netropsin

Netropsin is a natural product antibiotic produced by Streptomyces species. It is a small, rigid, cationic molecule classified as a diamidine that binds to DNA with high affinity.

Netropsin binds primarily to the minor groove of double-stranded DNA, showing a strong preference for AT-rich sequences. The interaction involves hydrogen bonding from the amidine groups and electrostatic contacts with the DNA phosphate backbone, allowing sequence-selective recognition without denaturing the duplex. The binding is generally reversible and does not disrupt base pairing.

Biological effects of netropsin arise mainly from its ability to block access to DNA by proteins. In vitro, it can inhibit transcription and replication by preventing transcription factors and polymerases from binding to promoter regions or progressing along the template, particularly at AT-rich sites. These properties make it a useful tool for studying DNA structure and sequence recognition, rather than a clinical antibiotic.

In molecular biology and biophysical research, netropsin is used to probe DNA conformation, to map AT-rich regions, and to explore the consequences of minor groove occupancy by ligands. It is often discussed together with distamycin, another minor groove binder with similar preferences. Because of toxicity and limited therapeutic value, netropsin is primarily a research reagent rather than a therapeutic agent.