What are the common methods for nucleic acid labeling?

In molecular biology, nucleic acids are typically modified enzymatically or chemically with tags (e.g. biotin, digoxygenin, fluorophores or modified nucleotides) that facilitate their visualization and/or purification. While these methods differ in technique, scalability and expense, both enzymatic and chemical methods can be used to label nucleic acids at either the 5' end, the 3' end or randomly throughout the molecule.

Enzymatic methods for labeling nucleic acids are relatively less expensive than chemical methods and often used for small-scale probe production. These methods use enzymes such as Terminal deoxynucleotidyl transferase (TdT), DNA polymerase or RNA polymerase to generate nucleic acid probes by catalyzing the incorporation of modified nucleotides during DNA replication.

In contrast, chemical methods are used for large-scale probe production because they offer greater flexibility and support for high volume reactions. Common chemical methods for labeling RNA molecules include periodate oxidation, while EDC-meditated conjugation and random chemical labeling using nonspecific crosslinkers can be used to label both DNA and RNA.