Development and validation of LC-MS/MS methods for the measurement of ribociclib, a CDK4/6 inhibitor, in mouse plasma and Ringer's solution and its application to a cerebral microdialysis study.

LC-MS/MS methods to measure ribociclib in mouse plasma and Ringer's solution were successfully developed and validated. Reverse phase chromatography was performed with gradient elution using C18 (100A, 50×4.6mm, 3µ) and C8-A (50×2.0mm, 5µ) columns for plasma and Ringer's samples, respectively. Mouse plasma samples were extracted using solid phase extraction method, whereas no extraction was required for the Ringer's solution samples. Analytes were detected using positive ion MRM mode. The precursor to product ions (Q1→Q3) selected for ribociclib and d6-ribociclib were (m/z) 435.2→252.1 and 441.2→252.1, respectively. The linear range of quantification of ribociclib was 62.5-10,000ng/ml for plasma method and 0.1-100ng/ml for Ringer's solution method. The results for the inter-day and intra-day accuracy and precision of quality control samples were within the acceptable range. The lower limit of quantitation (LLOQ) for plasma and Ringer's samples were 62.5ng/ml (S/N>30) and 0.1ng/ml (S/N>13), respectively, whereas the limit of detection (LOD) was 6.9ng/ml (S/N>7) and 0.05ng/ml (S/N>3), respectively. The developed methods were successfully applied to the analysis of ribociclib in mouse plasma and dialysate samples collected during a cerebral microdialysis study of ribociclib in a non-tumor bearing mouse.

The synthesis of tetra-modified RNA for the multidimensional control of gene expression via light-activated RNA interference.

Light-activated RNA interference (LARI) is an effective way to control gene expression with light. This, in turn, allows for the spacing, timing and degree of gene expression to be controlled by the spacing, timing and amount of light irradiation. The key mediators of this process are siRNA or dsRNA that have been modified with four photocleavable groups of dimethoxy nitro phenyl ethyl (DMNPE), located on the four terminal phosphate groups of the duplex RNA. These mediators can be easily synthesized and purified using two readily available products: synthetic RNA oligonucleotides and DMNPE-hydrazone. The synthesis of the tetra-DMNPE-modified duplex RNA is made possible by a remarkable regiospecificity of DMNPE for terminal phosphates (over internal phosphates or nucleobases) that we have previously identified. The four installed DMNPE groups effectively limit RNAi until irradiation cleaves them, releasing native, active siRNA. By using the described protocol, any process that is mediated by RNAi can be controlled with light. Although other methods exist to control gene expression with light by using specialized reagents, this method requires only two commercially available products. The protocol takes ∼3 d in total for the preparation of modified RNA.

Enhanced light-activated RNA interference using phosphorothioate-based dsRNA precursors of siRNA.

PURPOSE: To improve light-activated RNA interference by incorporating phosphorothioate linkages into the dsRNA used. The rationale behind this approach is that the groups have the potential to improve nuclease stability and therefore prevent cleavage of photolabile groups from the RNA termini prior to photolysis. METHODS: Photolabile groups (di-methoxy nitro phenyl ethyl or DMNPE) were incorporated into multiple double-stranded precursors of siRNA (dsRNA) that had six, two or no phosphorothioate linkages at the 3' and 5' ends of the strands. They were analyzed for their ability to toggle light-activated RNA interference with light and for serum stability. RESULTS: Incorporation of phosphorothioate linkages increased serum stability of all dsRNA examined. Presence of DMNPE groups reduced overall stability of the modified RNA relative to the analogous species without DMNPE modification. DMNPE-modified dsRNA with two phosphorothioate linkages in each strand significantly improved the window of expression toggled by light. CONCLUSIONS: Incorporating phosphorothioate groups into dsRNA both stabilizes them towards degradation by serum enzymes, as well as improves them as the basis for light-activated RNA interference.

Light-activated RNA interference using double-stranded siRNA precursors modified using a remarkable regiospecificity of diazo-based photolabile groups.

Diazo-based precursors of photolabile groups have been used extensively for modifying nucleic acids, with the intention of toggling biological processes with light. These processes include transcription, translation and RNA interference. In these cases, the photolabile groups have been typically depicted as modifying the phosphate backbone of RNA and DNA. In this work we find that these diazo-based reagents in fact react very poorly with backbone phosphates. Instead, they show a remarkable specificity for terminal phosphates and very modest modification of the nucleobases. Furthermore, the photo deprotection of these terminal modifications is shown to be much more facile than nucleobase modified sites. In this study we have characterized this regiospecificity using RNA duplexes and model nucleotides, analyzed using LC/MS/MS. We have also applied this understanding of the regio-specificity to our technique of light activated RNA interference (LARI). We examined 27-mer double-stranded precursors of siRNA ('dsRNA'), and have modified them using the photo-cleavable di-methoxy nitro phenyl ethyl group (DMNPE) group. By incorporating terminal phosphates in the dsRNA, we are able to guide DMNPE to react at these terminal locations. These modified dsRNA duplexes show superior performance to our previously described DMNPE-modified siRNA, with the range of expression that can be toggled by light increasing by a factor of two.