Oligo Synthesis FAQs


Custom DNA & RNA OligosSynthesis of custom-length oligos (5-150 bases) at 25 - 1000 nmol scales with a wide range of modifications available with HPLC, PAGE, and desalted purification options. Turnaround time starts at 4 business days, depending on scale and modification requirements. 

Oligos Retained for Sanger : Order an oligo for a Sanger sequencing order. Azenta will synthesize, dilute, and store the oligo on-site for up to 1 year.


Oligos are chemically synthesized using the industry-standard, solid-phase phosphoramidite method. Oligos are synthesized through a series of coupling reactions in the 3' and 5' direction.

The Azenta Custom DNA & RNA Oligos service can synthesize oligos between 5-150 bases.
Yes, Azenta offers synthesis of oligos containing degenerate bases using the standard IUPAC base nomenclature.

IUPAC Code Base
R A or G
Y C or T
M A or C
K G or T
S C or G
W A or T
H A, C, or T
B C, G, or T
V A, C, or G
D A, G, or T
N A, C, G, or T

Custom DNA & RNA Oligos service ships orders in as few as 4 business days depending on the modifications or purifications requested. Please refer to your order for specific turnaround time information.

Oligos Retained
for Sanger will be available for sequencing within 1-2 business days depending on the time the order is placed.


Custom DNA & RNA Oligos orders can only be delivered in dry format.

If primers arrive dry, we recommend briefly centrifuging the tube to ensure that the DNA is at the bottom of the tube. Resuspend the sample in a volume or concentration appropriate for your needs and vortex briefly to mix well. Let the sample sit for 1-2 minutes. Before use, vortex briefly again.

*Please note: the reconstitution solution is dependent on downstream applications and that TE may interfere with various enzymatic reactions.
Dry oligos are stable and can be stored at -20°C for 1 year. Resuspended primers at higher concentrations (≥100 µM, in TE or water) are stable for 6 months at -20ºC.

*Please note that repeated freezing and thawing will reduce stability and shelf life.
Purification Lengths (nt) Purity Recommended Uses
Desalted 5-90 >70% Standard sequencing and PCR primers
PAGE 11-150 >90% Long oligos
HPLC 5-90 >95% Modified oligos or oligos used in sensitive applications
Azenta synthesizes DNA oligos on a per-scale basis, which refers to the initial amount of material used in synthesis. Due to the inefficiency of the coupling reactions, yields are never equal to the initial amount of starting material. Yield is typically impacted by the nature and content of the sequence. Purification and modifications will also reduce the final yield delivered.

      Length (nt)       Scale    Purification              Target Yield*           
5-90 25 nmol Desalted 5 nmol
HPLC 2 nmol
50 nmol Desalted 10 nmol
HPLC 4 nmol
PAGE 2 nmol
100 nmol Desalted 20 nmol
HPLC 8 nmol
PAGE 4 nmol
200 nmol Desalted 50 nmol
HPLC 20 nmol
PAGE 10 nmol
1 µmol Desalted 300 nmol
HPLC 120 nmol
PAGE 60 nmol
91-150 100 nmol PAGE 2 nmol
200 nmol PAGE 5 nmol
1 µmol PAGE 25 nmol

* Guaranteed yield will be determined by the exact oligo length, scale, and purification, and will be shown on the oligo order receipt. Actual yield delivered will be ±10% of guaranteed yield.
Dye Max Ex (nm) Max Em (nm) Color Compatible Quenchers
6-FAM 495 520 Green BHQ-1, BHQ-2, ECLIPSE, TAMRA, Dabcyl
JOE 520 548 Orange BHQ-1, ECLIPSE, Dabcyl, TAMRA
TET™ 521 536 Orange BHQ-1, BHQ-2, ECLIPSE, TAMRA, Dabcyl
HEX™ 520 548 Pink BHQ-1, BHQ-2, ECLIPSE, TAMRA, Dabcyl
TAMRA 544 576 Rose BHQ-2, ECLIPSE, Dabcyl
ROX™ 576 601 Red BHQ-2, ECLIPSE
Cy®5 650 670 Violet BHQ-2 
Cy®3 550 570 Red BHQ-2, ECLIPSE
TexasRed® 583 603 Red BHQ-2, ECLIPSE
Azenta offers several options for synthesis and cost depends on the synthesis type, length, scales, modifications, and purifications required. Please contact dnaseq@azenta.com or +1-877- 436-3949 ext. 2 with pricing inquiries or reach out directly to your Sales Representative.
Yes, oligos containing RNA, LNA, 2-O-Me-RNA and other modified RNA nucleotides are available through our Custom Synthesis Service. Please submit an inquiry online through your Azenta account.