RNA double-helical fragments at atomic resolution: II. The crystal structure of sodium guanylyl-3′,5′-cytidine nonahydrate

(G–H) • –C and G–(C–H) • radicals derived from the guanine·cytosine base pair cause DNA subunit lesions

“…Interstrand hydrogen bonds are responsible for this pairing. The interatomic distances obtained in this work at C 1 symmetry by using the B3LYP͞DZPϩϩ level of theory do not compare well with the crystallographic conclusions (6,8). We do find agreement with the theoretical structures reported by Guerra et al (5) and Richardson et al (27).…”

“…The crystallographic data (6,8) available for the base pairs within DNA were compared with results predicted here ( Table 1). However the structures of the possible radicals that can be generated from primary radiation damage have never been explored experimentally.…”

“…Sophisticated experimental techniques have been used to investigate the causes and effects of DNA damage and also to determine structural features, as well as delving into the electron-binding ability of the bases and base pairs (1)(2)(3)(4). Some of the more advanced experimental and theoretical methods have also been applied to model systems in both the gas and liquid phases to estimate and predict the physical properties and to study hydrogen bonding in purine and pyrimidine base pairs (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19). Over the years, experimental crystallographic data and theoretical work on the isolated bases and base pairs seemed to disagree on the hydrogen bond lengths and interaction energies of the base pairs.…”

Polymeric metal–nucleotide complexes. The crystal structures of [(C9H12N3O8P)Cd(H2O).H2O] n and [(C9H12N3O8P)Co(H2O)] n formed between cadmium(II) or cobalt(II) ions and cytidine 5'-monophosphate

“…It involves the stacking between O(1 ') of a ribose ring and a neighbouring purine or pyrimidine base, such that O(1') is approximately equidistant from all the atoms of the base ring. These two types of base-stacking interactions have been reviewed by Bugg, Thomas, Sundaralingam & Rao (1971) and further described for the crystal structures of UpA (Sussman, Seeman, Kim & Berman, 1972), ApU (Seeman, Rosenberg, Suddath, Kim & Rich, 1976) and GpC (Rosenberg, Seeman, Day & Rich, 1976).…”

“…Possibly similar weak stacking interactions exist in other crystals without having been remarked upon, since secondary crystal-packing forces are generally not well understood. Rosenberg, Seeman, Day & Rich (1976)note differences in ribose conformations which appear to correlate with the presence or absence of stacking involving O(1') but any assessment is not yet quantitative. The sugar ring conformation in Cd-CMP is C(3')-endo while that in Co-CMP [where there is base-base rather than O(l')-base stacking] is C(2')-endo/C(l')-exo.…”