What is a four-base recognition sequence, and why does it often appear frequently in genomes?

• A. It is a four-base sequence that codes for a restriction enzyme.
• B. It is a four-base sequence involved in transcription initiation.
• C. It is a four-base sequence that forms a hairpin structure.
• D. It is a four-base recognition sequence recognized by restriction enzymes; with 4^4 = 256 possibilities, many sites occur randomly in genomes.

Answer: (D)

Restriction enzymes recognize short DNA sequences called recognition sequences. A four-base recognition sequence means a DNA stretch of four nucleotides that the enzyme can identify and usually cut near. Because each position can be one of four bases, there are 4^4 = 256 possible four-base sequences. If bases are distributed roughly at random, each specific four-base string occurs with probability 1/256 at any given position, so in a genome of substantial length you’ll find many such sites just by chance. In other words, short recognition sequences are common simply due to combinatorics and genome size, which is why four-base sites appear frequently in genomes. Real genomes may show biases due to base composition and repetitive elements, but the underlying idea remains that short sequences are expected to occur often.