Custom DNA Oligos

Synthesis and postprocessing in ultra high throughput.

• Available for all unmodified DNA oligos
• Deprotected and free from salt
• Accurate quantification - Variability of max. +/- 20% 
• Fast TAT of 1-3 working days up to 60mer, 0.01 - 1.0 µmol scale
• TAT of > 61 mer or 10.0 µmol scale 4-10 working days

Make use of a NightXpress delivery by placing your SaltFree Oligo order before 9:00 am CET

Minimum and average yields (OD) per scale and length:

The synthesis scale indicates the initial amout of 3'-bases. Average yields are statistical values and vary due to oligo sequences with GC content >50%, >3 purine streches, or strong secondary structures. 

HPSF is a size exclusion method by gel filtration and stands for High Purity Salt Free. 

• Available for all unmodified and some modified oligos
• Cleaned from chemicals and truncated sequences
• Free from any disturbing salts
• Accurate quantification - Variability of max. +/- 10% 
• Purity of >70 % for 18-35mer oligos
• Fast TAT of 1-4 working days up to 60mer, 0.01 - 1.0 µmol scale
• TAT of > 61 mer or 10.0 µmol scale 6-10 working days

Minimum and average yields (OD) per scale and length for unmodified oligos:

Minimum yields (OD) per scale for modified oligos:

The synthesis scale indicates the initial amout of 3'-bases. Average yields are statistical values and vary due to oligo sequences with GC content >50%, >3 purine streches, or strong secondary structures.

HPLC means High Performance Liquid Chromatography. The purification method with high separation efficiency.

• Available for all type of DNA oligos
• Removal of truncated sequences
• Accurate quantification - Variability of max. +/- 10% 
• Purity of ≥80 % for up to 120 mers
• TAT: 5-7 working days up to 60mer, 0.01 - 1.0 µmol scale
• TAT of > 61 mer or 10.0 µmol scale 10 working days

Minimum and average yields (OD) per scale and length for unmodified oligos:

Minimum yields (OD) per scale for modified oligos:

The synthesis scale indicates the initial amout of 3'-bases. Average yields are statistical values and vary due to oligo sequences with GC content >50%, >3 purine streches, or strong secondary structures.

Available fluorescent dyes and their characters at a glance

Product specifications:

• Synthesis scales from 0.01 to 1.0 µmol
• Purification options: HPSF, HPLC
• Sequence lengths: 5 - 80 bases
• Turnaround time: 3 - 5 working days

Spectra of fluorescent dyes

Although the data presented in this table have been checked for accuracy, the emission, absorption and extinction coefficient values may vary slightly with each oligonucleotide.

Available non-fluorescent modifications and their structures

Product specifications:

• Synthesis scales from 0.01 to 1.0 µmol
• Purification options: HPSF, HPLC
• Sequence lengths: 5-80 bases; 5-50 bases for some 3' modifications
• TAT: 2-4 working days

Amino-C6 [AmC6] Amino-C12 [AmC12]

5' Amino groups are often used for coupling the oligonucleotides to solid supports. Amino groups can also be used to attach secondary modifications such as fluorescent dyes or large molecules like digoxigenin.

Structure of 5' Amino C6    Structure of 5' Amino C12

Amino-C3 [AmC3] Amino-C6 [AmC6] Amino-C7 [AmC7]

3' Amino C7 and C3 can be used to block polymerase and exonuclease activity.

3' Amino C3 structure   3' Amino C6 structure   3' Amino C7 structure

Biotin [BIO]

Biotinylated oligonucleotides are known for their ability to bind to streptavidin. Biotin added at the 3' end can be used to block exonuclease digestion.

5' Biotin structure

Biotin-TEG [BIOTEG]

Biotin-TEG allows for an increase in binding to the streptavidin deep-binding pocket due to the fact that it has the longest linker arm from the Biotin group (e.g. used for hybridisation studies).

Biotin-TEG structure

Cholesterol [CHOL]

Cholesterol is a hydrophobic molecule. Coupled at the 3’ end of an oligonucleotide cholesterol has been established as a reliable courier through membranes and facilitates uptake into cells.

3' Cholesterol structure

Digoxigenin [DIG]

Digoxigenin is used primarily as a non isotopic label for oligonucleotides. Common applications include diagnostics, sequencing, and in-situ hybridisations.

Digoxigenin structure

Phosphate [PHO]

Phosphorylation allows the oligonucleotides to be used as a substrate for DNA ligase. 3' modifications can be used to block further extension by DNA. Terminal phosphates are also useful for enabling the ligation of two individual oligonucleotides together.

Phosphate structure

Thiol Modifier C3 [ThiolC3] Thiol Modifier C6 [ThiolC6]

It is used for the coupling of oligonucleotides to solid supports. Thiol can also be used for the attachment of fluorescent and non-fluorescent modifications.

3' Thiol C3 structure       5' Thiol C6 structure

Spacer, linkers, base & sugar modifications and their structures

Product specifications:

• Synthesis scales from 0.01 to 1.0 µmol
• Purification options: HPSF, HPLC
• Sequence lengths: 5-80 bases
• TAT: 2-4 working days

2'-Deoxyinosine [I]

2'-Deoxyinosine (INO) is a universal base that is less destabilising than mismatches found within a wobble or degenerated base.

2'-Deoxyinosine structure

2'-Deoxyuridine [U]

2'-Deoxyuridine (URI) are often used as a substitute for dT.

2'-Deoxyuridine structure

5-Methyl-dC [5MedC]

5-Methyl-dC stabilises the DNA duplex due to an increase in the melting temperature during the replacement of the dC.

5-Methyl-dC structure

Amino-C6-dT [AmC6dT]

Amino C6-dT allows internal modifications within the oligonucleotides sequence.

Amino C6-dT structure

Biotin-dT [BIOdT]

Biotin-dT can be used for an internal biotin modification (e.g. for hybridisation studies).

Biotin-dT structure

2',3'-dideoxyC [23ddC]

3'-ddC prevents extension by DNA polymerases and prevents degradation by 3'-exonucleases.

3'-ddC structure

dSpacer [Spd]

The dSpacer is used to create a stable abasic site within an oligonucleotide.

dSpacer structure

Spacer C3 [SpC3]

Spacer C3 can be coupled to the 3'-end and internally of an oligonucleotide sequence. This can prevent e.g. the elongation of the oligo during a PCR without a major influence to its annealing properties. Oligos with C3 spacers are therefore ideal hybridisation probes in PCR reactions.

C3 spacers structures

Wobbles [WOB] (defined ratio) 

The following IUB code is used to describe degenerated bases (wobbles). Wobbles are available with a defined and non defined ratios.

Dark quencher extends quenching efficiency in real-time PCR

Dabcyl [DAB] 400–550 nm

The Dabcyl quencher is a non-fluorescent dark quencher especially recommended for Molecular Beacons. It efficiently quenches various fluorescent dyes in the blue to green emission spectra, but it is not recommended for fluorophores emitting above 480 nm.

Dabcyl-dT [DABdT] 400–550 nm

Dabcyl-dT is a non-fluorescent internal quencher. It efficiently quenches various fluorescent dyes in the blue to green emission spectra. It can be used in addition to any other 3' quencher..

Eclipse [Eclip] 390-625 nm

Eclipse is a non-fluorescent dark quencher from Epoch Biosciences, Inc. This non-fluorescent dye with a maximum absorption at 522 nm effectively quenches a broad group of fluorescent dyes between emission ranges of 390–625 nm in Dual Labeled Probes and Molecular Beacons.

Tide Quencher 2 [TQ2] 440-580 nm

TQ2 is one of the Tide Quencher family developed by AAT Bioquest. It is the licence - free alternative to the BHQ1. With its quenching range from 440 - 580 nm TQ2 fits perfectly to FAM, JOE, Yakima Yellow and HEX.

BHQ1 [BHQ1] 480-580 nm

BHQ1 is one of the Black Hole Quencher from Biosearch Technologies, Inc. BHQ1 is an highly efficient dark quencher for Dual Labeled Probes, Molecular Beacons and FRET probes with an excellent spectral overlap for all dyes in the green to dark yellow emission spectrum.

BHQ1-dT [BHQ1dT] 480-580 nm

BHQ1-dT is one of the Black Hole Quencher from Biosearch Technologies, Inc. BHQ1-dT is an highly efficient quencher used for internal labelling for all dyes in the green to dark yellow emission spectrum. It can be used in addition to other 3' quenchers.

Tide Quencher 3 [TQ3] 510-620 nm

TQ3 is one of the Tide Quencher family developed by AAT Bioquest. It is the licence - free alternative to the BHQ2. With its quenching range from 510 - 620 nm TQ3 fits perfectly to HEX, CY3 and TAM but shows also good quenching activity for ROX and Texas Red.

BHQ2 [BHQ2] 520-650 nm

BHQ2 is the second Black Hole Quencher from Biosearch Technologies, Inc. in our portfolio. BHQ2 is a highly efficient dark quencher for Dual Labeled Probes, Molecular Beacons and FRET probes containing 5’ fluorophores in the dark green to orange emission sector.

BHQ2-dT [BHQ2dT] 560-670 nm

BHQ2-dT is one of the Black Hole Quencher from Biosearch Technologies, Inc. BHQ2-dT is an highly efficient quencher used for internal labelling for all dyes in red emission spectrum. It can be used in addition to other 3' quenchers.

BBQ 650 [BBQ650] 550-750 nm

The BlackBerry Quencher 650 is an excellent long wavelength quencher for Dual Labeled Probes, Molecular Beacons and FRET probes containing long wavelength dyes such as Cy5, Cy5.5 and other dyes in the red to near-infrared emission spectrum.

PTOs, the defense line against nucleases

Phosphorothioate (PTOs) are the most widely used nuclease resistant oligos for antisense applications.

In PTO oligos, a non-bridging oxygen is replaced by a sulfur atom. Therefore, PTOs are also known as "S-oligos". Phosphorothioate bounds can be introduced to an oligo

• at the 5'- or 3'-end
  Inhibits exonuclease degradation
• Internally 
  Limit the attack by endonucleases

Product specifications:

• Synthesis scales from 0.01 to 10 µmol
• Purification options: HPSF, HPLC
• Oligo lengths: 5-120 bases
• TAT: 2-4 working days

¹ The synthesis scale indicates the initial amount of 3'-bases
² There is no OD guarantee for oligos <18 and >35 bases or for oligos with multiple modifications

Good to know!

PTO oligos can show greater non-specific protein binding than unmodified phosphodiester (PO) oligos. They can lead to toxic effects or cause artefacts building when present in high concentrations.

These problems can be reduced or eliminated by using chimeric designs, which limit the number of phosphorothioate internucleoside linkages within the oligo. 

All relevant documents are provided in your online account:

• Oligo synthesis report
• Plate report
• Delivery note
• Quality report incl. QC spectra, if requested

To ensure a smooth ordering process, here are some hints how to order custom DNA oligos in plate format.

Ordering online:

• Up to 12 plates can be specified via file-upload or copy & paste
• One plate must contain a minimum of 12 oligos
• Modifications can be entered directly in the sequence
• Concentration and volume can be specified
• Plate copies as additional service can be selected
• A plate overview enables you to validate and edit single wells

Available plate types:

• 96well, 1.2 ml, round wells
• 96well, 0.8 ml, round wells
• 96well, 2.2 ml, deep well plates
• 96well, 0.2 ml PCR plates

Good to know:

Plate oligos are delivered in the selected plate type with the required volume (max. 500µl resp. 150µl for PCR Plates) for the selected concentration. 

For additional plate copies (aliquot-plates) or mixture plates the requested volume is taken from the mother plate.

The remaining oligos in the mother plate are always provided along with the plate copies or the mixture plates without additional charge.

Important for mixture plates:

• Define the plates for the forward and reverse primers (e.g. Plate1_ for, Plate1_ rev)
• Use the same primer names accompanied by the suffix “.for” or “.f” and “.rev” or ”.r”
• Select the concentration of the forward and reverse primers
• Specify the final concentration and volume of the primer mix in the order comment

Custom projects:

If you need additional plate formats, a special normalisation or pooling service, please send us your request!