We are dealing with 3 different primers which target 3 different genes of particular plant virus. The actual product size is about 422, 420, 380 bp and it was doing well for 2 years. But results are giving 100 bp extra size than desired ones (viz., 522+, 520+, 380+) from the samples of 3rd year onward.
Here what might be the reasons for this type of result? Is it needed to send for sequencing?
Please help us to solve from this problem.
Dear Ksds Roopa Kumar
Are you performing the PCR with the isolated virus gDNA or viral RNA transcribed into cDNA?
Dear Mr Kumar,
Are you performing multiplex PCR? Also, whether these results (additional 100 bp amplification) are consistent?
Dear Ksds Roopa Kuimar,
No doubt that sending your PCR products for sequencing and subjecting the results to BLAST analysis will yield essential clues about what is happening.
It is odd that ALL of your bands from all of your samples are 100 bp larger.
Double-check that you haven't made any changes to the DNA ladder that you are using as a size comparison.
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