Synthesis and hybridizing properties of oligodeoxynucleotide analogs containing methyleneformacetal

Aim To design and synthesize a new mixed backbone oligonucleotide (MBO). Methods In the presence of trimethylsilyl trifluoromethane-sulfonate (TMSOTf), condensation of 3′-O-(diphenylphosphinyloxy) methyl acetal (1) with 3′-protected deoxynucleoside (2 or 6) afforded dimers (3) or trimers (7) respectively. 5′-Hydroxyl and 3′-hydroxyl groups of these acetal-linked oligomers were protected by 4,4′-dimethoxytriphenylmethyl (DMTr) or by diisopropylamino-β-cyanothoxyphosphine respectively. Then, compounds 5 and 9) were incorporated into oligonucleotides by using the standard solid-phase synthesis of DNA with the phosphoramidite method. Results Six new oligonucleotides (ODN-II-ODN-VII) containing methyleneformacetal have been synthesized. The melting temperatures (T_m) of these ODNs with their DNA complements were determined. Conclusion The melting temperatures (T_m) of these modified ODNs were lowered about 0.8-1.2 ℃ per methyleneformacetal modification. These new ODNs can hybridize to DNA with only slightly less affinity than a control phosphodiester ODN, yet more work is necessary to study these modified ODNs and their biological activities.