Helene Sternglanz

Relationship between the mutagenic and base-stacking properties of halogenated uracil derivatives: The crystal structures of 5-chloro- and 5-bromouracil

Three-dimensional X-ray diffraction data were used to determine the crystal structures of 5-chlorouracil and 5-bromouracil, two mutagenic pyrimidine analogs that can substitute for thymine in DNA. Crystals of the two compounds are nearly isostructural. The space group is P21/c, with a equals 8.450(6), b equals 6.842(3), c equals 11.072(16) angstrom, beta equals 123.53(19) degrees for 5-chlorouracil, and a equals 8.598(3), b equals 6.886(1), c equals 11.417(5) angstrom, beta equals 123.93(3) degrees for 5-bromouracil. Intensity data were collected with an automated diffractometer. The structures were refined by full-matrix least-squares to R equals 0.058 for 5-chlorouracil and R equals 0.027 for 5-bromouracil. The analogs from planar, hydrogen-bonded ribbons that are nearly identical to those found in the crystal structure of thymine monohydrate. As in many other structures of 5-halogenated uracil derivatives, the bases assume a stacking pattern that permits intimate contacts between the halogen substituents and the pyrimidine rings of adjacent bases. This stacking pattern involves halogen contacts that are significantly shorter than normal van der Waals interactions. The crystallographic results provide additional evidence that halogen substituents influence the stacking patterns of uracil derivatives, while exerting little direct effect on the hydrogen-bonding properties. The observed stacking patterns are consistent with the hypothesis that altered stacking interactions may account for the mis-pairing between 5-halogenated uracil bases and guanine residues within double-helical nucleic acids.

Conformation of N6-Methyladenine, a Base Involved in DNA Modification: Restriction Processes

Crystal structures of N6,N9-dimethyladenine and N6-methyladenine hydrochloride were determined from three-dimensional x-ray diffraction data. The bases assume a conformation in which the N(6)-methyl group blocks one of the hydrogen-bonding sites normally used by adenine to form Watson-Crick pairs with thymine in double-helical DNA. When in this conformation, N6-methyladenine residues might alter the secondary structure of DNA. thereby preventing the scission of modified DNAs by restriction enzymes.

Conformations of N6-monosubstituted adenine derivatives: Crystal structure of N6-methyladenine

Abstract Three-dimensional X-ray diffraction data were used to determine the crystal structure of N6-methyladenine, a base that occurs in modified DNAs and in the anticodon loop of Escherichia coli tRNAVal. Crystals of N6-methyladenine are monoclinic, space group P 2 1 c , with a = 9.911(1), b = 5.850(1), c = 11.680(4) A and β = 92.49(2)°. Intensity data were collected with an automated diffractometer. The structure was solved by direct methods and refined by least-squares to R = 0.033. The conformation of the base is such that the methyl group is nearly coplanar with the purine ring and is pointing away from the imidazole moiety. This conformation is similar to that found for adenine derivatives with bulky substituents at the N(6) position. When in this conformation, N6-methyladenine could not form normal, complementary base pairs with thymine or uracil, and would therefore disrupt double-helical regions of nucleic acids. Such an effect might account for the biological roles of N6-methyladenine in modification and restriction processes, and in the anticodon loop of E. coli tRNAVal.

Crystal structures ofN(6)-methyladenine hydrochloride andN(6),N(9)-dimethyladenine

The crystal structures ofN (6)-methyladenine hydrochloride (6-MA·HCl) and ofN (6),N (9)-dimethyladenine (6,9-DMA) were determined by the use of X-ray diffractometer data. Crystals of 6-MA·HCl are monoclinic, space groupP21/m, witha = 9.3450(6),b = 6.5838(4),c = 7.3142(3) Å, β = 114.837(4) °, andZ = 2. Crystals of 6,9-DMA are monoclinic, space groupP21/c, witha = 12.045(3),b = 6.135(2),c = 23.27(1) Å, β = 111.79(3), andZ = 8. The crystal structures were refined by least-squares toR = 0.053 for 6-MA·HCl andR = 0.071 for 6,9-DMA. The N(1)-protonated adenine derivative in the 6-MA·HCl crystal structure and the two crystallographically independent adenine derivatives in the 6,9-DMA structure all assume conformations in which the methyl substituent at N(6) is in or near the purine plane, and is pointing away from the imidazole moiety.

Crystal structure of ethidium monoazide, a photoactive compound that reacts with nucleic acids

The crystal and molecular structure of ethidium monoazide, a photoactive derivative of ethidium, was determined from X-ray diffraction data. Crystals of 8-azidoethidium chloride monohydrate are monoclinic, space groupP21/c, witha = 8.336(5),b = 14.778(6),c = 16.873(5) Å, and β = 99.90(3) ° The crystals are poorly ordered, weakly diffracting, and unstable in air. Intensity data were collected with an automated diffractometer from a crystal that was sealed in a thin-walled glass capillary. The structure was solved by direct methods and was refined by least squares toR = 0.20 for the complete set of 2126 unique reflections, and toR = 0.11 for 724 reflections with1 > 2σ(I). The results demonstrate that the photoactive azide moiety is attached to the 8-position of the phenanthridinium moiety. This azide group is almost linear, is nearly in the plane of the phenanthridinium ring, and is oriented away from the phenyl substituent (i.e.,trans to the C(7)-C(8) bond). Possible models for intercalation complexes of 8-azidoethidium with double-helical nucleic acids were examined by modifying published coordinates from crystal structures of ethidium-dinucleotide complexes. When in the conformation observed in this crystal structure, 8-azidoethidium can be substituted for ethidium in the published complexes without suffering any unacceptable steric interactions.

Structural Properties of Purine and Pyrimidine Analogs

During the past thirty years, many analogs of naturally occurring purines and pyrimidines have been synthesized and tested for various biological effects [1–6]. A number of these compounds are effective metabolic inhibitors which are useful chemotherapeutically, and others have been valuable as mutagenic agents. In an effort to characterize the specific structural and biological properties of purine and pyrimidine analogs, many laboratories have been engaged in crystallographic investigations of these compounds. These studies have been directed specifically toward evaluating the effects exerted by various substituents on bond lengths and angles, preferred tautomer forms, conformations, hydrogen-bonding properties, and base-stacking interactions. In this paper we shall discuss some of these structural results. Rather than attempt a comprehensive review of purine and pyrimidine analogs, we shall examine four specific types of analogs that have been of special interest in our laboratory (Figure 1). The first type (Figure 1a) includes 5-halogenated uracil derivatives, in which a hydrogen atom of uracil or the methyl group of thymine is replaced by a halogen atom. The second type includes those analogs in which an oxygen atom of a natural base has been replaced by a sulfur atom (Figure 1b). The third type (Figure 1c), is composed of N6-monosubstituted adenine derivatives, and related 6-thiopurine derivatives. The fourth type includes purine nucleosides that possess bulky substituents at the 8-position (Figure 1d). Though these types of compounds represent only a fraction of the analogs that have been investigated, they encompass some striking examples of the mechanisms by which alterations of natural bases can cause subtle structural effects, that, in turn, may affect biological properties.