Nucleobase-Specific Recognition of DNA by Protamine

Salmon protamine wraps 35-bp DNA and shows nucleobase-specific recognition, preferring GC over AT at the major groove by a 2.6-to-1 ratio.

• Why it matters: It remains unclear whether intrinsically disordered, Arg-rich protamines can read DNA sequence rather than only charge, which matters for how paternal chromatin is silenced and remodeled.
• What they did: All-atom molecular dynamics simulations tested eight copies of salmon protamine (33 residues with 21 Arg) binding 35-bp DNA, then used additional 20-bp simulations and free-energy calculations.
• The result: Major-groove selectivity reverses at the minor groove, where AT overtakes GC by 2.1-to-1, yielding a moderate GC bias; experiments with 0–40% GC DNA show aggregation increases with GC and with G-tract shuffling.

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