Absence of Minor Groove Monovalent Cations in the Crosslinked Dodecamer C-G-C-G-A-[formula omitted]-T-T-C-G-C-G

Abstract

The structure of a crosslinked B -DNA dodecamer of sequence C-G-C-G-A-A-T-T-C-G-C-G has been solved to a resolution of 1.43Å. The dithiobis-propane crosslink, -CH2-CH2-CH2-S-S-CH2-CH2-CH2-, bridges N7 atoms of adenine bases 6 and 18 in the two central base-pairs within the major groove. The crosslink is sufficiently long that no bending is induced in the helix, which is essentially isostructural with the native unlinked dodecamer at 1.9Å. A constellation of solvent peaks tentatively fitted as a spermine molecule in that earlier analysis is now seen at higher resolution to be a well-defined octahedral magnesium hexahydrate complex in the major groove. One end of the duplex curves around that complex to produce a roll-bend near base-pairs 3-5, and an overall bend in helix axis, as has long been noted. Two other magnesium complexes connect the helices and help to knit the crystal lattice together. No evidence exists for partial sodium or potassium ion substitution for solvent water molecules within the minor groove spine of hydration, as had been suggested previously: not coordination geometry and environment, nor B values, nor calculated valence values, nor difference map analyses. Indeed, the very numbers that have been claimed in support of partial substitution by sodium or potassium ions are reproduced with the present crystals, which by chemical analysis contains only one trace sodium ion per 160bp, and one potassium ion per 41bp. In contrast, our crystals contain one Mg2+per base-pair, meaning that phosphate group charge neutrality is accomplished by divalent cations, not monovalent ions. Three of these magnesium cations per duplex are localized and visible in the X-ray analysis, and nine are disordered and invisible. Hence although binding of monovalent cations within the minor groove of A -tracts on occasion may be a consequence of groove narrowing, it cannot be the cause of that narrowing. Cations, contrary to what has been claimed, are not in charge.