Structural requirements for hybridization at the 5′-position are different in α-l-LNA as compared to β-d-LNA

The synthesis and biophysical evaluation of R and S-5′-Me-α-l-LNA nucleoside phosphoramidites and modified oligo-2′-deoxyribonucleotides is reported. Synthesis of the nucleoside phosphoramidites was accomplished in multi-gram quantities starting from diacetone glucose. The 5′-methyl group in the S configuration was introduced by reacting the sugar 5′-aldehyde with MeMgBr. Synthesis of the R-5′-Me isomer was accomplished from the S-5′-Me nucleoside by a late stage inversion using Mitsunobu conditions. Evaluation of the modified oligonucleotides in thermal denaturation experiments revealed that R-5′-Me-α-l-LNA showed similar RNA affinity as α-l-LNA while the S-5′-Me analog was less stabilizing. This result is in contrast to the β-d-series where the S-5′-Me isomer showed LNA-like affinity for RNA while the R-5′-Me group completely reversed the stabilization effect on duplex thermostability.