Chemical Synthesis of Selenium-Modified Oligoribonucleotides and Their Enzymatic Ligation Leading to an U6 SnRNA Stem−Loop Segment

2004-02-04T00:00:00Z (GMT) by Claudia Höbartner Ronald Micura
The derivatization of nucleic acids with selenium is highly promising to facilitate nucleic acids structure determination by X-ray crystallography using the multiwavelength anomalous dispersion (MAD) technique. The foundation for such an approach has been laid by Huang, Egli, and co-workers and was exemplified on small DNA duplexes. Here, we present a comprehensive study on the preparation of RNAs containing 2‘-<i>Se</i>-methylpyrimidine nucleoside labels. This includes the synthesis of a novel 2‘-<i>Se</i>-methylcytidine phosphoramidite <b>11</b> and its incorporation into oligoribonucleotides by solid-phase synthesis. Deprotection of the oligonucleotides is achieved in the presence of millimolar amounts of <i>threo</i>-1,4-dimercapto-2,3-butandiol (DTT). With this additive, oxidation products and follow-up side-products are suppressed and acceptable HPLC traces of the crude material are obtained, so far tested for sequences of up to 22-mers. Moreover, an extensive investigation on the enzymatic ligation of the selenium-containing oligoribonucleotides demonstrates the high flexibility of the selenium approach. Our target sequence, an U6 snRNA stem−loop motif comprising all naturally occurring nucleoside modifications beside the <i>Se</i>-label is achieved by ligation using T4 RNA ligase.