Thymidine(3',5')thymidine hydroxymethylphosphonate (10), the first oli
gonucleotide bearing hydroxymethylphosphonate function, and t-butylamm
onium 5'-O-monomethoxytritylthymidine 3'-O-acetoxymethylphosphonate (7
), oligonucleotide monomer, were synthesized using t-butylammonium O-m
ethylacetoxymethylphosphonate (4) as a novel phosphonylating agent. Hy
droxymethylphosphonate internucleotide linkage is stable at physiologi
cal pH and resistant to 3'- and 5'-exonucleases. While retaining the n
eutral character of the phosphonate modification, the presence of hydr
oxymethyl function increases hydrophilicity of hydroxymethylphosphonat
e oligonucleotide and its solubility in water compared to the parent m
ethylphosphonate analogue. Therefore, hydroxymethylphosphonate modific
ation can be used to fine-tune the physicochemical properties of antis
ense oligonucleotides. (C) 1994 Academic Press, Inc.