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For demanding applications such as multiplex PCR, cloning, mutagenesis, or antisense/RNAi methods, additional purification may be needed for your oligonucleotides. 


Purification services offered include PAGE and various types of HPLC. Purified, unmodified oligos 20−50 bases in length are provided with the guaranteed yields (Table 1). Purified oligos up to 60 bases that are provided with a purity guarantee receive QC by capillary electrophoresis (CE). The traces are available online in your account order history.*

Table 1. Yield guarantees for unmodified oligos of 25−50 bases, after purification.

Purification type100 nmol250 nmol1 µmol5 µmol10 µmol
PAGE2 nmol
6.5 nmol25 nmol125 nmol250 nmol
HPLC3.75 nmol
12.5 nmol50 nmol250 nmol500 nmol
IE-HPLC3.75 nmol
12.5 nmol50 nmol250 nmol500 nmol
RNase-Free HPLC3.75 nmol
12.5 nmol50 nmol250 nmol
500 nmol
Dual HPLC2 nmol
6.5 nmol25 nmol125 nmol250 nmol
Dual PAGE & HPLCN/A3 nmol12.5 nmol62.5 nmol125 nmol

* Purity and yield guarantees vary with oligo length, modifications, or sequence composition.

HPLC purification

High performance liquid chromatography (HPLC), a form of column chromatography, can be performed in one of two ways. Reverse-phase (RP) HPLC separates full-length oligo product from truncated products based on relative hydrophobicity. Ion-exchange (IE) HPLC separates full-length oligonucleotides from truncated species based on relative charge difference. IDT uses HPLC to purify unmodified oligos as well as oligos with complex modifications such as linkers, spacers, modified bases, and hydrophobic modifications. The type of HPLC selected is dependent on oligo sequence composition and characteristics.

PAGE purification

Polyacrylamide gel electrophoresis (PAGE) separates full-length product from shorter species based on electric charge. It reduces the amount (mass) of final oligo product; however, the increase seen in purity justifies the smaller yield. We strongly recommend PAGE purification for all oligos >60 bases in length.

RNase-free HPLC purification

Originally developed for isolating RNA oligos, RNase-free HPLC purification has been extended to DNA oligos for use in applications in which ribonucleases can be problematic. RNase-free HPLC purification is performed in an RNase-free environment: reagents, equipment, and lab surfaces are monitored for RNase contamination using RNaseAlert™ reagent.

Dual purification

For applications that demand the high oligo purity, we offer dual HPLC purification or dual PAGE and HPLC purification. Dual HPLC purification can be used to purify dual-labeled probes and Molecular Beacons bearing NHS ester modifications.

Which purification method?

The purification method you need depends on oligo composition and your research application. If you have questions regarding which type of purification is suitable for your oligos, our experts can provide guidance, contact us.