The restriction enzyme BamHI recognizes and cuts the DNA sequence: 5′ GIGATCC 3′ 3′ CCTAG/G 5′, where “/” indicates the position at which each strand is cut. Which of the following restriction enzyme sites will, if cut, produce fragments that can be directly ligated to DNA cut with BamHI? A. 5′ /GATC 3′ B. 5′ CC TAGG 3′ 3′ CTAG/ 5′ C. 5′ GGATCC 3′ 3′ CCTIAGG 3′ D. 5′ GGATCC 5′ 3′ GIGATCC 5′ E. 5′ CCTAGIG 3′ 3′ GIGATCC 5
The Correct Answer and Explanation is:
The restriction enzyme BamHI recognizes the sequence 5′ GGATCC 3′ and cuts between the G and A on both strands, resulting in sticky ends: 3′ CCTAGG 5′ (on the bottom strand) and 5′ GATCC 3′ (on the top strand). This creates a 5′ overhang of “GATC” on one end and a complementary overhang of “CCTAG” on the other end.
Now, in order for fragments cut by BamHI to be ligated to another DNA fragment, the two fragments must have complementary sticky ends that can base-pair. Let’s evaluate each option:
A. 5′ /GATC 3′
- This sequence would create a blunt end if cut at the position marked by “/”. Blunt-ended fragments do not have sticky overhangs and are much less efficient at ligation compared to sticky ends. Therefore, this option does not match.
B. 5′ CC TAGG 3′ 3′ CTAG/ 5′
- This is the recognition sequence for the restriction enzyme BamHI. When cut, it generates the sticky ends CCTAGG (on the bottom strand) and GATCC (on the top strand), exactly like BamHI cuts. Therefore, this sequence will produce the same overhangs as BamHI and can be ligated to DNA fragments cut by BamHI. This is a correct match.
C. 5′ GGATCC 3′ 3′ CCTIAGG 3′
- The first part, “5′ GGATCC 3′”, is the BamHI recognition sequence. However, the second part, “3′ CCTIAGG 3′”, contains an error (the “I” is not part of the correct sequence). This sequence is incorrect for ligation purposes because the overhangs do not match. This option is incorrect.
D. 5′ GGATCC 5′ 3′ GIGATCC 5′
- This sequence is malformed. The correct sequence would be 5′ GGATCC 3′, 3′ CCTAGG 5′, and the “GIGATCC” is not a valid sequence. Therefore, this option is incorrect.
E. 5′ CCTAGIG 3′ 3′ GIGATCC 5′
- This sequence is not a proper recognition site, as it contains “GIGATCC”, which is not a valid base sequence. Like option D, this sequence cannot form matching sticky ends. This option is incorrect.
Correct answer: B. 5′ CC TAGG 3′ 3′ CTAG/ 5′
