Protamine-DNA Condensates: Extreme DNA Compaction, Measurement of Bridging Forces, and Sequence Dependence

In sperm cells, protamine replaces histones to compact DNA 10−20 times more than in somatic cells. We characterized the extreme compaction of DNA by protamine using optical tweezers-based single-molecule pulling, bulk experiments, and all-atom molecular dynamics (MD) simulations (1). In the presence of protamine, single λ-DNA molecules form tangles that withstand forces strong enough (∼55 pN) for strand separation and shorten the contour length by up to 40% even at high forces, as well as bends and loops that rupture at 10-40 pN forces. MD simulations revealed that arginine sidechains of protamine form strong interactions with nucleobases, in the form of wedges between DNA strands and clamps over multiple bases. When mixed with protamine, double-stranded DNA forms aggregates but single-stranded (ss)DNA forms liquid droplets. Correspondingly, single-molecule pulling shows that ssDNA forms protamine-bridged liquid condensates that unravel sequentially, one bridge at a time. The bridging force, measured for the first time, is 11.3 ± 4.6 pN. ssDNA can form stem-loops, G-quadruplexes, and duplex segments. These structural elements allow protamine-DNA condensate properties to be tuned by the DNA sequence.



1. Ahlawat V, Dhiman A, Mudiyanselage HE, Zhou HX. 2024. Protamine-Mediated Tangles Produce Extreme Deoxyribonucleic Acid Compaction. J Am Chem Soc 146:30668-30677