Ion Localization on A-tract DNAs

N.V. Hud, V. Sklenár , and J. Feigon: "Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending", J. Mol. Biol. 286, 651-660 (1999). [abstract]

Model B-form duplex polymers of (left) d(GCA₄T₄)_n and (right) d(CGT₄A₄)_n. Violet surfaces designate the regions of preferential monovalent cation localization. Note that the reduced repulsion of phosphates across the minor groove due to monovalent cations localized in these regions of d(GCA₄T₄)_n would be expected to cause the duplex to bend concave towards the reader. Duplex d(CGT₄A₄)_n, rotated 90º with respect to d(GCA₄T₄)_n , would not be expected to exhibit an appreciable net macroscopic curvature, since two monovalent cation binding sites are located on opposite faces of the DNA for each T₄ A₄ sequence element. A, C, G and T bases are shown in red, orange, blue and green, respectively.