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615 or 660? Average MW of a DNA base pair

Average MW of a DNA bas

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#1 bao.tianle

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Posted 21 November 2012 - 02:05 AM

Hey guys. I have one question that quite confused. I was always taught the average weight for a ds DNA is 660. However, according to the Doležel et al., mean relative weight of one nucleotide pair is 615.8771. I am wondering what number should I follow when I do the caculation?
Thanks for help
Doležel J, Bartoš J,Voglmayr H, Greilhuber J (2003). "Letter to the editor: Nuclear DNA Content and Genome Size of Trout and Human". Cytometry 51A (2): 127–128. doi:10.1002/cyto.a.10013. PMID 12541287.

#2 leelee

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Excellent

Posted 21 November 2012 - 07:07 AM

I think the variability might depend on your sequence (as each nucleotide is slightly different)?

Try this Invitrogen page

#3 bao.tianle

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Posted 21 November 2012 - 07:15 AM

JesusPosted Image It seems even more complicated. I just want to know what number ppl normally used Posted Image
But thanks for your replyPosted Image

#4 John Forsberg

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Good

Posted 21 November 2012 - 02:41 PM

Based on that papers' calculations, the sizes of a base pair (accounting for loss of a water molecule on each strand in polymerization and a proton from each phosphate hydroxyl due to the pH) should be:

GC: 347.2207+307.1966-(4x1.0079+2x15.9994)-(2x1.0079)= 616.3711
AT: 331.2213+322.2079-(4x1.0079+2x15.9994)-(2x1.0079)= 615.383

average: 615.8771

Note that this reflects the loss of water and a proton from both strands.

Without accounting for the masses lost from the 2 waters or the 2 protons lost from the backbone phosphate, the masses end up being 654.4173 for GC and 653.4292, so an average of 653.9233. So I could see your original estimate of 660 roughly matching the value obtained if you just counted DNA as if it were a chain of AMP, TMP, GMP and CMP.

So yeah, that paper looks right.


edit: I have found references to masses of DNA with salt bound giving an average mass for a base-pair at roughly 660, so perhaps that's where your number comes from.

Edited by John Forsberg, 21 November 2012 - 02:42 PM.





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