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I am trying to calculate the exact weight of a given dsDNA.

On the Internet and the literature, different values for the av. molecular weight of one basepair are given :

I tried to calculate the average weight using following molecular weights:

molecule . weight
2'-Deoxyadenosin- 5'-monophosphate dAMP 331,22 g/mol
2'-Deoxycytidin- 5'-monophosphate dCMP 307,197 g/mol
2'-Deoxyguanosine 5'-monophosphate dGMP 347.2212 g/mol
2'-Deoxythymidine-5'-monophosphate dTMP 321.2005 g/mol
water H2O 18,01528 g/mol

adding the matching nucleoside monophosphates together and subtracting one water for each peptide-bond condensation (one on the sense; one on the antisense side); I get following formula for the average dsDNA basepair weight: $$ avg.BP.weight = \frac {(dAMP+dTMP-\ce{2H2O})+(dGMP+dCMP-\ce{2H2O})} {2} $$

resulting in : $$ \frac {(331,22+321.2005-36,03056)+(347.2212+307,197 -36,03056)} {2} = 617.3892 \frac{g}{mol} $$

which is very close but still 0.57081 short off the "best" literature value.

What am I missing?; Im trying to get this calculation as exact as possible.

Maybe i didn't consider some hydrogen or protons in bonds?

Thank you in advance!

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The different protonations forms are considered in the averaged Mw.
Removing two H2O is the step that makes your average different than the traditional 650Da per base pair. But you must remember that the last base pair in the sequence will have it's OH group so you need to add 17.008 gr/mol * 2 = 34.016 gr/mol.

The effect of this changes with the length of your sequence, here is a graph showing it. enter image description here Blue line is your calculation and red line is the one from literature.
Literature one is achieved around 60bp (I calculated Mw(63bps) = 617.93) and yours at 10^6.6 (Mw(10^6.6) = 617.3892085)

Why you need this calculation to be so exact? Knowing the length of you sequence and region can help. Remember that some regions are richer in one type of nucleotides (CpG islands, hairpin coding sites)

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  • $\begingroup$ Thank you for the precise answer and the great plot! I did this out of pure curiosity - I recognized that there where some inconsistencies (more generalizations) in the literature data so i tried to do my own calculations. I wrote a script to calculate the weight of an input sequence. My next goal would be to try to add the molecular weight of histones, linkerDNA , chaperones and the centromer, to calculate the total theoretical weight of the chromatin during metaphase. However i have now idea how to include variables like methylation. If you have further advice i would be truly thankful. :) $\endgroup$
    – user12256545
    Commented Feb 13, 2021 at 12:41
  • $\begingroup$ @user12256545 I try to be as doubtful as I can while modeling. If X happens in N stage how do I know it still happens in N+1 or K stage (everything in biology makes sense in retrospect but rarely in advance). Send me a message if you have code you'd like me to look at $\endgroup$
    – Hachiloni
    Commented Feb 13, 2021 at 20:00

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