Quality Control (QC) is an essential part of any oligonucleotide synthesis process. During synthesis, we perform online trityl monitoring of all oligonucleotides to control the coupling efficiency at each cycle. All oligonucleotides are routinely analyzed and measured by optical density (OD 260) measurement. All modified and randomly selected unmodified Oligonucleotides are analyzed by MALDI-TOF Mass Spectrometry (Matrix Assisted Laser Desorption/ Ionization Time Of Flight Mass Spectrometry).
According to your application, your oligonucleotide purity can be checked by a supplemental Quality Control.
- MALDI-TOF Mass Spectrometry analysis provides the most precise information about the length, deprotection-adduct and verification of the presence of labels for modified oligonucleotides. This is a very sensitive and very accurate technique for oligonucleotides over a broad range of lengths (up to 60 bases).
- Reverse-Phase UHPLC provides quantitative information about the purity level. This technique is mainly used for modified oligonucleotides and is very efficient for those of 15 to 40 bases long.
- Ion-Exchange UHPLC can also be performed to quantify the purity level of oligonucleotides. This technique is mainly used for unmodified oligonucleotides and is very efficient for those of 15 to 40 bases long.
- Fluorescence analysis provides qualitative information about your fluorescent oligonucleotides.
If Mass Spectrometry provides you an accurate qualitative information about the purity of the oligonucleotide, UHPLC will give you quantitative information about the purity level of the synthesized oligonucleotide.