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Crystallographic studies of DNA (oligonucleotides) and DNA/protein complexes

The objective of this project was to demonstrate that the crystal structure of DNA fragments is variable. Examples of Z-, B- and A-DNA duplexes in various environments were studied by X-ray crystallography. The structure of the hexamer pCGCGCG with canonical Z-DNA sequence was determined in 3 different crystal forms. The octamer pCCCGCGGG was studied as A-DNA in 5 crystal forms with progressively increasing compactness and as part of the dodecamer CGCCCGCGGGCG. The B conformation was represented by the CTAG sequence investigated as the central fragments of the dodecamer CGCTCTAGAGCG and the octamer CGCTAGCG, both with several duplexes in the asymmetric unit. Each sequence being studied in various environments demonstrated a structural variability. The CTAG structures compared among themselves and with the met-repressor / operator complex showed a similar low-high-low twist pattern. On the other hand in the trp-repressor / operator complex this tetranucleotide displays different conformational features. The CGCGCG sequence in the Z conformation also shows striking new features when compared with previously determined structures: base stacking between the ends of neighbour molecules is very variable and the bases in a duplex can have a large inclination with respect to the helical axis, which alters the overall shape of the molecule. The detailed structural comparison of 5 crystal forms of the octamer CCCGCGGG and the related dodecamer CGCCCGCGGGCG shows that both local and global structural parameters of the same A-DNA sequence vary significantly when the environment changes. A large helical twist and/or DNA bending provoke the locking of the major groove, the width of the groove decreases up to vanishing small values.

Two additional related studies are in progress. Three crystal forms of the tetramer GGCC have been obtained. The single crystal x-ray structure of the cro/DNA complex has also been determined with the duplex (GT)4.(AC)4 as a nonspecific DNA fragment.

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