Synthesis and Properties of ApA Analogues with Shortened Phosphonate Internucleotide Linkage

Abstract

A complete series of the 2 ′–5 ′ and 3 ′–5 ′ regioisomeric types of r(ApA) and 2 ′-d(ApA) analogues with the α-hydroxy-phosphonate C3 ′-O-P-CH(OH)-C4 ″ internucleotide linkage, isopolar but non-isosteric with the phosphodiester one, were synthesized and their hybridization properties with polyU studied. Due to the chirality on the 5 ′-carbon atom of the modified internucleotide linkage bearing phosphorus and hydroxy moieties, each regioisomeric type of ApA dimer is split into epimeric pairs. To examine the role of the 5 ′-hydroxyl of the α-hydroxy-phosphonate moiety during hybridization, the appropriate r(ApA) analogues with 3 ′(2 ′)-O-P-CH₂-C4 ″ linkage lacking the 5 ′-hydroxyl were synthesized. Nuclear magnetic resonance (NMR) spectroscopy study on the conformation of the modified sugar-phosphate backbone, along with the hybridization measurements, revealed remarkable differences in the stability of complexes with polyU, depending on the 5 ′-carbon atom configuration. Potential usefulness of the α-hydroxy-phosphonate linkage in modified oligoribonucleotides is discussed.

Keywords:

• α-Hydroxy-phosphonate linkage
• ApA analogues
• phosphonate internucleotide bond
• modified sugar-phosphate backbone
• NMR conformational study
• MDS study

Acknowledgments

Part of the special issue in honor of Vladimir Efimov.

Support by the grant 202/09/0193 (Czech Science Foundation) and Research Centers KAN200520801 (Acad. Sci. CR) and LC060061 (Ministry of Education, CR), under the Institute Research Project Z40550506 is gratefully acknowledged, as well as the support by Project No. MSM 0021620835 (Ministry of Education, CR) and the META Centrum supercomputing facilities provided under the research intent MSM 6383917201. The authors would also like to thank the staff of the Mass Spectrometry Group of IOCB AS, v.v.i. (Dr. Josef Cvačka, Head) for HR-MS spectra.