- to generate information on gene integrity and copy number (blot)
- to diagnose specific sequences and chromosomal aberrations (in situ hybridization)
- to simultaneously measure the relative expression of RNAs (microarray analysis)
- to discover protein-nucleic acid interactions (electrophoretic mobility shift assays or FRET)
Labels, Labels, Everywhere
Generally speaking, there are two types of nucleic acid labeling techniques: radioisotope labeling and non-radioactive labeling.- Radioisotope labeling: Considered as a conventional method for nucleic acid labeling, radiolabeled nucleotides are synthesized using ATP-gamma-32P or 35P. They are easily incorporated into nucleic acid sequences by traditional enzymatic means or by an organism of interest.
- Non-radioactive (chemical) labeling: Nowadays, non-radioactive nucleotide labels are more extensively used due to their relative speed, sensitivity, safety, and versatility. The most common labels are fluorescent ‘tags’ that are synthesized and incorporated into oligonucleotides, but you can also attach a variety of other molecules or proteins to chemically reactive groups like biotin, streptavidin, or fluorophores. Pre-labeled oligos are available from most oligo suppliers like as IDT DNA or Genewiz.

Sources: Jena Bioscience GmbH, Thermo Fisher Scientific, and New England Biolabs
* dNTP or NTP may be labelled with radioactive phosphate, hapten, or fluorophore.
Choosing a Labeling Method
When choosing a labeling system, consider the size and type of nucleic acid you’re working with. Large DNA, plasmid DNA, and RNA for blots and in situ hybridization can be labeled throughout by random incorporation of a covalently coupled label. While covalent probes produce excellent sensitivity, enzymatic methods are more economically convenient in the lab and can label copies of the sample (in PCR labeling). For shorter sequences like oligos, it may be more convenient to order a pre-labeled sample through a company that specializes in labeled DNA, like IDT or Genewiz. You should also think about the application you’ll be using your labeled nucleic acid in. For protein interaction studies, for instance, large fluorophore labels can interrupt interactions due to their steric hindrance and chemical properties. You can avoid this concern by using smaller labels or by labeling a site that is farther away from the interaction location. If you’re looking for signal amplification, secondary reporters such as antibody conjugates like avidin/streptavidin are an excellent choice. What nucleic labeling techniques and reporters have you used? Tell us in the comments below!References
- Ligasová, Koberna. DNA Replication: From Radioisotopes to Click Chemistry. Molecules. 2018 Nov 17;23(11). doi: 10.3390/molecules23113007.
- Jena Bioscience. https://www.jenabioscience.com/
- Thermo Fisher Scientific Nucleic Acid Labeling Brochure. https://www.thermofisher.com/us/en/home/life-science/dna-rna-purification-analysis/nucleic-acid-labeling.html
- New England Biolabs DNA and RNA Labeling. https://www.neb.com/products/dna-modifying-enzymes-and-cloning-technologies/dna-labeling/dna-labeling