Synthesis and Binding Poperties of Pyrimidine Oligodeoxynucleoside Analogs Containing Neutral Phosphodiester Replacements: The Formacetal and 3'-Thioformacetal Internucleoside Linkages

Article abstract of DOI:10.1021/jo00063a014

The replacement of the phosphodiester linkage with neutral, achiral, nuclease resistant entities is desirable for the development of oligonucleotide (ODN) analogs as therapeutic agents in either the antisense or antigene modes.Described herein is the use of the formacetal and 3'-thioformaacetal connections as phosphodiester backbone analogs.Pyrimidine dimer blocks containing these moieties were synthesized and incorporated into ODNs in alternating array with phosphodiester bonds, such that the ODNs had seven acetal and seven phosphodiester linkages.The binding properties of the resulting chimeric ODNs to single-stranded (ss) RNA and double-stranded (ds) DNA were then determined. ssRNA binding properties were determined by thermal denaturation (Tm) analysis, and the 3'-thioformacetal ODN/ssRNA duplex showed a 5.5 deg C enhancement in Tm relative to the phosphodiester ODN.The triple helix formation properties of the 3'-thioformacetal and formacetal ODNs were determined by footprint and restriction enzyme inhibition assays.The 3'-thioformacetal ODN binds to dsDNA with an affinity slightly less than the control ODN.The high affinity and specificity of an ODN containing the 3'-thioformacetal for the ssRNA target and the dsDNA target suggest that this linkage is a promising analog for both antisense and triple helix therapeutic applications.