Hello I am using two expression vectors (pCAGGS and pCDNA) for transforming a fragment of gene (2kbp). For transformation, I am using NEB 10 beta-competent E.coli cells. Issue? Although my gene of interest is transformed into the expression vector, a portion of the expression vector's nucleotide sequence is being removed or deleted.

Could anyone share their experience on this and how you overcame this problem?

Thanks in advance!