615 or 660? Average MW of a DNA base pair - (Nov/21/2012 )
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.
I think the variability might depend on your sequence (as each nucleotide is slightly different)?
Try this Invitrogen page
Jesus It seems even more complicated. I just want to know what number ppl normally used
But thanks for your reply
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
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.