Oligonucleotide Molecular Weight Calculator
What can our oligonucleotide calculator be used for?
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 oligonucleotide molecular weight 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
| A | C | G | T | U | Po | Ps | |
|---|---|---|---|---|---|---|---|
| DNA | dA | dC | dG | dT | – | o | s |
| RNA | A | C | G | – | U | o | s |
| 2’-OMe | mA | mC | mG | – | mU | o | s |
| 2’-F | fA | fC | fG | – | fU | o | s |
| 2’-MOE | moeA | moeC* | moeG | – | moeU* | o | s |
| 2’-cEt | cEtA | cEtC | cEtG | – | cEtU | o | s |
*The standard 2’-MOE nucleotides are 5-Me-C and 5-Me-U.
The oligo calculation relies on the formula described below:
M = M5′ + ∑ Ni Mi + ∑ Nj Pj
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!
How can our calculator be used to identify oligonucleotide properties?
An oligonucleotide calculator can be used to identify oligonucleotide properties by applying similar principles used in oligo calculations.
By entering oligonucleotide-specific details, such as the sequence, linkages, the calculator quickly provides physico-chemical properties like molecular weight and net charge, making it a handy tool for daily oligonucleotide preparation.
