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Calculating the molecular concentration of DNA

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Calculating the molecular concentration of DNA

Postby keetner » Sun Oct 07, 2012 7:49 pm

I'm not sure if you guys will be able to help me or not...but I thought I would at least try posting:

Image

In case the image is cut off: http://i.imgur.com/jlq9T.jpg

1) Look at the 660g/bp (it means g/mol of base pair); it is highlighted in pink
- I do not understand where this 660 is taken from. Some sources online have stated that the MW of base pairs in double stranded DNA is 660, and that a single strand base is 330.
- If this is the case, wouldn't each base pair technically have different masses? A-T vs C-G?

2) Why do we multiply by two? The question says "find molar concentration of single strands of DNA..."
-If 660 is the mass of a base pair, isn't it taking in account the mass of both strands? Because right now, it seems like we've multiplied by two to account for the other strand.

3) Why do we multiply by Avogadro's number?
- I assume it's to 'cancel' out the mol unit
- However, I thought the point of this question was to find the MOLAR concentration, so would it not be in mol/L?

I should have asked my professor in advance, but I fell behind in studying...unfortunately.

Any help or input would be greatly appreciated.

Thank you.
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Re: Calculating the molecular concentration of DNA

Postby JackBean » Sun Oct 07, 2012 8:00 pm

1) of course they do, but this is an average ;)

2) probably because you've used molecular weight of base pair

3) yeah, by that you get the number of molecules. No reason to make that since both are equivalents. But I would guess it's because of the last sentence "10^13 ssDNA strands per liter and that's a lot"
http://www.biolib.cz/en/main/

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Postby keetner » Sun Oct 07, 2012 8:13 pm

Thanks for the response!

I'm still confused as to why you would multiply by two (my second question).
If 660 is the mass of the base PAIRS, I assume we are including the mass of both strands. So to me, before we multiply by two, the mass of a double strand DNA would be ~3.29x10^-11.

It's confusing because would it not make more sense to divide by two? That way we are getting the mass of each strand...

OR if we had actually multiplied by two, we would use 330 instead of 660.

I hope I've made some sense...

Thanks again.
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Re:

Postby Cat » Sun Oct 07, 2012 9:32 pm

keetner wrote:Thanks for the response!

I'm still confused as to why you would multiply by two (my second question).
If 660 is the mass of the base PAIRS, I assume we are including the mass of both strands. So to me, before we multiply by two, the mass of a double strand DNA would be ~3.29x10^-11.

It's confusing because would it not make more sense to divide by two? That way we are getting the mass of each strand...

OR if we had actually multiplied by two, we would use 330 instead of 660.

I hope I've made some sense...

Thanks again.


Because 660 is NOT the mass of the bp. It's an average Molecular Weight of a DNA bp. Therefore, it's 660g/mole = 1 bp (so it's actually 660 (g/mole)/bp - that is why the answer is in g/mole). Now 1 mole of dsDNA = 2 moles of ssDNA since each molecule becomes 2 molecules when dissociated. And that is where 2 comes from.
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Re: Calculating the molecular concentration of DNA

Postby keetner » Sun Oct 07, 2012 11:11 pm

Hrm...

I think the (gram/mol)/bp is throwing me off. With dsDNA, it's 660 but with ssDNA, it's 330. Also, I think I was under the impression that if you had the MW of a base pair in DNA, you would divide that MW in half so you could get the MW of each base. Though I guess that would make no sense since we're talking about concentration?? mol/L? So by denaturing the dsDNA, is the solution becoming "more concentrated" with ssDNA? And like you said, the ratio of dsDNA:ssDNA is 1:2 -- and like any ol' stoich problem, you would have to times by two in this case.

But if we were STRICTLY talking about MASS and not concentration, then my logic in thinking you would divide by two would not be wrong, would it?

Yes...? Hopefully?!

I'm not sure if I'm not the right track, but if we were to pretend that dsDNA was CH4 and that ssDNA was C2H6; keeping molar ratio 2:1. You obviously wouldn't divide CH4 by 2 to get the value for C2H6...cause that makes no sense. I'm guessing it's the same idea here with DNA, then?

Sorry if this post is a bit scattered, since most of it is just my rambling/thinking. I also apologize for my chemistry skills right now, haha. It's just been so long since I've had to do any calculations like this. Plus, I think I've developed the bad habit of just doing things without really understanding why you do them (units in stoich and what not). But I really do appreciate the help.

Thank you again!
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Postby JackBean » Mon Oct 08, 2012 2:07 pm

Concentration of 2 ng/ml of dsDNA will still be 2 ng/ml of ssDNA after denaturation. Concentration of 2 mmol/ml of dsDNA will be 4 mmol/ml of ssDNA after denaturation.
http://www.biolib.cz/en/main/

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Re: Calculating the molecular concentration of DNA

Postby keetner » Mon Oct 08, 2012 6:53 pm

Ahh, I get it. That's what I was thinking. You basically summed up my messy post in two short sentences.
Thanks again for the help + clarification you guys :).
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