Real Science and Other Adventures

Restriction enzyme recognition sites – the oldest palindromes

Madam, I’m Adam.

A fast never prevents fatness.

Never odd or even.

These are all palindromes – the letters are the same whether they’re read backwards or forwards. But bacteria invented palindromes long, long before we did. Many bacterial restriction enzymes recognise palindromes in DNA.

Restriction enzymes are commonly used by bacteria to cut and destroy the DNA of invading viruses. Each restriction enzyme recognises a certain sequence of base pairs. This is one of the strands in the sequence recognised by the enzyme EcoRI (which is found in the bacteria E. coli):

ecori-site-no-nos

DNA has two different ends: a 5′ end and a 3′ end. We read DNA from the 5′ end towards the 3′ end. This is also the direction nucleotides are added when the DNA is copied(replicated or transcribed). So we can write this strand with a 5′ end on the left and a 3′ end on the right like this:ECORI SITE.png

But DNA has two strands. Each base partners with its complement – G with C  and A with T. The two strands for the EcoRI restriction site are written like this:

ECORI SITE head up.pngNote that the 5′ end is on the left in the top strand and on the right in the bottom strand. The two strands are heading in opposite directions – we call this antiparallel. Reading each strand like this – 5′ to 3′ – they are the same (5′-GAATTC-3′).

I think it helps visualise and understand the symmetry if you write the lower strand upside down like this:

ecori-site-up-down

That way it really does look the same whether you’re sitting in your chair or standing on your head. It looks symmetrical like a palindrome should.

 

 

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One comment on “Restriction enzyme recognition sites – the oldest palindromes

  1. Pingback: Using restriction enzymes to cut and paste | Real Science and Other Adventures

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This entry was posted on October 1, 2016 by in DNA tools and techniques, VCE Biology and tagged , , , .
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