Oligonucleotide analogues containing 4'-C-(hydroxymethyl)uridine: synthesis, evaluation and mass spectrometric analysis.

2',3'-Di-O-tert-butyldimethylsilyl-4'-C-(hydroxymethyl)uridine was synthesized and converted into the phosphoramidite building blocks 9 and 13. Novel oligodeoxynucleotide analogues containing 4'-C-hydroxymethyl linked phosphodiester internucleoside linkages and 3'-hydroxyl linked phosphodiester internucleotide linkages were synthesized on an automated DNA-synthesizer. The latter modification introduced an additional 4'-C-hydroxymethyl functionality. Oligodeoxynucleotides with one or two modifications in the middle or in the ends of 17-mers, 15-mers and 14-mers have been evaluated with respect to hybridization properties and enzymatic stability. Compared to unmodified oligomers, 3'-end-modified oligodeoxynucleotides were stabilized towards 3'-exonucleolytic degradation, but showed moderately to strongly lowered hybridization properties towards complementary DNA. However, more promising results were obtained in melting experiments with complementary RNA where only small decreases in melting temperature were detected. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) was used to identify products from syntheses of the modified oligodeoxynucleotide analogues.