The Roles of Hydrogen Bonding and Sterics in RNA Interference

Effect of north bicyclo[3.1.0]hexane 2'-deoxy-pseudosugars on RNA interference: a novel class of siRNA modification

North bicyclo methanocarba thymidine (T(N)) nucleosides were substituted into siRNAs to investigate the effect of bicyclo[3.1.0]hexane 2'-deoxy-pseudosugars on RNA interference activity. Here we provide evidence that these modified siRNAs are compatible with the intracellular RNAi machinery. We studied the effect of the T(N) modification in a screen involving residue-specific changes in an siRNA targeting Renilla luciferase and we applied the most effective pattern of modification to the knockdown of murine tumor necrosis factor (TNF-α). We also showed that incorporation of T(N) units into siRNA duplexes increased their thermal stabilities, substantially enhanced serum stabilities, and decreased innate immunostimulation. Comparative RNAi studies involving the T(N) substitution and locked nucleic acids (LNAs) showed that the gene-silencing activities of T(N) -modified siRNAs were comparable to those obtained with the LNA modification. An advantage of the North 2'-deoxy-methanocarba modification is that it may be explored further in the future by changing the 2'-position. The results from these studies suggest that this modification might be valuable for the development of siRNAs for therapeutic applications.

Hydrogen-bond-guided self-assembly of nucleotides on a receptor-array surface

The hydrogen-bond-guided self-assembly of 5'-ribonucleotides bearing adenine(A), cytosine (C), uracil (U), or guanine (G) bases from aqueous solution on a lipid-like surface decorated with synthetic bis(Zn(II)-cyclen) (cyclen=1,4,7,10-tetraazacyclodododecane) metal-complex receptor sites is described. The process was studied by using surface plasmon resonance spectroscopy. The data show that the mechanism of nucleotide binding to the 2D template is influenced by the chemistry of the bases and the pH value of the solution. In a neutral solution of pH 7.5, the process is cooperative and selective with respect to Watson-Crick pairs (A-U and C-G), which form stable double planes in accordance with the Chargaff rule. In a more acidic solution at pH 6.0, the interactions between complementary partners become non-cooperative and the surface also stabilizes mismatched and wobble pairs due to the pH-induced changes in the receptor coordination state. The results suggest that hydrogen bonding plays a key role in the self-assembly of complementary nucleotides at the lipid-like interface, and the cooperative character of the process stems from the ideal matching of the orientation and chemistry of all the interacting components with respect to each other in neutral solution.

Modifications in small interfering RNA that separate immunostimulation from RNA interference

Synthetic small interfering RNA (siRNA) can suppress the expression of endogenous mRNA through RNA interference. It has been reported that siRNA can induce type I IFN production from plasmacytoid dendritic cells, leading to off-target effects. To separate immunostimulation from the desired gene-specific inhibitory activity, we designed RNA strands with chemical modifications at strategic positions of the ribose or nucleobase residues. Substitution of uridine residues by 2'-deoxyuridine or thymidine residues was found to decrease type I IFN production upon in vitro stimulation of human PBMC. Thymidine residues in both strands of a siRNA duplex further decreased immunostimulation. Fortunately, the thymidine residues did not affect gene-silencing activity. In contrast, 2'-O-methyl groups at adenosine and uridine residues reduced both IFN-alpha secretion and gene-silencing activity. Oligoribonucleotides with 2'-O-methyladenosine residues actively inhibited IFN-alpha secretion induced by other immunostimulatory RNAs, an effect not observed for strands with 2'-deoxynucleosides. Furthermore, neither 5-methylcytidine nor 7-deazaguanosine residues in the stimulatory strands affected IFN-alpha secretion, suggesting that recognition does not involve sites in the major groove of duplex regions. The activity data, together with structure prediction and exploratory UV-melting analyses, suggest that immunostimulatory sequences adopt folded structures. The results show that immunostimulation can be suppressed by suitable chemical modifications without losing siRNA potency by introducing seemingly minor structural changes.