DNA Labeling
Nucleic acids may be labeled at their 5´ end, their 3´ end, or throughout the molecule depending on the application. For hybridization reactions (Southern or northern blotting) it is usually advantageous to generate high specific activity probes with label distributed throughout the nucleic acid, through techniques such as nick translation, random priming, by PCR or in vitro transcription using labeled dNTPs or NTPs. For applications involving protein interactions, such as gel-shift assays or pull-downs, it is generally beneficial to generate end-labeled probes to prevent steric interference of the interaction. This can be achieved with end-labeling protocols or with PCR using primers bearing the required modification.
New England Biolabs offers a number of reagents and kits suitable for labeling single-stranded or double-stranded DNA and RNA at either the molecule ends or randomly throughout the nucleic acid.
Recommended Products for DNA Labeling:
| Application | Label | Reaction | Recommended Enzyme |
| DNA 5´ End Labeling | γ-32P rATP |  |
T4 Polynucleotide Kinase |
| Labeling by PCR | α-32P dNTP, Biotin-dNTP, Fl-dNTP |  |
Taq DNA Polymerase |
| DNA 3´ End Labeling | α-32P dNTP, Biotin-dNTP, Fl-dNTP |
  |
Klenow Fragment (3´ → 5´ exo-) |
| Single Nucleotide Terminator Labeling | Fl terminator nucleotide |  |
Therminator DNA Polymerase |
| Random Priming | α-32P dNTP, Biotin-dNTP, Fl-dNTP |
 |
Klenow Fragment (3´ → 5´ exo-) |
| Nick Translation | α-32P dNTP, Biotin-dNTP, Fl-dNTP |
 |
DNA Polymerase I (E. coli) |
Choose Type:
Protocols for DNA Labeling
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