An unknown DNA molecule was cleaved using several restrictio

An unknown DNA molecule was cleaved using several restriction enzymes individually and in various combinations. The DNA fragment sizes were determined by agarose gel electrophoresis and the restriction enzyme recognition sites were mapped. Subsequently, the DNA was sequenced and an extra recognition site was found for one of the enzymes. However, all the other mapping data was consistent, within experimental errors, with sequence data. What are the simplest explanations for this discrepancy? Assume the DNA sequence had no errors.

Solution

The extra fragment generated could be due to the partial digestion of the DNA fragment. When the amount of restricion enzyme is low it cuts the sequence partially. This sequenses can be of same size to other digested sequences and hence cannot be distinguised properly on the gel electrophoresis. But during sequencing the presence of the extra recognition site can be detected. An alternative explationation could be that the restriction site is very close to other restriction site, hence the fragment obtained would be very small which could run off the agarose gel and could not be detected on the gel.