12 votes
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Are alleles equally sized?

In general, alleles don't have to be the same size. Two major examples which come to mind are the Huntingtin gene and FMR1. Huntingtin is the causative gene of Huntington's disease. In people with ...
R.M.'s user avatar
  • 1,554
5 votes

Why does hemoglobin electrophoresis in sickle cell trait gives two bands but not three?

This is a really interesting question and again reminds of how ignorant we are about things as subtle as this which otherwise should have been an obvious question. First of all, although there seems ...
Polisetty's user avatar
  • 3,687
5 votes
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How does SDS-PAGE separate based on mass?

You are correct that molecule mobility depends on the mass-to-charge ratio, and this means that different sized molecules with the same $\frac{m}{q}$ will have the same acceleration. However, the ...
acvill's user avatar
  • 8,286
4 votes
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Are longer and shorter DNA similarly charged?

Each phosphate group has a single negative charge. Not just the terminals. The reason gel electrophoresis works so well with DNA is that charge is linearly proportional to size. The longer the ...
Karl Kjer's user avatar
  • 7,657
4 votes
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Why would I see no bands in DNA gel electrophoresis of red blood cells?

It is a trick question. Red Blood Cells (RBC) are anucleated in mammals. You are not going to be able to extract anything about chromosome 1 from RBC. By the way, if you want to know how they got ...
Remi.b's user avatar
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4 votes

Why do you have to submerge your gel in buffer before adding DNA

This has a very simple reason: Adding the buffer later poses the risk to wash out your sample from the well as well as mixing samples. There is another reason: It makes loading easier. The sample is ...
Chris's user avatar
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3 votes

Why is gel used in electrophoresis?

In gel electrophoresis, the gel is the mechanism by which macromolecules of different sizes are separated. By loading the gel with amino acids (or proteins or DNA), you start all of the samples ...
porkchop's user avatar
  • 111
3 votes
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Why does my gel have such poor resolution?

Although your tech is referring to your DNA samples, your ladder also indicates there is some room for improvement of your running technique. -20C for a week should not have impacted the quality of ...
tswei's user avatar
  • 344
3 votes

Agarose gel Ladder smear

Are you sure that your TBE is at the right dilution? And that you're using TBE to make the gel and also as the buffer for running? That sort of wavy line looks like what you might get if you'd made ...
mykinz's user avatar
  • 41
3 votes

Quantifying DNA in a band on gel electrophoresis

All three methods could be used to measure the amount of DNA. However in practice, method 2 (estimation by dye brightness) typically works best in a normal workflow. It really depends on what you plan ...
tswei's user avatar
  • 344
3 votes
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What do we call this adjustable platform used to ensure that something is positioned strictly level in a lab?

I remember using those for agarose gels as an undergraduate, though using them for PAGE doesn't make a lot of sense unless your bench is seriously out of level. Anyways, they can be called levelling ...
canadianer's user avatar
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3 votes
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What is meant by 4 –12% or 8% SDS-PAGE?

Do the percentage values refer to the percentage of acrylamide in the gel? Yes. The 8% gel is 8 g acrylamide per 100 mL. The “4-12%” gel is a gradient gel, which are useful for separating proteins ...
acvill's user avatar
  • 8,286
3 votes
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Electrodes in non-conducting fluid? Are they neutral? Electrolysis, Electrophoresis

Electrodes are neutral, but they are held at different potential. This is similar to the current flow in a wire: although current flows, the wire remains neutral, i.e., no charge is accumulated (...
Roger V.'s user avatar
  • 3,842
3 votes

Can I column purify instead of gel extract?

Yes, this is perfectly possible. There are a few small caveats though: do not overload the column with too much DNA, as this will result in lower yields also do not load an amount of DNA which is too ...
Chris's user avatar
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3 votes

Why do we choose to use agar instead of agarose in various microbial applications?

Agarose is indeed more expensive than agar because it is purified from agar, i.e. it is agar minus the agaropectin. Agaropectin is heterogeneous, and modified with acidic side-groups. The consequence ...
CaroZ's user avatar
  • 392
2 votes

Why my proteins are migrating like this on SDS-page?

It's a guess, as I haven't run a algae sample on SDS-PAGE, but your migration problems might be due the algal polysaccharides that are present in your sample. Check if your protein purification ...
BioGeo's user avatar
  • 137
2 votes

What are the possible reasons to get extra unrecognized band in agarose gel electrophoresis?

Looks like genomic DNA contamination to me. More importantly, does it really matter? I certainly appreciate the curiosity but, if your objective is cloning, I would just keep going and then do some ...
canadianer's user avatar
  • 17.7k
2 votes

What are the pros & cons of site-directed mutagenesis? What are the alternatives?

The 'Quickchange' method is probably what you want. If you are worried about self complementary (which you shouldn't be too much) you can actually stagger the primers so they are not fully ...
mimat's user avatar
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2 votes
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What are the pros & cons of site-directed mutagenesis? What are the alternatives?

SDM will be the perfect tool for this mission, unless the plasmid in question is very large (20+ kb). When you have performed the SDM, digest the products with dpnI to remove the original plasmids, ...
Jeppe Nielsen's user avatar
2 votes
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Why marker and control are loaded in the beginning or ending lane of the gel?

No important reason. It is for esthetics, and also for ease of description in figure legends. One could argue that it might be confusing to have the markers or the control in the middle, but since the ...
Karl Kjer's user avatar
  • 7,657
2 votes

Agarose gel Ladder smear

Try going even higher with the agarose concentration, as it looks like you have decent separation of the small bands and poor separation of the large bands. Also try a fresh batch of agarose. I ...
Jeppe Nielsen's user avatar
2 votes
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Optimizing Gel Electrophoresis: Ampere, Volts and Buffer concentrations

As far as I know you can either adjust the ampere or the voltage as both is dependent of the resistance from the buffer. Which means that I would suggest you to let the voltage as it is. As the ...
TheGreenOne's user avatar
2 votes
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Gel electrophoresis and foam

Gas bubbles are foamed by electrolysis of water, generating bubbles of hydrogen gas on the negative electrode and oxygen gas on the positive electrode. As for the foam itself... I am guessing there ...
JayCkat's user avatar
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2 votes
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During DNA foot-printing, what is the purpose of radioactively labeling only one end of the DNA fragment?

Preamble Although there is a Wikipedia page with a general account of DNA footprinting, this perhaps does not put sufficient emphasis on the general strategy, making reference to the Maxam & ...
David's user avatar
  • 25.2k
2 votes
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PCR and large-scale PCR

I made the large-scale in a falcon tube and then moved the mixture to PCR tubes each containing 50 μL, so the PCR conditions should be the same as the single PCR amplification If all reagent ...
acvill's user avatar
  • 8,286
1 vote

How to confirm secondary structure formation of Precursor miRNA on gel?

Disclaimer: Although I have attempted northern blots for miRNA, I haven't actually done the kind of experiment you are talking about. First of all you need controls. A negative control: a same ...
WYSIWYG's user avatar
  • 35.5k
1 vote

What causes DNA gel electrophoresis bands to swirl?

It can possibly be one of two problems: Either the gel poorly prepared, in that it was cooled for too long, resulting in parts that solidified before pouring it into the mold. This I have seen before,...
Roelof Coertze's user avatar
1 vote
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DNA Sequencing - Sanger termination method: What effects will more ddNTPs in solution have on the resolution on agarose gel via electrophoresis?

You are correct. The greater the ratio of ddNTPs to dNTPs, the more frequently ddNTPs will terminate the reaction, resulting in shorter mean fragment size. However, Sanger sequencing is not done with ...
Karl Kjer's user avatar
  • 7,657
1 vote

Blackgram leaves. SDS page. Phosphate buffer method

You should de-stain your gel longer. I can see at least one thick band at the top, but without de-staining longer you are probably missing other fainter bands. Also, please explain what you mean by "...
Guillaume's user avatar
  • 715
1 vote

PCR products with no band in gel

My first guess would be that you're using too much template DNA for these conditions. Your wells light up quite a bit, 448 ng is also on the high side. Try lower concentrations of template DNA (1-100 ...
VonBeche's user avatar
  • 1,473

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