Oligo Configuration Options

Our oligos are available in a range of synthesis scales, purification options, and modifications. Many different applications demand different scale or purity to work well when it comes to custom DNA oligo synthesis. Learn more here about how to choose the best oligo configuration for your applications.

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To assist in the selection process, we have compiled a list of available options and guidelines below:

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

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Understanding why oligos sometimes require purification

Following DNA synthesis, the completed DNA chain is released from the solid support by incubation in basic solutions such as ammonium hydroxide. This solution contains the required full-length oligo but also contains all of the DNA chains that were aborted during synthesis (failure sequences). If a 20-mer was synthesized, the solution would also contain 19 mer failures, 18 mer failures, 17 mer failures etc. The amount of failure sequences present is influenced by the coupling efficiency. These failure sequences can compete with the full-length product in some applications such as PCR, and may therefore need removing before the oligo can be used successfully.

Purification options offered

Purification methodDescriptionBenefit
(25 nm: 10–100 nt;
50 nm: 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.
(50 nm–1 µm, 7–55 nt)
Based on reverse phase chromatography; removes failure sequences from the completed synthesis.Provides full-length sequences needed in some applications.
(50 nm+, 10–55 nt)
Reverse Phase High Performance Liquid Chromatography (HPLC) removes failure sequences or unincorporated label the same way as cartridge purification.Guarantees highly purified primer required in some applications (>=85% full length).
(200 nm+, 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.

Purity guide by application

ApplicationSuggested purification option
AFLP analysisDesalted oligos have been used successfully for Amplification Restriction Fragment Polymorphisms.
AntisenseHPLC-purified oligos are cited most frequently in references for antisense studies. See Minimum Yields chart for HPLC purification yields.
First-strand cDNA synthesis for generation of librariesGenerally oligos for first strand cDNA synthesis for library construction have some sequence at the end which codes for 5´ restriction endonuclease cloning sites. Therefore, it is best to use full-length, Cartridge, HPLC, or PAGE-purified oligos.
Fluorescent sequencingAll four purity grades have worked successfully forour scientists.
Gel shift assaysCartridge, HPLC, and PAGE-purified oligos are recommended for gel shift assays, so as to have a homogeneous population of DNA fragments.
GENETRAPPER screeningPAGE-purified oligos are recommended. Primers should be phenol extracted and ethanol precipitated prior to use in the tailing reaction in GeneTrapper System. If desalted purity oligos are purchased they can be PAGE-purified using the PAGE purification protocol.
Isothermal sequencingDesalted oligos are sufficient for this application, along with Cartridge, HPLC, and PAGE-purified oligs.
MicroarraysStandard desalted oligos are sufficient for printing onto arrays.
PCRDesalted oligos work fine for standard PCR. Higher purity options will also work.
PCR using oligos with critical 5´ sequences (e.g., restriction endonuclease sites, RNA polymerase promoters)Cartridge, HPLC, and PAGE-purified oligos are best for the greatest efficiency. Since oligos are synthesized 3´ to 5´, incomplete oligos (n-x oligos) will be missing the 5´ sequence. It is important to use full-length oligos that have the 5´ sequence present, otherwise there will be a population of PCR products missing the sequence intended to be installed before PCR.
Production of cloning adaptersFull-length oligos work best for efficient cloning. Utilize cartridge, HPLC, or PAGE-purified oligos for full length.
Site-directed mutagenesisFull-length (e.g., Cartridge, HPLC, and PAGE-purified) oligos as a rule tend to give the highest percentage of mutagenized clones (especially if the intended mutation is close to the 5´ end of the oligo). Desired mutations have been obtained using desalted oligos. However, some wild-type parental vector clones tend to carry over.

Please email us if you need a different modification from the options below.

5′ Modifications

Review our selection of generic modifications, fluorescent dye modifications, and Molecular Probes dyes.
NOTE: Modification names with an asterisk (*) indicate products that are HPLC purified.

Modification name Electronic ordering codeAbsorption maximum (nm)Emission maximum (nm)Extinction coefficient (OD/mole) at 260 nm
Generic modifications
Amine (Primary)AMNNANANA
Fluorescent dye modifications
*These products are HPLC purified

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 Dye RGAGreen50453278,000
Rhodol Green DyeRGBGreen49652363,000
Rhodamine Green-XRGCGreen50352874,000
Rhodamine Red-XRRARed560580129,000
Texas Red-XTRXRed583603136,000
*These products are HPLC purified

Internal 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′ 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/mole) At 260 nm

Do you need to order a DNA or RNA oligo with a special modification but can’t find it on our Custom Oligo pages? Then order them by contacting our Custom Oligo Services team.

Bringing you more

We are proud to offer an enhanced selection of custom oligonucleotide options that do not appear on our standard modification menus.  

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.

Frequently Asked Questions

Q. What modifications are available?
A. Our synthesizers allow us to use any commercially available modification and add them to your oligo. We also offer post-synthesis labeling with fluorescent dyes such as our superior Alexa Fluor dyes.

Q. What scales are available?
A. We can manufacture from 200 nmol to 1 gram scales in a variety of purities. Just let us know what you need.
Q. What purity selections do you offer?
A. We offer standard desalted, HPLC, and in vivo purifications.

Q. Do you offer custom siRNA libraries?
A. We can offer plated sets of siRNAs designed to your list of favorite targets. Contact us today for a quote.

Start your project now! Get our order form and begin the process. A project manager will respond to your inquiry within 2 business days.

For more information, call 800.955.6288 option 8, x46116 (US only), or email us at Custom Oligo Services.  


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