Nucleic acid conversion data

1. Determining the copy number of a template (dsDNA)

where n is the copy number; c is the concentration vs quantity in µg; m is the molecular weight (MW) of the molecule in Da.

Example: 1 kb ds linear DNA molecule has approximate MW of 6,49 · 10 ⁵ Da. 1 µg of this molecule equal to 9,2 · 10 ¹¹ copies.

2. Determining the molecular weight of an deoxyoligonucleotide (ssDNA)

m = (ndG · 328,2 + ndA · 312,2 + ndT · 303,2 + ndC · 288.2) + (mi · nbp) + (m5'end + m3'end),

where m is the molecular weight (MW) of the molecule in Da; n is the number of a corresponding base in the oligonucleotide; mi is the molecular weight (MW) of the counter ion; nbp is the length of the oligonucleotide; m5'end and m3'end are the atom masses at the 5' and 3' ends of the oligonucleotide respectively. Add (17 + 2 · mi) for phosphorylated oligonucleotides and substract (61 + mi) for dephosphorylated oligonucleotides. No phosphate is present at the 5´ end of strands made by primer extension. The atomic masses of the most common oligonucleotide counter-ions are:

Na (23), K (39,1), Li (6,9)

Example: The oligonucleotide dGdAdAdTdTdCdCdGdAdTdCdGdAdTdCdT (Na salt) has an approximate MW of 5270,2 Da. The molar mass of dsDNA can be calculated by doubling the molecular masses of both strands. Approximate molecular mass of a bp in DNA is 649 Da.

3. Determining the molecular weight of an ribooligonucleotide (RNA)

m = (nrG · 344,2 + nrA · 328,2 + nrU · 305,2 + nrC · 304.2) + 159,

where m is the molecular weight (MW) of the molecule in Da; n is the number of a corresponding base in the oligonucleotide; mi is the molecular weight (MW) of the counter ion. Addition of 159 to the MW takes into account the MW of a 5´ tri-phosphate.

Example: The oligonucleotide GAAUUCCGAUCGAUCU has an approximate MW of 5088,2 Da. The molar mass of RNA can be calculated using following formula: average mass of a ribonucleotide base x number of bases. Approximate molecular mass of the ribonucleotide is 340,5 Da.