Oligonucleotides crystal structure

Sponer, ]., Kypr, ]. (1993). Theoretical analysis of the base stacking in DNA choice of the force field and a comparison with the oligonucleotide crystal structures. Journal of Biomolecular Structure Dynamics, 11, 111. 

In 1994 and 1995, two crystal structures of hammerhead ribozymes [31,32] and a structural analysis based on fluorescence resonance energy transfer studies [41] were published. In case of the crystal structure analyses, both ribozyme variants contained certain modifications that had been introduced to avoid self-cleavage [31,32]. In one case a DNA-analog of the substrate oligonucleotide was used [31], in the other case the all-RNA substrate contained a I -O-CR modification at the attacking 2 -OH group to avoid cleavage in the crystal [32] for reviews see [8,42,43]. 

In an oligonucleotide-drug hydrate complex, the appearance of a clathrate hydrate-like water structure prompt a molecular dynamics simulation (40). Again the results were only partially successful, prompting the statement, "The predictive value of simulation for use in analysis and interpretation of crystal hydrates remains to be established." However, recent molecular dynamics calculations have been more successful in simulating the water structure in Ae host lattice of a-cyclodextrin and P-cyclodextrin in the crystal structures of these hydrates (41.42). 

Vicens, Q. Westhof, E. Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding a site. Chem. Biol. 2002, 9, 747-755. 

Teplova, M., et al. (2002). Covalent incorporation of selenium into oligonucleotides for X-ray crystal structure determination via MAD proof of principle. Multiwave-length anomalous dispersion. Biochimie 84, 849-858. 

Vicens, Q. and Westhof, E. (2003). Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide. /. Mol. Biol. 326,1175-1188. 

Detailed studies of the structures (including crystal structures) of the formed adducts of cisplatin with oligonucleotides and DNA (again from several sources). 

Figure 2.37 Two views of the crystal structure of [Rh(R, R-Me2trien) (phi)]3+ bound within an eight-base-pair oligonucleotide. (Reproduced with permission from [18] 1999, American Chemical Society).

C.A. Hunter, X.-J. Lu, DNA Base-stacking interactions A comparison of theoretical calculations with oligonucleotide X-ray crystal structures. J. Mol. Biol. 265, 603-619 (1997)... 

The N-H- -N bonds constitute about a quarter of the hydrogen bonds in the purine and pyrimidine crystal structures (see Thble 7.14). The proportion is much smaller in the nucleosides and nucleotides Thble 7.12, where they compete with the stronger O-H- -O and N-H- -O interactions. In combination with N - H O=C, the N - H N bonds form the Watson-Crick and related base-pair configurations in purine and pyrimidine crystal structures, and in the oligonucleotides and nucleic acids. 

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