Our oligos are available in a wide variety of synthesis scales, purification options, and modifications. Many different applications demand different scale or purity to work well when it comes to DNA oligo synthesis. To assist in the selection process, we have compiled a list of available options and guidelines below.

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Oligonucleotide modification selection guides

Synthesis scale for PCR applications

When ordering custom oligos for PCR applications, the scale of synthesis determines the number of reactions provided. The table below assumes a 100 µl PCR reaction and a final oligo concentration of 0.1 to 0.5 µM.

Scale of synthesisEstimated number of reactions
25 nmole500 to 2,500
50 nmole1,000 to 5,000
200 nmole4,000 to 20,000
1 µmole20,000 to 100,000
10 µmole100,000 to 1,000,000

The standard scales listed above are available for oligos delivered in tubes or plates. Oligos delivered at higher quantities and based on a specific final yield are also available through our large-scale synthesis service. Submit a request for larger quantities by detailing your special request online.

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Oligo purification options

Purification methodDescriptionAdvantagesLimitations
(25 nmol: 10–100 nt;
50 nmol: 5–100 nt)
Oligos are processed through normal phase chromatography column which removes salts but not failure sequences.A salt-free DNA solution, ready-to-use; suitable for many PCR and sequencing applications without further purification.Doesn’t remove truncated sequences (i.e., internal deletions or 5’ truncations).
(50 nmol–1 µmol, 7–55 nt)
Based on reverse phase chromatography; removes failure sequences from the completed synthesis.Provides full-length sequences needed in some applications.Doesn’t remove internal oligonucleotide deletions. Only available for certain scales (50 nmol–1 µmol) and oligonucleotide lengths (7–55 bp).
(50 nmol+, 10–55 nt)
Reverse phase high performance liquid chromatography (HPLC) removes failure sequences or unincorporated label the same way as cartridge purification.Helps ensure highly purified oligo required in some applications (≥85% full length).Not available for small-scale oligonucleotide synthesis (i.e., 25 nmol). More ideal for shorter oligonucleotides (10–55 bp). Secondary structures can complicate purification.
(200 nmol+, 7–100 nt)
Method used to differentiate full-length product from failure sequences based on size and conformation.Provides the highest percentage of full-length oligos (≥85%) required for certain demanding applications such as mutagenesis or adapter production.Not available for small-scale oligonucleotide synthesis (i.e., 25 nmol). Significant reduction in final yield. Not compatible with certain oligonucleotide modifications.

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Please submit a special request if you need a different modification from the options below.

5′ oligo modifications

Review our selection of generic modifications, fluorescent dye modifications, and Molecular Probes dyes.

NOTE: Oligos containing modifications with an asterisk (*) require HPLC purification.
Modification name Electronic ordering codeAbsorption maximum (nm)Emission maximum (nm)Extinction coefficient (OD/mol) at 260 nm
Generic modifications
Amine (Primary)AMNNANANA
Fluorescent dye modifications
*Oligos containing this modification require HPLC purification.

Molecular Probes dyes
Dye*Electronic ordering codeColorAbsorption maximum (nm)Molar emission maximum (nm)Extinction coefficient (cm -1M -1)
Alexa Fluor 488488Green49051971,000
Alexa Fluor 532532Green53255381,000
Alexa Fluor 546546Yellow556573104,000
Alexa Fluor 555555Orange/yellow555565150,000
Alexa Fluor 594594Orange59061773,000
Alexa Fluor 647647Red650655239,000
Alexa Fluor 660660Red663690132,000
Alexa Fluor 750750Purple749755240,000
Bodipy FLBDAFar Red50251082,000
Bodipy 530/550BDB53455177,000
Bodipy 493/503BDC50050979,000
Bodipy 558/569BDE55956897,000
Bodipy 564/570 BDF563569142,000
Bodipy 576/589BDG57558883,000
Bodipy 581/591BDH581591136,000
Bodipy FL-XBDI50451085,000
Bodipy TR-XBDJ58861668,000
Bodipy TMRBDK54457056,000
Bodipy R6GBDL52854770,000
Bodipy R6G-X BDM52954773,000
Bodipy 630/650BDN625640101,000
Bodipy 650/665BDP651660100,000
Cascade Blue DyeCSBBlue40042028,000
Marina Blue DyeMNBBlue36245919,000
Oregon Green 514OGBGreen50652685,000
Oregon Green 488OGCGreen49552176,000
Oregon Green 488-XOGDGreen49451784,000
PACIFIC BLUE DyePFBBlue41645136,000
Rhodamine Green DyeRGAGreen50453278,000
Rhodol Green DyeRGBGreen49652363,000
Rhodamine Green-XRGCGreen50352874,000
Rhodamine Red-XRRARed560580129,000
Texas Red-XTRXRed583603136,000
* Oligos containing any of these modifications require HPLC purification.

Internal oligo modifications

Review the list of available internal modifications and their electronic ordering codes.

Alternative basesElectronic ordering codeDescription
Deoxyuracil UUseful with UDG for ligase-free cloning.
Deoxyinosine IDeoxyinosine has the capacity to base-pair with all four bases; however, it does so with varying affinities. The order of stabilities for the different combinations, from greatest to least stable, reported by Martin et al. are as follows: I:C, I:A, I:T, and I:G. I:C pairs were found to be slightly less stable than A:T pairs (Martin FH, Castro MM et al. (1985) Nucleic Acids Res.13: 8927.)
Phosphothiates (see below)A sulfur is substituted for one of the oxygens in the phosphodiester bonds between the nucleotides. This linkage is to the 3′ side of the designated base.
A-Phosphorothioate F 
C-Phosphorothioate O 
G-Phosphorothioate E 
T-Phosphorothioate Z 
Mixed bases* Degenerate bases—Equal amounts of the designated bases are delivered by the synthesizer
A+C+G+T N 
A+C+G V 
A+T+G D 
T+C+G B 
A+T+C H 
A+T W 
C+G S 
T+G K 
A+C M 
C+T Y 
A+G R 
*Mixed bases may be designated at any position for the 50 nmole scale and above. For the 25 nmole scale, mixed bases may be designated for any except the 3'-most base. Mixed bases are achieved by having the synthesizer deliver an equal amount of each base at the given base addition. Differences in coupling efficiency may result in the end product being slightly skewed toward the base that couples with the highest efficiency.

3′ oligo modifications

NOTE: Not all modifications are available at all scales and purifications. Modifications other than internal mixed bases are not available for oligos ordered for Next-Day delivery. Please contact technical support for more information.

Dye nameElectronic ordering codeAbsorption maximum (nm)Emission maximum (nm)Extinction coefficient (OD/mol) at 260 nm

Additional oligo modifications

Do you need to order a DNA or RNA oligo with a unique modification not listed? Contact our Custom Oligo Services team

We are proud to offer an enhanced selection of custom oligonucleotide options that do not appear on our standard modification options. Each order is treated as a special project by our dedicated services team. Upon completion, the project is reviewed by our Technical, Quality, and Manufacturing teams to deliver the best the industry has to offer.

Start your project now! A project manager will respond to your inquiry within two business days. Submit a special request online to begin the process

For Research Use Only. Not for use in diagnostic procedures.