Fig. 3. HU binding motifs. (A) Nick, ds-DNA connected with ds-DNA. HU arms interact with the 3′ DNA branch; the 5′ DNA branch is curved and interacts with the HU body. (B) 3′-overhang, ds-DNA connected with ss-DNA. HU arms interact with the ds-part of the molecule while the flexible ss-part interacts with the HU body. α1 and α3, α helices 1 and 3 of HU; N, their N-termini. Points indicate positively charged HU residues and DNA phosphates.