5'-Position Modifications


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 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.


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”).


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)