Synthesis, Thermodynamic Behavior, and Enzymatic Properties of Oligonucleotides Containing Nucleoside Analogs.

The focus of this research is on base modified nucleosides. By generating these nucleosides we hope to find information about the role of base-stacking in the stability of the DNA duplex and generate nucleoside analogues that could be used as conversion agents or in ambiguous positions in probes and primers. The target nucleosides included one C-nucleoside 5-(2\u27-deoxy-beta-D-ribofuranosyl)-2-hydroxypyrimidine and four 4-substituted pyrazole nucleosides; 1-(2\u27-deoxy-beta- D-ribofuranosyl)-4-iodopyrazole, 1-(2\u27-deoxy-beta- D-ribofuranosyl)-4-, 1-(2\u27-deoxy-beta- D-ribofuranosyl)-4-propynylpyrazole, and 1-(2\u27-deoxy-beta- D-ribofuranosyl)-4-(2-thiazolyl)pyrazole. The C-nucleoside was of interest because of its potential anti-viral and anti cancer activity and its potential to function as a convertide . There are several potential routes for the synthesis of C-nucleosides. The two routes we attempted were based on a palladium catalyzed Heck type coupling and a Grignard reaction. Neither route was successful. The palladium coupling was hindered mostly by the poorly defined reaction conditions and the complex mix of product produced. It was initially hampered by the difficulty in obtaining the requisite glycals for the reaction. This problem; however, was addressed by generating protected glycals by the treatment of appropriately protected thymidines with hexamethyldisilazane. The Grignard coupling route produced mostly addition of the base to the toluoyl protecting group. In addition both methods may have been hindered by acid lability of the base. The pyrazole nucleosides were easily synthesized by addition of the sodium salt of the base to a p-toluoyl protected 1-chlororibose. The pyrazole nucleosides were then converted to the phosphoramidites and incorporated into oligonucleotides using standard solid phase coupling conditions. Once incorporated into oligonucleotides the relative stabilities of the nucleosides were measured by thermodynamic melting. Overall the thiazolylpyrazole nucleoside was the most stable and the iodopyrazole was the least stable. The propynylpyrazole and the nitropyrazole were similar. All four nucleosides showed a preference for the purines and were lease stable versus dC. The nucleosides were also found to function in PCR reactions. The initial preference for the natural nucleoside incorporated versus each modified nucleoside was a dC; however, this is most likely a result of impure starting materials