LNA guanine and 2,6-diaminopurine. Synthesis, characterization and hybridization properties of LNA 2,6-diaminopurine containing oligonucleotides

Abstract

LNA guanine and 2,6-diaminopurine (D) phosphoramidites have been synthesized as building blocks for antisense oligonucleotides (ON). The effects of incorporating LNA D into ON were investigated. As expected, LNA D containing ON showed increased affinity towards complementary DNA (Δ T m +1.6 to +3.0 °C) and RNA (Δ T m +2.6 to +4.6 °C) ON. To evaluate if LNA D containing ON have an enhanced mismatch sensitivity compared to their complementary LNA A containing ON thermal denaturation experiments towards singly mismatched DNA and RNA ON were undertaken. Replacing one LNA A residue with LNA D, in fully LNA modified ON, resulted in higher mismatch sensitivity towards DNA ON (ΔΔ T m −4 to >−17 °C). The same trend was observed towards singly mismatched RNA ON (ΔΔ T m D–a = −8.7 °C and D–g = −4.5 °C) however, the effect was less clearcut and LNA A showed a better mismatch sensitivity than LNA D towards cytosine (Δ T m +5.5 °C).