3’-End labeled oligonucleotides can be used as sequence-specific protein binding or nucleic acid hybridization probes e.g. for EMSA, Northern or Southern blots. Compared to internal, random labeled probes, the label is located at the 3‘-End only and less likely interferes with probe binding.
The combination of (poly)-HRP-conjugated Biotin/Digoxigenin detection reagents with AF 488 (Alexa Fluor® 488)-, AF546 (Alexa Fluor® 546)- or AF594 (Alexa Fluor® 594)-labeled tyramide further increases detection sensitivity of up to 100-fold.
Figure 1 Terminal deoxynucleotidyl Transferase (TdT) template-independently transfers labeled nucleotides to the 3’-OH group of ssDNA/oligonucleotides. The number of nucleotide and thus label incorporation depends on the type of nucleotide ((dd)UTP) and type of label (n = 1 for labeled ddUTP, n = 1 - 3 (average) for labeled UTP, n > 1 for labeled dUTP (multiple label, tail length is highly nucleotide specific).
| Kit | Label | # of Label | Labeling principle similar to … |
|---|---|---|---|
| BIO 3‘-End Oligonucleotide Labeling Kit with Biotin-11-UTP | Biotin | 1-3 | Biotin 3‘-End DNA Labeling Kit (Pierce/Thermo Scientific) |
| DIG 3‘-End Oligonucleotide Labeling Kit with Digoxigenin-11-ddUTP | Digoxigenin | 1 | DIG Oligonucleotide 3‘ End Labeling Kit, 2nd generation (Roche) |
| 3‘-End Oligonucleotide Labeling Reagent Kit | nucleotide dependent | nucleotide dependent | - |
