guanylyl-(3--5-)-guanosine and cytidylyl-(3--5-)-cytidine

We have solved the single crystal X-ray structure of the synthetic DNA hexamer d(CCGCGG). The central alternating tetramer forms a Z-DNA duplex. The initial cytosine of each strand of the duplex swings out and forms a Watson-Crick base-pair with the terminal guanine of a symmetry-related molecule. Thus, two symmetry-related DNA molecules form a twin with intermolecular base-pairs at both ends. Such a twin is additionally stabilized by a sodium ion located on a dyad axis between two DNA duplexes. The total structure has recombination-like features. It also provides a model for B/Z junctions. The crystal used in this study belongs to space group C222(1) with a = 34.33 A, b = 44.04 A and c = 38.27 A. The structure was solved by molecular replacement using partial models, and refined by molecular dynamics simulated annealing and positional treatment. The refinement has been concluded with an R-factor of 18.5% for 2377 reflections with F > or = 2 sigma (F) in the resolution region 8.0 to 1.92 A. The asymmetric unit contains two strands of d(CCGCGG) and 38 water molecules.

Topics: Crystallization; Crystallography, X-Ray; Dinucleoside Phosphates; DNA; Models, Molecular; Molecular Structure; Nucleic Acid Conformation; Oligodeoxyribonucleotides; Recombination, Genetic

The reaction of cyanomorpholinoadriamycin (CMA) with DNA results in the formation of sequence-specific complexes with DNA. These complexes were revealed as blocked transcripts in an in vitro transcription assay--of 14 high-intensity blockages detected in the 120 bp probed in this assay, 12 were prior to GpG or CpC sequences. Slow read-through past the first few sites exhibited first-order kinetics, with half-lives of 25-200 min. Bidirectional transcription footprinting revealed nine high-intensity sites, eight of which were defined by a GpG element (nontemplate strand). Reaction of CMA with single-strand DNA, followed by a primer-extension assay, revealed four major blockages all of which were at GpG sites on the initial single-strand DNA. From a combination of these three experimental approaches, it appears that CMA yields dominantly intrastrand cross-links between adjacent guanine residues. Since CMA is also known to form interstrand cross-links, these appear to occur at GpC sequences but are minor in comparison to the extent of formation of intrastrand cross-links.

Topics: Alkylation; Base Sequence; Cross-Linking Reagents; Dinucleoside Phosphates; DNA; DNA Fingerprinting; DNA, Single-Stranded; Doxorubicin; Kinetics; Molecular Sequence Data; Transcription, Genetic