Partial digest in restriction mapping

In summary, scientists can use the sum of the sizes of restriction fragments to determine if the DNA has been completely digested. If the sum is greater than the original size of the DNA, it indicates an incomplete digestion. This is because incomplete digestion results in additional fragments, making the sum larger than the original size.
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Mycelium
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Homework Statement


The question:
Scientists need to take precautions when they carry out restriction mapping. They need to make sure that the enzyme they have used has completely digested the DNA. One check they may carry out is to add the sizes of the fragments together. How could scientists use this information to show that the DNA has not been completely digested?

Homework Equations

The Attempt at a Solution


I know that it would be indicative of a partial digest if the sum of the fragments was greater than the size of the original fragment, but I don't understand why it would be so?
 
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Well, let's say you have a 10 kb linear DNA that gets cut into a 4 kb and 6 kb piece. What bands do you expect to see in a complete digest, and what is the sum of the sizes of the bands? If the digest is incomplete, what fragments do you expect to see, and what is the sum of the sizes of the bands?
 
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  • #3
Ygggdrasil said:
Well, let's say you have a 10 kb linear DNA that gets cut into a 4 kb and 6 kb piece. What bands do you expect to see in a complete digest, and what is the sum of the sizes of the bands? If the digest is incomplete, what fragments do you expect to see, and what is the sum of the sizes of the bands?
Okay, I think I get it. So if it was complete, you would see only 4kb and 6kb fragments. If incomplete, there would be 10kb pieces along with the 4 and 6 kB pieces so it would seem as though you had a 20kb piece originally?
 
  • #4
Yup. Incomplete digestion essentially gives "extra" bands that will make the sum of the sizes of the bands larger than the original piece of DNA.
 
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What is a partial digest in restriction mapping?

A partial digest in restriction mapping is a method used in molecular biology to identify and map the locations of restriction sites on a DNA sequence. It involves using a limited amount of a restriction enzyme to cut the DNA in specific locations, resulting in a partial digest pattern that can be compared to known restriction maps to determine the sequence's location.

How is a partial digest performed?

A partial digest is performed by first isolating the DNA sequence of interest and then incubating it with a limited amount of a restriction enzyme. The enzyme will cut the DNA at specific restriction sites, resulting in fragments of varying lengths. The fragments are then separated using gel electrophoresis, and the resulting band pattern can be compared to known restriction maps to determine the sequence's location.

What are the advantages of using a partial digest in restriction mapping?

One advantage of using a partial digest is that it allows for the identification of multiple restriction sites on a single DNA sequence in a single experiment. It is also a more cost-effective method compared to full digestion, as it uses a smaller amount of the expensive restriction enzyme.

What are the limitations of using a partial digest in restriction mapping?

One limitation of using a partial digest is that it can result in overlapping fragments, making it difficult to accurately determine the exact location of restriction sites. Additionally, some restriction enzymes may not work well with this method, leading to incomplete digestion and inaccurate results.

How is a partial digest pattern interpreted in restriction mapping?

A partial digest pattern is interpreted by comparing the resulting band pattern to known restriction maps. By identifying the size and location of the bands, the sequence's location and the number of restriction sites can be determined. The pattern can also be used to confirm the presence or absence of specific restriction sites on a DNA sequence.

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