Geertrui Schuerman1,2 , Luc Van Meervelt1
1 Laboratorium voor
Macromoleculaire Structuurchemie, K.U.Leuven, Celestijnenlaan
200F, B-3001 Heverlee, Belgium
2 Laboratorium voor
Analytische Chemie en Medicinale Fysicochemie, K.U.Leuven, Van
Evenstraat 4, B-3000 Leuven, Belgium
e-mail: geertrui.schuerman@chem.kuleuven.ac.be
Keywords: DNA, daunomycin, DNA-drug
interaction, conformational flexibility
The combined use of high energy synchrotron source together with cryotechniques (100 K) enabled us to collect high quality data to 1.1A resolution for the daunomycin-d(CGCGCG) complex. The data:parameter ratio obtained was comparable to that of small molecules and therefore, for the first time, allowed for unrestrained least-squares refinement of an oligonucleotide.
The refined structure has a final R1-value of 10.2% (wR2=27.5%) and contains 65 water molecules. The structural pattern that emerges from the refinement proves that the conformation of the sugar-phosphate backbone is considerably more flexible than previously seen. All phosphates (as well as one sugar) not situated at a drug-intercalation step, are found to adopt two or more distinct conformations. Also the water structure surrounding these phosphates shows clearly double conformations. The conformational flexibility is further reflected in the sugar puckering which shows much more variation in present structure compared to the same structure at room temperature[1]. The puckering mode for the single sugar 3 conformation observed in the room temperature structure appears to be the average of the puckering modes found in the two possible conformations for sugar 3 in present structure.
Therefore it seems that, while room temperature
data collections provide us with an average view of the crystal
structure, cryocooling enables us to get a far more detailed
picture of the real structure.
1. A.H.-J. Wang, Y.-G. Gao, Y.-C. Liaw & Y.-K. Li, Biochemistry 30 (1991) 3812-3815.