Oligonucleotide calculator

Our Oligo calculator is a new tool that we implement to make life of oligonucleotide chemists easier. The handy and simple interface of this calculator makes it a convenient tool to use on daily basis for oligo calculation. Similarly to different oligonucleotide calculators that can be found on the internet, our Oligo calculator will provide the molecular weight of the desired oligonucleotide with or without a DMT group and 2’-O modifications.

To use Bachem’s Oligo calculator, chose first if your oligonucleotide sequence contains a DMT (4,4’-dimethoxyltrityl) protecting group in the 5’ end by selecting the button DMT. Then, type in your sequence with the nucleotide and the linkage in clicking the buttons of the Oligo calculator.
To obtain the molecular weight of your oligonucleotide, you only have to press calculate! You can then copy the result of the oligonucleotide calculator into your clipboard.

How does the Oligo calculator work?

The oligonucleotide calculator is a very useful tool to help chemists calculate oligonucleotide molecular weight with or without modifications. With the Oligo calculator and its easy use, chemists can have access to an oligonucleotide properties calculator, which will provide in one click the mass of the desired oligonucleotide.

You will have first to enter your sequence using the symbol described below on the table. In order to add more flexibility to the oligo calculation, you can choose whether your linkage is a phosphodiester or phosphothioate. For this, you should enter between all of the nucleotides that compose your sequence, the type of linkage by pressing the relevant button Po or Ps.

As an example, if your oligonucleotide is the DNA sequence ACGT with full phosphotioate linkages, you should type in: AsCsGsT

 ACGTUPoPs
DNAdAdCdGdT-os
RNAACG-Uos
2’-OMemAmCmG-mUos
2’-FfAfCfG-fUos
2’-MOEmoeAmoeC*moeG-moeU*os
2’-cEtcEtAcEtCcEtG-cEtUos

*The standard 2’-MOE nucleotides are 5-Me-C and 5-Me-U.

The oligo calculation relies on the formula described below:

M: Molecular weight of the oligonucleotide sequence

M5’: Molecular weight of the 5’ end

Ni: Number of the nucleotides residues

Mi: Molecular weight of the nucleotides residues

Nj: Number of the phospho linkages

Pj: Molecular weight of the phospho linkages

 

With these explanations in hands, you are ready to use our oligo calc!

Oligonucleotide Calculator

Oligonucleotide Calculator