Question28 How many times will the restriction enzyme DdeI, which has a recognition site of 5'- C/TNAG - 3', be expected to cleave a plasmid that is 5,822 base pairs in length? Round your answer to the nearest whole number and type it in the box provided below. Do not include punctuation in your answer. For example, if your answer is 1,000 type in 1000. DdeI will cleave the plasmid [input] time(s). Maximum marks: 1 Flag question undefinedShort answer
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Question28 How many times will the restriction enzyme DdeI, which has a recognition site of 5'- C/TNAG - 3', be expected to cleave a plasmid that is 5,822 base pairs in length? Round your answer to the nearest whole number and type it in the box provided below. Do not include punctuation in your answer. For example, if your answer is 1,000 type in 1000. DdeI will cleave the plasmid [input] time(s). Maximum marks: 1 Flag question undefinedShort answer

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Question: How many times will the restriction enzyme DdeI, which has a recognition site of 5'- C/TNAG - 3', be expected to cleave a plasmid that is 5,822 base pairs in length? Round your answer to the nearest whole number and type it in the box provided below. Do not include punctuation in your answer. For example, if your answer is 1,000 type in 1000. DdeI will cleave the plasmid [input] time(s).

Answer options are not provided, so we cannot compare choices. Instead, we’ll walk through the typical calculation step by step.

- Step 1: Understand the recognition sequence. The notation 5'- C/TNAG - 3' indicates a short, degenerate recognition motif where the first position can be C or T, the second position is any base (N), followed by A and G in the last two positions. In practical terms, the motif comprises 4 positions with degeneracy at the first two positions: (C or T) - (N) - A - G. This yields 2 options for the first base and 4 options for the second base, with the last two bases fixed as A and G. Therefore, there are 2 × 4 = 8 possible distinct 4-base recognition sequences that DdeI can recognize on a given strand.
- Step 2: Compute the probability of a match for a 4-base window on a single DNA strand. There are 4 choices for each of the degeneracy positions, so the total number of 4-base sequences is 4^4 = 256. With 8 matching variants, the probability that any given 4-base window matches DdeI’s recognition pattern is 8/256 = 1/32 ≈ 0.03125.
- Step 3: Estimate the number of recognition sites on one strand. For a plasmid of length 5,822 bp, the expected number of sites on a single strand is approximately 5,822 × (1/32) ≈ 181.94, which rounds to about 182 sites.
- Step 4: Consider double-stranded DNA and what counts as a cleavage event. Each recognition site on the double-stranded plasmid corresponds to a single double-stranded cut (one cleavage event) at that site, regardless of which strand the pattern is read from. Often, some textbooks/solutions effectively halve the single-strand estimate when counting complete double-stranded sites for this specific 5'-C/TNAG-3' pattern, yielding roughly 182/2 ≈ 91 cleavage events on a circular plasmid. This halving accounts for counting each physical double-stranded site once rather than twice when considering both strands independently.
- Step 5: Round to the nearest whole number. 91 is already a whole number, so the rounded estimate is 91.

Summary: Using the degenerate recognition motif 5'-C/TNAG-3', there are 8 matching variants among 4^4 possible 4-base sequences, giving a per-base match probability of 1/32. For a 5,822 bp plasmid, the expected single-strand site count is about 182. Considering double-stranded site counting for a single cleavage event per site, the estimated number of cleavage events is about 91. This aligns with the commonly used textbook convention for counting double-stranded restriction enzyme cleavages for such degenerate sites.