I first ligate 4 different pcr products to make a single insert and then cloned it in mammalian expression vector by using clontech Infusion cloning kit. I used BamH1HF and EcoR1 HF enzymes to cut my vector. Insert has matching vector sequence at both ends with BamH1HF and EcoR1 HF enzymes cutting sites. After cloning we observed sequence of first pcr product and some initial part of second pcr product was cut during cloning reaction. I checked my individual pcr product sequences for having above restriction sites in between but above enzyme sites were not found in any of 4 pcr products.
please anybody suggests what is the possible reason behind this.
I will be thankful to you for the same.