Elongational flow studies on conformational change in DNA induced by DNA‐binding protein HU

Interaction of DNA‐binding protein HU from Bacillus stearothermophilis (HUBst) with coliphage T2 DNA was investigated by observing an elongational flow‐induced birefringence, Δ n , of a T2‐phage DNA aqueous solution at various HU concentrations. Localized flow birefringence was observed in the pure elongational flow region, and the strain rate dependence of Δ n had a critical strain rate ϵ˙ c for the appearance of flow birefringence at all of the HU concentrations examined, indicating that a coil–stretch transition occurred at ϵ˙ c in each DNA–HU system. For strain rates larger than ϵ˙ c , Δ n increased rapidly and then gradually, approaching a plateau value. The value of ϵ˙ c increased with an increase in HU concentration. Analysis based on the relationship between ϵ˙ c and the Rouse–Zimm relaxation time revealed that the increase in ϵ˙ c with increase in HU can be explained by the decrease in the size of the DNA–HU complex. The plateau birefringence value, Δ n p , decreased at small HU concentrations but did not change at larger HU concentrations. Considering that Δ n p is related to the orientational order parameter of segments, it was concluded that there were at least two stages in the process of compaction of DNA induced by HU. © 2003 Wiley Periodicals, Inc. Biopolymers 68: 486–496, 2003