Oligo Synthesis FAQs

Custom DNA & RNA Oligos : Synthesis 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.