Synthesis and thermal stabilities of oligonucleotides containing 2′-O,4′-C-methylene bridged nucleic acid with a phenoxazine base

Abstract

We designed and synthesized a novel artificial 2′-O,4′-C-methylene bridged nucleic acid (2′,4′-BNA/LNA) with a phenoxazine nucleobase and named this compound BNAP. Oligodeoxynucleotide (ODN) containing BNAP showed higher binding affinities toward complementary DNA and RNA as compared to ODNs bearing 2′,4′-BNA/LNA with 5-methylcytosine or 2′-deoxyribonucleoside with phenoxazine. Thermodynamic analysis revealed that BNAP exhibits properties associated with the phenoxazine moiety in DNA/DNA duplexes and characteristics associated with the 2′,4′-BNA/LNA moiety in DNA/RNA duplexes.