Gel electrophoresis, TLC techniques

[SaintJude]

There are always those MCAT questions that tests if you understand the rationale behind conventional components of common experiments. So I have two:

1.) As part of creating a copy of the gel electrophoresis results, why does dipping the page into a basic solution denature the DNA fragments into single strands?

2.) Why do chemists consistently use Iodine vapor to stain TLC ?

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[MedPR]

There are always those MCAT questions that tests if you understand the rationale behind conventional components of common experiments. So I have two:

1.) As part of creating a copy of the gel electrophoresis results, why does dipping the page into a basic solution denature the DNA fragments into single strands?

2.) Why do chemists consistently use Iodine vapor to stain TLC ?

Glad you asked these questions. It reminded me that I have to review the important lab techniques!

1. Basic solution will denature DNA by interrupting the hydrogen bonds between strands. Acidic solution will also interrupt the hydrogen bonding between the two strands, but it will also hydrolyze the bonds within the single strand.

2. I believe the Iodine is used to stain the compound. It is also preferred over other staining methods because Iodine will react pretty readily (I assume because it is a good nucleophile?) and also be removed readily because it is a good leaving group. I think the point of using iodine versus another coloring agent is that it doesn't cause any changes, it just binds so you can see the compound.

 

[TXKnight]

There are always those MCAT questions that tests if you understand the rationale behind conventional components of common experiments. So I have two:

1.) As part of creating a copy of the gel electrophoresis results, why does dipping the page into a basic solution denature the DNA fragments into single strands?

2.) Why do chemists consistently use Iodine vapor to stain TLC ?

I am not sure I understand your question, but for the sake of trying to answer: both acidisc and basic conditions denature DNA. Basic conditions are preferred in molecular biology techniques for the most part. NaOH can be used for this. If you think about this in the context of stability, it may be easier to see how the hydroxide ions interfere with the hydrogen bonding that hold base pairs together.

 

[MedPR]

I am not sure I understand your question, but for the sake of trying to answer: both acidisc and basic conditions denature DNA. Basic conditions are preferred in molecular biology techniques for the most part. NaOH can be used for this. If you think about this in the context of stability, it may be easier to see how the hydroxide ions interfere with the hydrogen bonding that hold base pairs together.

I think the question is why basic solution and not any other of the denaturing agents we've learned about. Acidic solution will interfere with the hydrogen bonding, ethylmercaptan will break the disulfide bonds. Heat will break bonds, urea will break bonds, etc.

Why base over any of those? Because base will only break apart the two strands rather than also destroying the single strands like other denaturing agents.

 

[SaintJude]

Thanks, MedPr! On point.