-3′   Sense   Exon 3 (1st segment)   61  
5′-GGCCATCTCCTCGTAGTCGC-3′   Antisense   Exon 3 (1st segment)   61  
5′-AGCTGCTGGAGGCTGTGGAC-3′   Sense   Exon 3 (2nd segment)   61  
5′-CTGACTCGCCTTCCCTAGGG-3′   Antisense   Exon 3 (2nd segment)   61  
5′-CAACAGGGACCTCCTCTCTATC-3′   Sense   Exon 4   62  
5′-CTGCACACACAGGGACAGCAG-3′   Antisense   Exon 4   62  
5′-GTACCTGGCCCTGGGGCTGCTG-3′   Sense   Exon 5   66  
5′-GATTCCCACCCCAGTGCCAGCT-3′   Antisense   Exon 5   66  
5′-CACTCACCCCTGCAGGCACCTGA-3′   Sense   Exon 6   60  
5′-GCACCGCCCAGACCCTGGCGG-3′   Antisense   Exon 6   60  
5′-CAGCATGCATCCTAGGCAGTTCA-3′   Sense   Exon 7a   65  
5′-TCTGAGAGTCACCTGCTGTGGCT-3′   Antisense   Exon 7a   65  
5′-AGGTCTCTTCCAGCCCTCAGTCT-3′   Sense   Exon 7b (1st segment)   61  
5′-CCTTTGCAGCTGGGCAGGATGTT-3′   Antisense   Exon 7b (1st segment)   61  
5′-AAGCCAGCACTCCTGCCATCACA-3′   Sense   Exon 7b (2nd segment)   61  
5′-CTGTAAGAGCATGGGCTGGAGGA-3′   Antisense   Exon 7b (2nd segment)   61  
5′-GTGTTCTGCACAGGTGCTTGC-3′   Sense   Exon 8   63  
5′-GTTGTTGGCCAGAGCTCAGAG-3′   Antisense   Exon 8   63  
5′-CACCCCAGAGCTCTCTGTGAC-3′   Sense   Exon 9 (1st segment)   65  
5′-CTCGCCAGGTAGGTCTGGGCCA-3′   Antisense   Exon 9 (1st segment)   65  
5′-ACTCAAGAACCTGGCCCAGACCT-3′   Sense   Exon 9 (2nd segment)   62  
5′-CAGGACCTGGGAATGCTGTGATG-3′   Antisense   Exon 9 (2nd segment)   62  
5′-CTGGAGGCTGTGGACGCGCGGTA-3′   Sense   M4   55  
5′-TCTTCTGGATGCTGCGGCGGAA-3′   Antisense   R7   55  
5′-AGTGTACGCCTTCTCCATCAAAG-3′   Sense   M2   55  
5′-CTTGCAGCCCTCACAGGCGCTG-3′
 
Antisense
 
RJ
 
55
 

The table lists the sequence of the 14 sets of primers generated to amplify the PML exons. The primers were designed at the exonic-intronic boundaries to produce PCR products of various sizes, ranging from approximately 500 to 300 base pairs (bp). PCR products greater than 400 bp were digested with MboII (second fragment of exon 2 and second fragment of exon 7b) or BamHI (first fragment of exon 7b). The primers (M4, R7, M2, RJ) used to amplify and sequence the PML-RARα fusion gene are also reported.

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