We designed and synthesized two novel thymidine analogs: (S)-5′-C-aminopropyl-thymidine and (S)-5′-C-aminopropyl-2′-β-fluoro-thymidine.

An RNA aptamer that binds with high affinity and specificity to human immunoglobulin G (IgG) is a 24-mer single-stranded oligonucleotide containing 2′-fluoro pyrimidine nucleotides. Using X-ray crystallographic analysis, a Ca 2+ ion was reported as being located near the G7 phosphate of the RNA aptamer. Surface plasmon resonance analysis showed that the RNA aptamer could not bind to IgG in a buffer without Ca 2+ ions. To elucidate the role of Ca 2+ ions in the binding of the RNA aptamer to IgG, we performed molecular dynamics simulation for the RNA aptamer/IgG complex with and without Ca 2+ ions in a solvent. In the presence of Ca 2+ ions, the RMSD of the RNA aptamer backbone remained below approximately 3.0 Å from the crystal structure during a 1,500-ns simulation. The distance between the centroids of the RNA aptamer and IgG was maintained between the centroids in the crystal structure. However, in the absence of Ca 2+ ions, the RMSD increased and the structure of the RNA aptamer changed from the initial structure. These results indicate that Ca 2+ ions play a role in maintaining the conformation of the RNA aptamer to the binding form.