Stereochemistry of nucleic acids and their constituents. X. solid‐slate base‐slacking patterns in nucleic acid constituents and polynucleotides

Abstract

SynopsisThe base-stacking patterns in over 70 published crystal structures of nucleic acid constituents and polynucleotides were examined. Several recurring stacking patterns were found. Base stacking in the solid state apparently is very specific, with particular modes of interaction persisting in various crystalline environments. The vertical stacking of purines and pyrimidines in polynucleotides is similar to that observed in crystals of tiucleic acid constituents. Only partial base overlap was found in the majority of the structures examined. Usually, the base overlap is accomplished by positioning polar substituents over the ring system of an adjacent base. The stacking interactions are similar to those found in the crystal structures of other polar aromatic compounds, but are considerably different from the ring-ring interactions in nonpolar aromatic compounds. Apparently, dipole-induced dipole forces are largely responsible for solid-state base stacking. It is found that halogen substituents affect, base-stacking patterns. In general, the presence of a halogen substituent results in a stacking pattern which permits intimate contact between the halogen atom and adjacerit purine or pyrimidine rings. Considering differences in the stacking patterns found for halogenated and nonhalogenated pyrimidines, a niodel is proposed to account for the mutagenic effects of halogenated pyrimidineo.

Structures of two dideoxynucleosides: 2',3'-dideoxyadenosine and 2',3'-dideoxycytidine

“…The glycosidic bonds, CI'-N9 in (1) and CI'-N1 in (2), have X torsion angles of 264.1 (2) and 203.2 (2) ° , respectively, and both molecular conformations are anti although that of (1) is on the borderline with the syn conformation (X=270°). The C1'-O4' bond is significantly shorter than the C4'-O4' bond in conformity with the observations of Bugg, Thomas, Sundaralingam & Rao (1971). In general, other molecular dimensions in both molecules are comparable with similar compounds.…”

Pyridazine nucleosides. The structure and conformational analysis of 5-hydroxy-2-(1-β-D-ribofuranosyl)-3(2H)-pyridazinone

“…The C(3)-C(4) bond lies directly on top of N(1). The bond-over-ring type of overlap seen here is not as common as having a single polar group or atom sit over the adjacent ring but it is known (Bugg, Thomas, Sundaralingam & Rao, 1971) and the overlap here is similar to what is seen in the crystal structure of 9-methyladenine (Stewart & Jensen, 1964).…”

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

“…4. The degree or extent of overlap is approximately one third of the normal (Bugg, Thomas, Sundaralingam & Rao, 1971).…”

“…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).…”