Kondo Jiro

Abstract In this study, we report the synthesis of 2′-formamidonucleoside phosphoramidite derivatives and their incorporation into siRNA strands to reduce seed-based off-target effects of small interfering RNAs (siRNAs). Formamido derivatives of all four nucleosides (A, G, C and U) were synthesized in 5–11 steps from commercial compounds. Introducing these derivatives into double-stranded RNA slightly reduced its thermodynamic stability, but X-ray crystallography and CD spectrum analysis confirmed that the RNA maintained its natural A-form structure. Although the introduction of the 2′-formamidonucleoside derivative at the 2nd position in the guide strand of the siRNA led to a slight decrease in the on-target RNAi activity, the siRNAs with different sequences incorporating 2′-formamidonucleoside with four kinds of nucleobases into any position other than 2nd position in the seed region revealed a significant suppression of off-target activity while maintaining on-target RNAi activity. This indicates that 2′-formamidonucleosides represent a promising approach for mitigating off-target effects in siRNA therapeutics.

Abstract The combination of mass spectrometry and single crystal X‐ray diffraction of HPLC‐purified DNA‐stabilized silver nanoclusters (DNA‐AgNCs) is a powerful tool to determine the charge and structure of the encapsulated AgNC. Such information is not only relevant to design new DNA‐AgNCs with tailored properties, but it is also important for bio‐conjugation experiments and is essential for electronic structure calculations. Here, the efforts to determine the structure of a HPLC‐purified green emissive DNA‐AgNC are presented. Unfortunately, the original DNA‐AgNC, known to have four valence electrons, could not be crystallized. By modifying the stabilizing DNA sequence, while maintaining the original spectroscopic properties, several mutants could be successfully crystallized, and for one of them, single crystal X‐ray diffraction data provided insight into the silver positions. While the DNA conformation is not resolved, the described approach provides valuable insight into the class of green and dual emissive DNA‐AgNCs with four valence electrons. These results constitute a roadmap on how to improve crystallization and crystal quality for X‐ray diffraction measurements.