Question

An endonuclease has a recognition sequence that is 6 nucleotides long. The first 3 bp (double stranded) are:

GGC

CCG

What will be the next 3 nucleotides in the top strand?

Answer 1

An endonuclease or a restriction nuclease has a recognition site that is a palindromic sequence. This means that it remains unchanged when we read it from left to right and from right to left. Again, in the dsDNA it will be complimentary in the two strands.

Here, the first three bases out of 6 total bases are GGC. Since the sequnce when reading in the 5' to 3' on one strand must match when reading in the same direction on the 5' to 3' complimentary strand, so the restriction site must have the first three bases in the bottom strand to be GGC in 5' to 3' direction as well. So the sequnce is:

5' - G G C G C C - 3'

3' - C C G C G G - 5'

So the next three NTs in the top strand will be GCC.

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