An automated algorithm for sequence confirmation of chemically modified oligonucleotides by tandem mass spectrometry.

We have developed a tandem mass spectrometry (MS/MS) data analysis program for confirmation of sequence of chemically modified oligonucleotides. The method is based on the analysis of deconvoluted MS/MS data for fragment ions from three charge states and comparison of these data against a set of computer-generated masses from expected fragmentation patterns. The algorithm compares the experimental masses not only against the fragment set predicted for the expected sequence but also against a wider test set covering all next-neighbor position switches of the original sequence and all pairwise swaps of nucleosides, which in synthesis would result in molecules with masses within a preset mass tolerance.

Reversed-phase high-performance liquid chromatography method for simultaneous analysis of two liposome-formulated short interfering RNA duplexes.

Gene silencing induced by short interfering RNA (siRNA) has proven to be useful in genomic research and has great potential for therapeutic applications; however, siRNAs are not readily bioavailable. Cationic liposomes offer effective protection of drug product from nucleases and enable distribution to desired target organs. The amount of siRNA in the formulation must be determined accurately.

Evaluation of the safety, tolerability and pharmacokinetics of ALN-RSV01, a novel RNAi antiviral therapeutic directed against respiratory syncytial virus (RSV).

Small interfering RNAs (siRNAs) work through RNA interference (RNAi), the natural RNA inhibitory pathway, to down-regulate protein production by inhibiting targeted mRNA in a sequence-specific manner. ALN-RSV01 is an siRNA directed against the mRNA encoding the N-protein of respiratory syncytial virus (RSV) that exhibits specific in vitro and in vivo anti-RSV activity. The results of two safety and tolerability studies with ALN-RSV01 involving 101 healthy adults (65 active, 36 placebo, single- and multiple dose, observer-blind, randomized dose-escalation) are described.

4-(4'-Methyltetrafluorophenyl)-2,3,5,6-tetrafluorobenzyl bromide: a new electrophoric derivatizing reagent.

Commercially-available 4,4'-dimethyloctafluorobiphenyl was converted in a single step to 4-(4'-methyltetrafluorophenyl)-2,3,5,6-tetrafluorobenzyl bromide (MTFP-TFBBr) for the purpose of providing a new electrophoric derivatizing reagent. When reacted with this reagent, 2-fluoro-O6-(2'-hydroxyethyl)hypoxanthine, a model analyte, gave a mixture of isomeric products (apparently substituted at N7 and N9, analogous to its known reaction with pentafluorobenzyl bromide), and 53 femtograms of the mixture was detected at S/N = 10 by gas chromatography electron capture mass spectrometry (GC-EC-MS). As intended, the volatility of the MTFB-TFBBr derivative was much less (two-fold) than that of the corresponding pentafluorobenzyl derivative.