Functionalized porous silicon surfaces as DESI-MS substrates for small molecules analysis.

In desorption electrospray ionization mass spectrometry (DESI-MS), the type of surface in addition to low gas and solvent flow rates help to avoid the "splashing of solvent" or "washing effect", by which samples are promptly removed from the surface by the spray. These effects operate on smooth surfaces and generally result in unstable signals as the spray moves over the spot. The aim of this work is to compare the performance of functionalized porous silicon surfaces (pSi) for small molecules analysis with regard to the stability of the signal and the limits of detection (LODs) observed in DESI-MS. The results showed that functional groups, like 1-decene and heptadecafluoro-1,1,2,2-tetrahydrodecyl trimethoxysilane, on pSi surface provides a good alternative for dried spot analysis by DESI-MS, improving stability of the signal and the LODs. This improvement is possible because the dual process containing the weak sample-surface interactions of the hydrophobic characteristic of the functional groups and increasing the surface area of interaction between the sample and the thin solvent film created by the DESI spray, resulting in more effective dissolution of the analyte in the spray solvent without fast removal of the sample.

Global organization of a positive-strand RNA virus genome.

The genomes of plus-strand RNA viruses contain many regulatory sequences and structures that direct different viral processes. The traditional view of these RNA elements are as local structures present in non-coding regions. However, this view is changing due to the discovery of regulatory elements in coding regions and functional long-range intra-genomic base pairing interactions. The ∼4.8 kb long RNA genome of the tombusvirus tomato bushy stunt virus (TBSV) contains these types of structural features, including six different functional long-distance interactions. We hypothesized that to achieve these multiple interactions this viral genome must utilize a large-scale organizational strategy and, accordingly, we sought to assess the global conformation of the entire TBSV genome. Atomic force micrographs of the genome indicated a mostly condensed structure composed of interconnected protrusions extending from a central hub. This configuration was consistent with the genomic secondary structure model generated using high-throughput selective 2'-hydroxyl acylation analysed by primer extension (i.e. SHAPE), which predicted different sized RNA domains originating from a central region. Known RNA elements were identified in both domain and inter-domain regions, and novel structural features were predicted and functionally confirmed. Interestingly, only two of the six long-range interactions known to form were present in the structural model. However, for those interactions that did not form, complementary partner sequences were positioned relatively close to each other in the structure, suggesting that the secondary structure level of viral genome structure could provide a basic scaffold for the formation of different long-range interactions. The higher-order structural model for the TBSV RNA genome provides a snapshot of the complex framework that allows multiple functional components to operate in concert within a confined context.

Specific disruption of transthyretin(105-115) fibrilization using "stabilizing" inhibitors of transthyretin amyloidogenesis.

Transthyretin (TTR) is a cerebrospinal fluid and serum protein that undergoes ordered aggregation (amyloidogenesis) in familial amyloidotic polyneuropathy (FAP) and senile systemic amyloidosis (SSA). It is now widely accepted that dissociation of the native TTR tetramer is a precondition for amyloidogenesis; thus, molecules that stabilize the tetramer have received much attention as potential TTR amyloidosis inhibitors. Many of these inhibitors bind to the thyroxine (T(4)) binding pocket and interact specifically with a section of the TTR sequence, corresponding to residues 105-115, that is implicated in amyloidogenic propensity. In this work, we study the effects of "stabilizing" inhibitors on ordered aggregation of TTR(105-115) peptide. We show that molecules known to bind full-length TTR at the T(4) site are potent, specific inhibitors of ordered aggregation, while molecules that do not interact with TTR exhibit milder, nonspecific disruption through a "hyperbundling" effect. Our results suggest that, in addition to annealing the native tetramer, "stabilizing" inhibitors may also directly disrupt amyloidogenic aggregation of TTR monomers through specific interactions with the exposed TTR(105-115) sequence.