Continuous monitoring of enzyme reactions on a microchip: application to catalytic RNA self-cleavage

Assay for glucosamine 6-phosphate using a ligand-activated ribozyme with fluorescence resonance energy transfer or CE-laser-induced fluorescence detection

A naturally occurring aptazyme, the glmS ribozyme, is adapted to an assay for glucosamine 6-phosphate, an effector molecule for the aptazyme. In the assay, binding of analyte allosterically activates aptazyme to cleave a fluorescently labeled oligonucleotide substrate. The extent of reaction, and hence analyte concentration, is detected by either fluorescence resonance energy transfer (FRET) or capillary electrophoresis with laser-induced fluorescence (CE-LIF). With FRET, assay signal is the rate of increase in FRET in presence of analyte. With CE-LIF, the assay signal is the peak height of cleavage product formed after a fixed incubation time. The assay has a linear response up to 100 (CE-LIF) or 500 microM (FRET) and detection limit of approximately 500 nM for glucosamine 6-phosphate under single-turnover conditions. When substrate is present in excess of the aptazyme, it is possible to amplify the signal by multiple turnovers to achieve a 13-fold improvement in sensitivity and detection limit of 50 nM. Successful signal amplification requires a temperature cycle to alternately dissociate cleaved substrate and allow fresh substrate to bind aptazyme. The results show that aptazymes have potential utility as analytical reagents for quantification of effector molecules.

Bioengineering and Bioinformatics Summer Institutes: meeting modern challenges in undergraduate summer research

Summer undergraduate research programs in science and engineering facilitate research progress for faculty and provide a close-ended research experience for students, which can prepare them for careers in industry, medicine, and academia. However, ensuring these outcomes is a challenge when the students arrive ill-prepared for substantive research or if projects are ill-defined or impractical for a typical 10-wk summer. We describe how the new Bioengineering and Bioinformatics Summer Institutes (BBSI), developed in response to a call for proposals by the National Institutes of Health (NIH) and the National Science Foundation (NSF), provide an impetus for the enhancement of traditional undergraduate research experiences with intense didactic training in particular skills and technologies. Such didactic components provide highly focused and qualified students for summer research with the goal of ensuring increased student satisfaction with research and mentor satisfaction with student productivity. As an example, we focus on our experiences with the Penn State Biomaterials and Bionanotechnology Summer Institute (PSU-BBSI), which trains undergraduates in core technologies in surface characterization, computational modeling, cell biology, and fabrication to prepare them for student-centered research projects in the role of materials in guiding cell biology.

Hybrid Dynamic Coating with n-Dodecyl β-d-Maltoside and Methyl Cellulose for High-Performance Carbohydrate Analysis on Poly(methyl methacrylate) Chips

Hybrid dynamic coating using n-dodecyl beta-d-maltoside (DDM) and methyl cellulose (MC) has been developed for suppression of analyte adsorption and electroosmotic flow (EOF) in a poly(methyl methacrylate) (PMMA) channel. The adsorption of APTS-labeled sugars in a PMMA channel was obviously suppressed with DDM dynamic coating; however, EOF was reduced only by a factor of approximately 25%, resulting in irreproducible separations. In contrast, both analyte adsorption and EOF in a PMMA channel were efficiently minimized with MC coating; however, concentrated MC above 0.3% was required to achieve high-performance separations, which greatly increased viscosity of the solution and caused difficulties during buffer loading and rinsing. In addition, n-dodecyltrimethylammonium chloride did not show observable effects on reducing analyte adsorption, although it has the same hydrophobic alkyl chain as DDM. These results strongly indicated that the polysaccharide moiety of surface modifiers has a specific affinity to surface charges and is crucial to achieving efficient and stable dynamic coating on the PMMA surface. Hybrid dynamic coating with 0.25% DDM and 0.03% MC was found to minimize both analyte adsorption and EOF in a PMMA channel to a negligible level, while still keeping a low viscosity of the solution. High-speed and high-throughput profiling of the N-linked glycans derived from alpha1-acid glycoprotein, fetuin, and ribonuclease B was demonstrated in both single-channel and 10-channel PMMA chips using DDM-MC hybrid coating. We propose that DDM-MC hybrid coating might be a general method for suppressing analyte adsorption and EOF in polymer MCE devices. The current MCE-based method might be a promising alternative for high-throughput screening of carbohydrate alterations in glycoproteins.