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DNA Labeling

Nucleic acids are readily labeled with tags that facilitate detection or purification. A variety of enzymatic or chemical methods are available to generate nucleic acids labeled with radioactive phosphates, fluorophores, or nucleotides modified with biotin or digoxygenin for example.

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


Terminal™ Transferase



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)

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Protocols for DNA Labeling