DNA Oligos for Next Generation Sequencing Applications

Do you need NGS adaptors, fusion primers or any other specific primers for your next generation sequencing project? Due to its vast experience in the area of oligonucleotide synthesis (25 years) as well as next generation sequencing (8 years), Microsynth exactly knows the quality requirements for NGS oligos. Therefore, you will be in good hands at Microsynth when requesting NGS oligos only, or equally when outsourcing your entire NGS project.

In order to get a price quotation for NGS oligos, please contact us (info@microsynth.ch).

Your Overall Benefits Include:

  • High purity due to stringent HPLC purification1

  • High quality: QC check by means of MALDI-TOF or analytical PAGE

  • Validated production process: our own NGS group is regularly using this type/grade of oligo

  • Broad applicability: recommended for any kind of NGS application and technology (e.g. Illumina, Ion Torrent, 454)

  • Additional useful features: typical Microsynth characteristics such as fast delivery, high yields and excellent technical service

How to Order?

Important: Please first contact us at Microsynth and request your offer (volume discounts are possible!)

Option 1: When ordering NGS primers, please proceed as follows:

  • Enter our webshop, click on DNA and metRNA in the “Oligonucleotide” domain

  • Select either Normal Entry in order to type or copy/paste the desired sequence information etc. or alternatively select Upload Entry by using our convenient Excel Template (can be downloaded during ordering)

  • Important: You must use the prefix “NGS_” ahead of your oligo name (e.g. NGS_Cart_fw01), select either 0.2 µmol or 1.0 µmol scale and further choose HPLC purification

  • Follow the further instructions

Option 2: When ordering primers for Illumina amplicon sequencing, please proceed as follows:

  • Use the dedicated “Order Form_Illumina_AmpliconDeepSeq” (can be downloaded in the right column under “Related Downloads”; in this context see also our application note “Amplicon Deep Sequencing”)

  • Specify now the locus-specific sequences for your first-step PCR primers and then select your desired indexed forward and reverse primers

  • Enter our webshop, click on DNA and metRNA in the “Oligonucleotide” domain and then on Upload Entry

  • Follow the further instructions


1 At this place it is crucial to emphasize the importance of oligonucleotide purity for NGS applications. Most researchers take into account the n-x side products when they consider oligonucleotide purity, but do not ask their oligo suppliers for post-synthetic processes that have been optimized in terms of oligo cross-contamination arising from different customer orders. As a consequence many suppliers use cheaper high-throughput methods (e.g. Cartridge purification) to purify NGS oligos, which however is especially prone to cross-contamination. As a consequence, even a small amount of cross-contamination which is harmless in less sensitive applications (e.g. PCR or Sanger), may become a severe problem in the NGS data analysis since incorrect amplification products are likely to be sequenced as well. Therefore, Microsynth has established a specific process for production of NGS oligos that is based on a stringent HPLC purification procedure where the elimination of cross-contamination is given the highest priority. 


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