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)