5'-Position Modifications
5'-Phosphate
The unmodified synthesis has only 3'- and 5'-hydroxy groups. 5'-Phosphate oligonucleotides for cloning are offered as a 5'-modification to the regular synthesis.
5'-Amino
5'-Amino modification is a primary amine linked to the carbon-5 of the 5'-ribose via a C3, C6, C12 or C2OC2-phosphate-linker. Amino-C4 and -CX are also possible (See “Amino groups and Carboxy-dT” under “Internal or 5'-positions”). Additionally different spacers are possible (See “Spacers” under “Internal or 5'-positions”). Please note that 5'-amino-C3 is not available with HPLC purification.
5'-Biotin
The standard coupling of a Biotin to the 5' end of an oligonucleotide is done including a C6 linker, but C4 or our CXS linker is also optional (See “Biotin” under “Internal or 5'-positions”). Additionally, different spacers are possible (See “Spacers” under “Internal or 5' positions”).
5'-Thiol
The 5'-Thiol modification is linked to the 5'-carbon of the ribose via a C6-phosphate-linker. 5'-Thiololigonucleotides are delivered dry and trityl-protected. Protocol for removal of the trityl-group prior to use is supplied. The Thiol modification can also be obtained from a disulfide (See “Miscellaneous” under “Internal or 5'-positions”). For more spacing different spacers are possible (See “Spacers” under “Internal or 5'-positions”).
5'-Fluorescent Dyes
Please refer to our dye selection chart for available 5’-fluorescent dyes modifications. 5' modification with dyes includes the fluoresceins ABI-dyes HEX, TET, 6-FAM and the VIC analog CAL Fluor® Orange, the Rhodamines TAMRA and ROX, the Texas Red analog CAL Fluor Red 610 and the LC Red 640 analog CAL Fluor Red 635.
| Dye | Abs. max. | Em. max. | Abs. coef. |
| 6-FAM | 494 | 517 | 83 |
| TET | 522 | 538 | 73 |
| HEX | 535 | 553 | 73 |
| CAL Fluor Orange 560 | 540 | 561 | 94 |
| Quasar® 570 (Cy3 analog) | 550 | 570 | 150 |
| TAMRA | 560 | 583 | 89 |
| CRF-610 (Cy3.5 analog) | 581 | 596 | 150 |
| ROX | 587 | 607 | 82 |
| Texas Red | 596 | 615 | 85 |
| CAL Fluor Red 610 | 590 | 610 | 108 |
| CAL Fluor Red 635 | 616 | 635 | 112 |
| Quasar 670 (Cy5 analog) | 649 | 670 | 250 |
| Quasar 705 (Cy5.5 analog) | 678 | 704 | 250 |
Abs. coef.: Molar Extinction Coefficient x 1000 (cm-1M-1)
