Video Transcript
The diagram provided shows the
mechanism of the restriction enzyme EcoRI. Reading five prime to three prime,
what sequence does this restriction enzyme recognize to cut?
This question asks us about a
specific restriction enzyme, EcoRI. Let’s review what restriction
enzymes are and how they can be used to manipulate DNA.
Restriction enzymes are useful
tools in biotechnology because they can be used to cut specific DNA sequences so
they can be combined in interesting ways. They were originally discovered in
bacteria as a way for bacteria to defend themselves from viruses. They do this by cutting viral DNA
into pieces, so the virus is restricted from carrying out its life cycle.
There are many different
restriction enzymes, and each has its own target DNA sequence that it recognizes and
cuts. This is called a recognition
sequence. These recognition sequences are
palindromes, meaning they’re read the same way forwards and backwards. The word “racecar” is an example of
a palindrome, because it reads “racecar” whether we read it in one direction or the
other.
The DNA sequence GGATCC is an
example of a palindrome and is the recognition sequence for the restriction enzyme
BamHI. GGATCC is the sequence on the five
prime to three prime strand. And when we read it in this
direction, it reads as GGATCC. If we look at the sequence on the
opposing three prime to five prime strand, we see that it is also GGATCC when we
read it in the five prime to three prime direction.
So when we’re talking about
palindromes in DNA, the sequence on the five prime to three prime strand is the same
as the sequence on the opposing strand when read in the five prime to three prime
direction. In terms of how this enzyme cuts
DNA, we can see this here. Each restriction enzyme, in
addition to having a unique recognition sequence, has a specific cutting
pattern.
Now that we’ve covered the basics
regarding restriction enzymes and how they cut DNA using their recognition
sequences, let’s try to answer our question.
In this question, we’re provided
with a sequence of DNA and the cutting pattern of the restriction enzyme EcoRI. In order to figure out what the
recognition sequence is, we can do this by figuring out where the palindrome is. If we focus on the region where the
cut is, on the five prime to three prime strand, it’s AATT. We can see that this is a
palindrome, because on the opposite strand in the reverse direction it’s also
AATT. There might be more of the
sequence, so let’s keep going.
The next base over is a G on the
five prime to three prime strand. And on the three prime to five
prime strand, it’s also a G, so this is part of the palindrome too. If we go over another base, we have
a C on the five prime to three prime strand. But on the opposite strand in
reverse, this is a T. So, the palindrome doesn’t extend
this far, and this position isn’t part of the recognition sequence.
So, the indicated sequence must be
the recognition sequence. On the five prime to three prime
strand, it reads GAATTC. And on the three prime to five
prime strand, it reads GAATTC when read in the five prime to three prime
direction. This is a palindrome.
Therefore, the sequence that EcoRI
recognizes in the five prime to three prime direction is GAATTC.
