Molecular structure of the core-modified siRNA duplexes containing diastereomeric pair of [C6'(R)-OH]- versus [C6'(S)-OH]-carba-LNAs suggests a model for RNAi action.

Molecular structures of native and a pair of modified small interfering RNA-RNA duplexes containing carbocyclic [6 '-(R)-OH/7 '-(S)-methyl]- and [6 '-(S)-OH/7 '-(S)-methyl]-carba-LNA-thymine nucleotides, which are two diastereomeric analogs of the native T nucleotide, incorporated at position 13 in the antisense (AS) strand of siRNA, have been simulated using molecular mechanics/dynamics techniques. The main aim of the project has been to find a plausible structural explanation of why modification of siRNA at T(13) position by the [6 '(R)-O-(p-Toluoyl)-7 '(S)-methyl]-carba-LNA-Thymine [IC(50) of 3.32 ± 0.17 nM] is ca 24 times more active as an RNA silencing agent against the target HIV-1 TAR RNA than the [6 '(S)-O-(p-Toluoyl)-7 '(S)-methyl]-counterpart [IC(50) of 79.8 ± 17 nM] [1]. The simulations reveal that introduction of both C6 '(R)-OH and C6 '(S)-OH stereoisomers does not lead even to local perturbation of the siRNA-RNA duplex structures compared to the native, and the only significant difference between 6 '(S)- and 6 '(R)-diastereomers found is the exposure of the 6 '-OH group of the 6 '(R)-diastereoisomer toward the edge of the duplex while the 6 '-hydroxyl group of the 6 '(S)-diastereoisomer is somewhat buried in the minor groove of the duplex. This rules out a hypothesis about any possible local distortion by the nature of chemical modification of the siRNA-target the RNA duplex, which might have influenced the formation of the effective RNA silencing complex (RISC) and puts some weight on the hypothesis about the 6 '-hydroxy group being directly involved with most probably Ago protein, since it is known from exhaustive X-ray studies [2, 3] that the core residues are indeed involved with hydrogen bonding with the internucleotidyl phosphates. Further systematic investigation is in progress to map the position-dependent functional and nonfunctional interactions of the modified [6 '(R or S)-O-(p-Toluoyl)-7 '(S)-methyl]-carba-LNA-T with the Ago2 protein of the RISC.