Question Video: Identifying the Sequence that is Recognized by EcoRI | Nagwa Question Video: Identifying the Sequence that is Recognized by EcoRI | Nagwa

Question Video: Identifying the Sequence that is Recognized by EcoRI Biology • Third Year of Secondary School

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The diagram provided shows the mechanism of the restriction enzyme EcoRI. Reading 5′–3′, what sequence does this restriction enzyme recognize to cut?

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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.

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