EcoRI Restriction Site Frequency in 4 Mbp DNA Sequence 

The EcoRI restriction site frequency in 4 Mbp DNA sequence is a key concept in molecular biology for GATE Life Sciences exams. With equal nucleotide probabilities, this question tests probability calculations for restriction endonuclease sites.

Solution Explanation

EcoRI’s recognition site is a specific 6-base pair sequence (GAATTC), and in random DNA with equal nucleotide probabilities, it occurs about every 4,096 bp on average.

The expected frequency of the EcoRI site in a 4 Mbp (4,000,000 bp) DNA sequence is calculated as total length divided by 46, since there are 4 nucleotides and a 6-bp site: 4,000,000 / 4,096 ≈ 976.56, so roughly 976 or 977 times.

This assumes non-overlapping sites and ignores edge effects in a linear sequence, which is standard for such problems.

Option Analysis

  • (A) 976: Correct, as 4,000,000 ÷ 4,096 = 976.5625 (integer part 976).
  • (B) 46: Incorrect; this might assume a 10-bp site (410 ≈ 1M, but wrong length) or miscalculation.
  • (C) 64: Incorrect; 64 = 43, for a hypothetical 3-bp site (e.g., 4M / 64 = 62,500).
  • (D) 1000: Incorrect; approximate (4M / 4,000 = 1,000), perhaps rounding 46=4,096 to 4,000.

EcoRI Recognition Sequence

EcoRI recognizes the palindromic 6-bp sequence 5′-GAATTC-3′, cleaving between G and A to produce sticky ends.

In random DNA, each position has 1/4 chance per base, so probability per site is (1/4)6 = 1/4096.

Step-by-Step Calculation

For a 4 Mbp (4,000,000 bp) sequence:

  • Expected sites = 4,000,000 × (1/4,096) ≈ 976.56.
  • Thus, ~976 occurrences (option A).

Parameter Value
DNA Length 4,000,000 bp
Site Length 6 bp
Possible Sequences 46 = 4,096
Frequency 4M / 4,096 ≈ 976

Why Other Options Fail

  • 46: Wrong site length assumption (e.g., 8-10 bp).
  • 64: Matches 43 for 3-bp site.
  • 1000: Rough estimate ignoring exact 4,096.

This aligns with competitive exam patterns like GATE Life Sciences, emphasizing biotech tools.