Problem 1: Restriction Fragment Analysis

Question: A 9 kb circular plasmid is digested with EcoRI alone (3 fragments: 4 kb, 3 kb, 2 kb) and BamHI alone (2 fragments: 6 kb, 3 kb). When digested with both, 5 fragments are produced. How many EcoRI sites and BamHI sites are there?

Solution:

• EcoRI alone → 3 fragments = 3 EcoRI cuts = 3 EcoRI sites (3+3+2+1 is wrong; circular: n cuts = n fragments). Verify: 4+3+2 = 9 kb ✓
• BamHI alone → 2 fragments = 2 BamHI cuts = 2 BamHI sites. Verify: 6+3 = 9 kb ✓
• Double digest → 5 fragments = 3+2 = 5 total cuts (confirmed: 3 EcoRI + 2 BamHI = 5 cuts → 5 fragments) ✓

Answer: 3 EcoRI sites and 2 BamHI sites.