DNA techniques content video: restriction enzymes and DNA libraries quiz - Q4

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mcatacct1
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Joined: Sat Oct 26, 2019 4:35 pm

DNA techniques content video: restriction enzymes and DNA libraries quiz - Q4

Post by mcatacct1 » Wed Feb 12, 2020 6:52 pm

Q: select all of the applications for which restriction enzymes are used.

I selected...

-Gene cloning via insertion of genes into plasmid vectors
-recognizing and cleaving foreign DNA

I did not include...

-Repairing DNA damage in small bacterial clones
-Distinguishing certain alleles by SNP recognition

The answer told me I'm incorrect, but I'm not understanding what specifically I failed to include or shouldn't have included. I also was unsure what a "SNP recognition" was. Could you tell me which answer choices were suppose to be included, and what a SNP recognition is if possible? Thank you for your time.
NS_Tutor_Mathias
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Re: DNA techniques content video: restriction enzymes and DNA libraries quiz - Q4

Post by NS_Tutor_Mathias » Thu Feb 13, 2020 1:52 pm

"SNP recognition" refers to sequencing portions of a person's genome to detect single nucleotide polymorphisms, a simple and common type of mutation. Through genome-wide assocation studies (GWAS) such polymorphisms have been linked to a variety of diseases. A smaller number of SNPs have stronger (sometimes experimental) evidence linking them to metabolic defects.

A common way of performing this analysis is through the use of restriction enzymes that may provide alternate fragments if a mutation is present (particularly when either the SNP or WT provide a binding site for a particular restriction enzyme), rather than performing a more cost and labor intensive form of sequencing.

Any answer choice in which a restriction enzymes were involved should be included, whether working in its normal biological role or as a repurposed tool in molecular biology.
mcatacct1
Posts: 65
Joined: Sat Oct 26, 2019 4:35 pm

Re: DNA techniques content video: restriction enzymes and DNA libraries quiz - Q4

Post by mcatacct1 » Sun Feb 23, 2020 11:48 pm

thank you for the reply! Just to clarify with an example...

So if someone has sickle cell where glutamate (GAG) goes to valine (GUG) we'd say they have a SNP. But to determine this empirically we get some restriction endonuclease that normally cuts between G-A producing some number of fragments (let's say 4) when glutamate is present. But when we have valine present we only get 3 fragments. So we can run the fragments through a gel electrophoresis, and because the results of the gels are different we can say the DNA sequences are different. Is that example an accurate representation of how restriction endonucleases would be used?
NS_Tutor_Mathias
Posts: 616
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Re: DNA techniques content video: restriction enzymes and DNA libraries quiz - Q4

Post by NS_Tutor_Mathias » Mon Feb 24, 2020 1:43 pm

That is exactly it.

Small clarifications though:
The restriction endonuclease is likely to recognize at least 4 bases. Useful endonucleases often recognize at least 6, and often palindromic sequences. And since this is DNA, the template strand equivalents would be CTC and CAC.

So if this endonuclease were to recognize CCAC, it would cut in the case of the SNP being present and not in the case of the SNP being absent. Producing 2 fragments if the SNP is present and just one if it is not.

Of course, in reality, the target sequence may occur in several locations and so more than just those fragments may appear - which I assume is what you were getting at with 3 vs 4 fragments.

So it sounds to me like you got the big picture down perfectly, which is what really matters for understanding experimental design!
mcatacct1
Posts: 65
Joined: Sat Oct 26, 2019 4:35 pm

Re: DNA techniques content video: restriction enzymes and DNA libraries quiz - Q4

Post by mcatacct1 » Wed Feb 26, 2020 12:50 am

Thank you so much!
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