COLLABORATION IN BASIC SCIENCE AND ENGINEERING (COBASE)

Working in Plavec's Laboratory

Janez Plavec of the Slovenian National Institute of Chemistry spent June and July 2000 working with Nicholas Hud at his lab in Atlanta. Thanks to their complementary skills and expertise, the two colleagues were able to lay the foundation for collaborative research on DNA-cation interactions, specifically focusing on cation binding by non-B-form DNA structures.

Plavec and his research team in Slovenia had previously determined the solution-state structure of the DNA oligonucleotide d(G4T4G3). Despite their progress in identifying this molecule’s quadrupex structure, however, the number and location of bound cations within this structure remained unclear. Meanwhile, Hud had developed techniques for localizing cation binding on nucleic acids by using the isotopically-labeled ammonium ion (15NH4+) as a chemical probe in NMR spectroscopy. During Plavec’s visit this past summer, he was able to learn Hud’s techniques and apply them to his research on d(G4T4G3) and related molecules.

The two months of intense collaborative work during Plavec’s visit resulted in the collection of a significant amount of data, which is currently being analyzed and prepared for publication. Hud reports that the results "have the potential for a significant impact in the area of DNA quadruplex research. There have been numerous speculations on the role of DNA quadruplexes in vivo based upon in vitro experiments. Our results suggest that at least some of these experiments are only applicable to a very small set of sample conditions, and that the folding of DNA molecules that contain G-quartets may be even more sensitive to solution conditions than previously appreciated."

Beyond these research results, the colleagues reaped other benefits thanks to the visit. Plavec learned several new methods for preparing nucleic acid samples and gained experience with the NMR pulse programs used in his host’s lab. Hud and one of his graduate students, Brian Mutschler, gained new insights from their visitor on the collection, processing, and interpretation of NMR spectroscopy data. As for the future, Plavec and his graduate students are completing some follow-up experiments related to the project back home in Ljubljana, and Hud hopes to visit Plavec’s lab during 2001. The two colleagues intend to apply for NSF funding as soon as the manuscript describing their initial results can be completed.

Nicholas Hud

Janez Plavec