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DNA Oligos for Next Generation Sequencing Applications

DNA Oligos for Next Generation Sequencing Applications
The quality and purity of NGS primers and adapter sequences are critical for the success of every next generation sequencing project. Due to its vast experience in the area of oligonucleotide synthesis (>30 years) as well as next generation sequencing (>10 years), Microsynth exactly knows the key 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.

Features and Benefits

High Quality
  • Optimized production process to ensure suitable purity and low levels of cross contamination.
  • Stringent quality control (online trityl monitoring and MALDI-TOF MS or analytical PAGE)


Fast Production
  • NGS oligos: ≤ 2 d
Excellent Technical Support
  • Trained and experienced scientists are happy to support you.
User-friendly Online Ordering System
  • Easy-to-use online portal with a series of helpful tools (e.g. order tracking & history, convenient search and re-order option


Cost Effective
  • Very competitive pricing
  • High guaranteed yields


  • Availability of current modifications (5’-Phosphate, PTO, 5-Me-dC etc.)
  • Application independent of the instrument or technology
  • Analytical HPLC available
  • Certificate of Analysis available
  • Various delivery formats possible (dried, liquid, tubes, 96-well plates etc.)
  • Possibility to outsource the entire NGS project (from isolation to bioinformatics)

Synthesis Scales


Synthesis Scale Purification Length Restriction Guaranteed Yield Production Time [wd]
0.04/0.2 umol  IEX-HPLC 40 – 80 2 OD 3 - 5
1.0 umol  IEX-HPLC 40 – 80 6 OD 3 - 5

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.

Therefore many suppliers use cheaper high-throughput methods (e.g. reversed-phase cartridge purification) to purify NGS oligos, which however are 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. A typical example is the risk of barcode misinterpretation in multiplexing experiments where index adapters containing the MID (multiplex identifier) or barcode are used.

Consequently, Microsynth has established and validated a specific process for production of NGS oligos that is based on either stringent HPLC purification procedure where the elimination of cross-contamination is given the highest priority. 

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 in the blue “DNA/RNA Synthesis” 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 (up to 65 mers)

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); 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 in the blue “DNA/RNA Synthesis” domain and then on Upload Entry

Follow the further instructions