Even after repeating Sanger sequencing for a particular genetic region, heterozygous band peaks can be seen for a particular nucleotide position, only with one of the primers used for bi-directional sequencing but the heterozygous peaks are absent when read with the other primer. This phenomenon is getting repeated again and again. Does it happen with anyone also? What does this signify? Only machine error or error in dNTP polymerisation? Or is it due to some differences in chemical reactions associated with the polymerase that we use during single primer extension reaction?
One way of getting this result is to have a polymorphism under the 3' end of one sequencing primer. The product has both sequences but the primer that anneals to both products shows the 2 bases of the snp but the other primer only anneals to the perfect homology on one amplimer and cannot sequence the allele associated with the mismatched snp. Effectively you may be creating an ARMS technique situation in your sequencing reaction. Move your primers out about 50 bases and your sequence may show the change or just move them out a few bases and the problem should go away. Quite often in these cases the checker gel of the Het sample will also show a slightly larger than expected band on the agarose gel
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