Exact average molecular weight of a dsDNA basepair

Question

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 :

660 g/mol (probably wrong),
other sources say 617.96 g/mol
Thermofisher gives 607.4 g/mol
(https://www.thermofisher.com/de/de/home/references/ambion-tech-support/rna-tools-and-calculators/dna-and-rna-molecular-weights-and-conversions.html)

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!

Hachiloni · Accepted Answer

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.

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)

Exact average molecular weight of a dsDNA basepair

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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