Oligo Synthesis

Sentebiolab carries out high-quality primer synthesis using the world’s most advanced high-throughput DNA synthesis and purification systems. With fast next-day delivery and low prices, we provide our high-quality primers to researchers and clinicians. Our high-throughput system is able to meet the annual oligo needs of Turkey. By using Biolytic (USA) Dr. Oligo™ DNA/RNA Synthesizer, 96 oligos can be simultaneously synthesized separately with a yield of >99.95%. Using Dr. Oligo™, our lab routinely performs synthesis of oligos up to 125 bp in length at standard 50 nmol, 100 nmol, and 200 nmol scales. Furthermore, using the fully automated Dr. Oligo™Processor, we carry out routine purification of our synthesized oligos including removal of organic salts (desalting) and DMT-ON (Oligonucleotide Purification Column (OPC)-Reverse Phase (RP)-HPLC grade).

If desired, we also provide “degenerate primer syntesis” services and offer Ion Exchange (IE)-HPLC grade purification.

senteligo™

We offer senteligo™ brand RP-HPLC grade quality primer products at 200 nmol scale. The advantages of using senteligo™ include: high quality, OPC (RP-HPLC grade) purification, competitive prices, fast delivery (delivery within 24 hours), and quality guarantee.

General Information

Oligonucleotides are short strands of DNA. Oligonucleotides (primers) are used in many molecular and genetic manipulations such as PCR. They are also used to determine base sequences in a DNA strand and identify mutations in DNA.

Sentebiolab synthesizes cost-effective nucleotide sequences for you that can be used in molecular biology studies. The primers we produce undergo quality control testing. The oligonucleotide synthesis process is based on tetrazole catalysis with phosphoramidite monomers.

Phosphoramidite is a normal nucleotide except that it contains a protecting group such as trityl. These groups block reactive amine, hydroxyl and phosphate groups. The protecting groups prevent undesired side reactions and ensure production of the desired product. After the synthesis process is complete, these protecting groups are removed.

The first phosphoramidite molecule attaches to a solid surface from the 3’ end and synthesis progresses in the 3’ to 5’ direction. The solid surface that the protected nucleotides bind is a 5-micrometer glass bead that contains pores and canals of controlled size for the initial nucleotide to adhere.

Phosphoramide based synthesis is carried out via the serial repetition of 4-step cycles and is completed once the next nucleotide is bound to the 5’ terminus. These 4 steps are deprotection, coupling, capping, and stabilization, respectively.


Primer purification methods:

This section is designed to help you choose the purification method most suited for your application. During oligo synthesis, every nucleotide is added to the growing chain successively. In each assembly cycle, nucleotides are unable to be added to a small fraction of the oligo chains. This results in the production of a mixture of both full-length and truncated sequences. During oligo synthesis, the separation of support and removal of protecting groups results in residual products, which are removed by purification.

For some applications, it is very important that only full-length (n) oligos are present. For other applications, the presence of shorter oligos (n-1, n-2, etc.) does not affect experimental results.

Desalting
Oligonucleotides produced by Sentebiolab are purified by the desalting method. The desalting process is used to clean up side products and residues that are produced during synthesis. This method is useful for oligos up to 35 bp and PCR applications.
OPC
With the OPC method, incorrect sequences, side products, and impurities are removed. With this method, the primers obtained can be used for sequencing, PCR, hybridization probes and gene synthesis. OPC purification is recommended for oligonucleotides up to 70 bases in length.
HPLC Reverse-phase
This separation technique is based on the difference in hydrophobicity between the products of the desired length and shorter sequences. HPLC purification of oligos using fluorophores is a productive method. The lipophilic characteristic of fluorophores creates an excellent environment for the removal of impurities after synthesis. Furthermore, RP-HPLC is a preferred method for large-scale syntheses. Since the lipophilic-based separation will result in shortened oligos, this method is not recommended for oligos less than 50 bases long.

Synthesis, Delivery and Storage Conditions

Storage Conditions Temperature Maximum Storage Duration
Lyophilized -20 °C < 1 year
Lyophilized Room temperature ≤ 1 month
Re-suspended -20 °C < 6 months
Re-suspended Room temperature ≤ 1 week

Purification options include standard purification, OPC (RP-HPLC grade) and IO-HPLC.

Standard desalting (removal of small molecule impurities) is available for every oligonucleotide. If desired, orders within Ankara can be delivered via cold chain as 100 uM normalized stock concentration.

Prior to drying, the OD and A260 values are calculated and the necessary amount of TE or H2O to be added to produce a stock solution is determined. This information is given to the customer as a report at the time of product delivery.

Lyophilized primers can be stored at room temperature. Re-suspended primers must be stored at -20 °C. For long-term storage of your primers, dissolve with TE Buffer and avoid freeze-thaw cycles. Dilute the amount to be used and store this as aliquots.

Ordering Information

  • Our synthesis days are Monday, Wednesday and Thursday.
  • Orders received by 10:00 on Monday and Wednesday for oligos less than 40 bases long and at 50 nmol scale will be ready the following day at 16:00.
  • Orders received by 16:00 on Monday and Wednesday for oligos less than 40 bases long and at 100 nmol scale will be ready the following day at 16:00.
  • Orders received by 16:00 on Thursday for oligos less than 40 bases long and at 200 nmol scale will be ready the following day at 16:00.
  • Orders are manufactured in the order in which they are received. If the synthesis capacity is filled that day, your order will be added to the next synthesis.
  • Orders for 40 or more oligos are considered as bulk orders. For delivery time, please contact us.
  • Oligonucleotides purified by OPC will be delivered two days after the synthesis.
  • Oligonucleotides that are longer than 40 bases are considered as long oligos. For delivery time, please contact us.

To submit an order, please fill in the form and send by email to order@sentebiolab.com.tr

✚ Order Form


Scale and Purification Selection Guide – by Application

Desalted OPC (RP-HPLC Grade) IE-HPLC
Up to 40 bases Up to 60 bases Up to 150 bases
50 nmol PCR
100 nmol PCR, RT-PCR PCR, Sequencing, RT-PCR, Next Generation Sequencing, Microarray
200 nmol PCR, RT-PCR PCR, Sequencing, RT-PCR, Next Generation Sequencing, Microarray Sequencing, RT-PCR, Aptamer
senteligo™ PCR, Sequencing, RT-PCR, Next Generation Sequencing, Microarray


Terms of Guarantee

Sentebiolab guarantees your primers. The primers are guaranteed for 3 months. If desired, primers can be re-synthesized within the 3-month guarantee period. Primers less than 15 bp or above 40 bp are not included in the guarantee. Primers with mistakes in the sequence that you provide or primers that are not stored according to the storage conditions after delivery are also not covered by the guarantee.

Additional conditions for the guarantee to hold:

  • Primer sequence must previously have been shown to work.
  • Primer sequence must be published in an international journal.

Quality Control


The synthesized primers are routinely checked by gel electrophoresis to ensure only a single band was produced. Furthermore, we perform quality control by PCR and gene synthesis experiments. In each oligo production, during the many deblock steps that are carried out, the synthesis efficiency is checked by trityl analysis. The synthesis results are presented as a report with the OD 260 value as measured by NanoDrop spectrophotometer. Monthly LC-MS analysis ensures continued quality assurance.