Oligonucleotides are assembled via solid-phase synthesis. In that way, nucleotides are attached according to the sequence of choice leading to chain growth. It is generally accepted that chemical reactions never reach 100% conversion. However, in state-of-the-art oligonucleotide synthesis, coupling yields of up to 99.5% are achieved. With the unreacted 0.5% of the strands, chain assembly stops and truncated sequences form as side products. Depending on the intended application, it is advantageous to remove these shorter sequences from the full-length product.


RP-HPLC Purification

Oligos <50 nt in length can be well purified via RP-HPLC (reverse-phase high-performance liquid chromatography). Through this purification approach, preferably residual, n-x truncated oligos (lacking the hydrophobic DMT protection group at the 5’ end) are removed. This results in a ≥85% purity of the targeted oligonucleotide. RP-HPLC is useful for a higher level of purity that is required for more demanding applications, such as cloning, DNA fingerprinting, real-time PCR, FISH, etc.

Potential Applications:

Molecular cloning

DNA fingerprinting

Real-Time PCR and digital PCR*


* The primer and qPCR probes are compatible with all commercially available supermixes


IEX-HPLC Purification

IEX-HPLC (ion-exchange high-performance liquid chromatography) is a preferred purification method for longer oligonucleotides (40-80 nt). Through this purification approach, residual n-x truncated oligos are removed in an efficient way. Whereas RP-purification yields very good results for oligos < 50 nt, IEX purification is superior for longer oligonucleotides. (40-80 nt). For oligos with this length, IEX results in ≥85% purity of the targeted oligonucleotide. IEX is useful for a higher level of purity of long oligonucleotides required for more demanding applications, such as direct cloning or NGS applications.

Potential Applications:

Molecular cloning (direct cloning)

NGS Applications



HPLC Purification & Dialysis

Dialysis as an add-on to HPLC is recommended if oligos need to be present in a physiological state. This purity level is strongly recommended when performing in vivo experiments (e.g. in mice).

Potential Applications:

Antisense experiments

Cell culture studies

Physical Chemistry and Structure Analysis (NMR, MS, etc.)

Contact Us

Medical Innovation Ventures Sdn. Bhd (Mediven)

Plot 88F, Lintang Bayan Lepas 10,
Bayan Lepas Industrial Park,
Bayan Lepas Free Industrial Zone Phase 4,
11900 Bayan Lepas, Pulau Pinang, Malaysia.

Tel: +604-3052730 / Fax: +604-3052730