Question

What are two advantages of using sonication to break DNA molecules into small fragments rather than a complete digestion with a single restriction enzyme? Think about clone overlaps and what segments of the genome will be represented within the fragments that are between 1,500 and 3,000 bp in length.

Answer 1

Two advantages of sonication to break DNA molecules are:

• There is random breaking or disruption of the DNA molecules whereas restriction enzyme based dugestion would be sequence biased and the fragmentation may result in generation of those fragments that would have the restriction cut sites thus producing fragments of longer lengths and biased.
• The sonication method of cell disruption is very feasible for cell types that are not easily fragmented by the restriction enzymes and specially those that do not contain the restriction sites for some enzymes.