I have difficulties finding a formula for the calculation of the molecular mass (g/mol) of an amplicon (double stranded). On the internet and in literature I find different formulas giving different results. Can someone please help me with this?
The approximate weight of a double stranded oligonucleotide is length * 618 (654 - 2* H2O per bp), not taking into account a possible terminal phosphate group.
It depends on your application for the value as to how accurate you need the value to be. As Christian said above, length x 618 is a reasonable approximation for most cases.
However if you are using this value to convert between a concentration in ng/µL and copies/µL it is more appropriate to take into account the base composition, as each of the bases has a different mass. I have linked to an online calculator that will determine the mass of an amplicon taking into account the base composition.
If you are using the value for an application such as mass spectroscopy, then the appropriate value to use needs to take into account the relative abundance of isotopes for each of the elements involved and is a bit trickier. I don't know of an online calculator that will do this, we did it from scratch.
http://www.basic.northwestern.edu/biotools/oligocalc.html
Thank you for your responses! I want to calculate the molecular mass of the amplicon to calculate the gene copy number [(concentration amplicon (g/l) x 6.022 x 10^23 (molecules/mol))/ molecular mass amplicon (g/mol)].
@Jacob: Can I then use the simplified formula or is it better to use the online calculator?
Kindest regards,
Audrey
The simplified formula is good enough for that. As you have dsDNA, the difference between a AT and a GC pair is just one Dalton, so less than 0.2%. That should be insignificant compared to the errors that arise from quantification.
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