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.
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 synthesis | Estimated number of reactions |
|---|---|
| 25 nmole | 500 to 2,500 |
| 50 nmole | 1,000 to 5,000 |
| 200 nmole | 4,000 to 20,000 |
| 1 µmole | 20,000 to 100,000 |
| 10 µmole | 100,000 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.
Oligo purification options
| Purification method | Description | Advantages | Limitations |
|---|---|---|---|
| Desalt (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). |
| Cartridge (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). |
| HPLC (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. |
| PAGE (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. |
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.
| Electronic ordering code | Absorption maximum (nm) | Emission maximum (nm) | Extinction coefficient (OD/mol) at
| |
|---|---|---|---|---|
| Generic modifications | ||||
| Aldehyde | ALD | NA | NA | NA |
| Amine (Primary) | AMN | NA | NA | NA |
| Biotin | BIO | NA | NA | NA |
| Phosphate | PHO | NA | NA | NA |
| Thiol | THL | NA | NA | NA |
| Fluorescent dye modifications | ||||
| Fluorescein | FLO | 494 | 520 | 31,500 |
| HEX | HEX | 535 | 553 | 31,580 |
| ROX* | ROX | 576 | 601 | 22,500 |
| TET | TET | 522 | 538 | 16,255 |
| TAMRA* | TAM | 565 | 580 | 32,300 |
| *Oligos containing this modification require HPLC purification. | ||||
| Molecular Probes dyes | |||||
|---|---|---|---|---|---|
| Dye* | Electronic ordering code | Color | Absorption maximum (nm) | Molar emission maximum (nm) | Extinction coefficient
|
| Alexa Fluor 488 | 488 | Green | 490 | 519 | 71,000 |
| Alexa Fluor 532 | 532 | Green | 532 | 553 | 81,000 |
| Alexa Fluor 546 | 546 | Yellow | 556 | 573 | 104,000 |
| Alexa Fluor 555 | 555 | Orange/yellow | 555 | 565 | 150,000 |
| Alexa Fluor 594 | 594 | Orange | 590 | 617 | 73,000 |
| Alexa Fluor 647 | 647 | Red | 650 | 655 | 239,000 |
| Alexa Fluor 660 | 660 | Red | 663 | 690 | 132,000 |
| Alexa Fluor 750 | 750 | Purple | 749 | 755 | 240,000 |
| Bodipy FL | BDA | Far Red | 502 | 510 | 82,000 |
| Bodipy 530/550 | BDB | – | 534 | 551 | 77,000 |
| Bodipy 493/503 | BDC | – | 500 | 509 | 79,000 |
| Bodipy 558/569 | BDE | – | 559 | 568 | 97,000 |
| Bodipy 564/570 | BDF | – | 563 | 569 | 142,000 |
| Bodipy 576/589 | BDG | – | 575 | 588 | 83,000 |
| Bodipy 581/591 | BDH | – | 581 | 591 | 136,000 |
| Bodipy FL-X | BDI | – | 504 | 510 | 85,000 |
| Bodipy TR-X | BDJ | – | 588 | 616 | 68,000 |
| Bodipy TMR | BDK | – | 544 | 570 | 56,000 |
| Bodipy R6G | BDL | – | 528 | 547 | 70,000 |
| Bodipy R6G-X | BDM | – | 529 | 547 | 73,000 |
| Bodipy 630/650 | BDN | – | 625 | 640 | 101,000 |
| Bodipy 650/665 | BDP | – | 651 | 660 | 100,000 |
| Cascade Blue Dye | CSB | Blue | 400 | 420 | 28,000 |
| Marina Blue Dye | MNB | Blue | 362 | 459 | 19,000 |
| Oregon Green 514 | OGB | Green | 506 | 526 | 85,000 |
| Oregon Green 488 | OGC | Green | 495 | 521 | 76,000 |
| Oregon Green 488-X | OGD | Green | 494 | 517 | 84,000 |
| PACIFIC BLUE Dye | PFB | Blue | 416 | 451 | 36,000 |
| RGA | Green | 504 | 532 | 78,000 | |
| Rhodol Green Dye | RGB | Green | 496 | 523 | 63,000 |
| Rhodamine Green-X | RGC | Green | 503 | 528 | 74,000 |
| Rhodamine Red-X | RRA | Red | 560 | 580 | 129,000 |
| Texas Red-X | TRX | Red | 583 | 603 | 136,000 |
| * 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 bases | Electronic ordering code | Description |
|---|---|---|
| Deoxyuracil | U | Useful with UDG for ligase-free cloning. |
| Deoxyinosine | I | Deoxyinosine 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. |
| F | ||
| C-Phosphorothioate | O | |
| 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 name | Electronic ordering code | Absorption maximum (nm) | Emission maximum (nm) | Extinction coefficient (OD/mol) at 260 nm |
|---|---|---|---|---|
| Biotin | BIO | NA | NA | NA |
| Phosphate | PHO | NA | NA | NA |
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
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