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uM molecule versus basepair calculation

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#1 fume711



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Posted 14 December 2010 - 05:19 PM

Not really a homework question but not sure which forum I would ask calculation questions. I've been doing a bunch of calculations converting nanodrop ng/ul to uM and ran into an interesting dilemma.

Scenerio 1) Whenever purchasing primers, they usually come lyophilized in nmol that is calculated from A260 and converted with the epsilon value to get a nmol in molecule form, not nmoles of basepair so length matters. ie: 107 nmols = 107 nmols of molecules, not 107 nmols of bases.

Scenerio 2) When i convert dsDNA from nanodrop ng/ul, i usually convert by 660 g / 1 mol bp without taking into account the dsDNA length, giving a uM in bp rather than molecule. Units can still come out to uM meaning micromoles of basepair / L.

My question: Is it general practice to assume moles in DNA conversions automatically refer to moles of molecules rather than moles of basepair, and as such I should add in the length of the DNA in the calculation.

Example online calculators such as promega and ABI / roche take into account the length or molecular weight (which indirectly takes into account the length) and label the answer as pM for example, but don't specify pmoles of molecules / L or pmoles of basepairs / L. The calculations do correspond to pmoles of molecules / L but I wanted to see whether this is general practice throughout the community. Nanodrops give a tangible ng/ul value taking into account the physical bases via beers law does it not?

Thanks and hope it's not too confusing.

#2 mdfenko


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Posted 15 December 2010 - 11:10 AM

statements of concentration are always referring to molecules, not base pairs. if they want to speak about base pairs they will specifically say so.
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#3 fume711



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Posted 17 December 2010 - 08:31 PM

Thanks for the reply. Is that just general accepted knowledge or is there a reference..or is that working off of chemistry where concentration is per molecule, not each carbon within the molecule kind of analogy?...just too used to being a scientist that's always asked to show "proof"....but thanks for the reply though!

Edited by fume711, 17 December 2010 - 08:32 PM.

#4 bob1


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Posted 18 December 2010 - 07:52 PM

Concentration is ALWAYS for the molecule unless specified, this is convention that has been around as long as we have been able to work out concentration and is regulated/standardised by IUPAC.

Unfortunatly you have been calculating your concentrations incorrectly - though they are easily converted if you know the length of your DNA/RNA.

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