Highly efficient on-DNA amide couplings promoted by micelle forming surfactants for the synthesis of DNA encoded libraries

DNA encoded libraries (DELs) represent powerful new technology for finding small molecule ligands for proteins and are increasingly being applied to hit finding in medicinal chemistry. Crucial to the synthesis of high quality DELs is the identification of chemical reactions for their assembly that proceed with very high conversion across a range of different substrates, under conditions compatible with DNA-tagged substrates. Many current chemistries used in DEL synthesis do not meet this requirement, resulting in libraries of low fidelity. Amide couplings are the most commonly used reaction in synthesis of screening libraries and also in DELs. The ability to carry out highly efficient, widely applicable amide couplings in DEL synthesis would therefore be highly desirable. We report a method for amide coupling using micelle forming surfactants, promoted by a modified linker, that is broadly applicable across a wide range of substrates. Most significantly, this works exceptionally well for coupling of DNA-conjugated carboxylic acids (N-to-C) with amines in solution, a procedure that is currently very inefficient. The optimisation of separate procedures for coupling of DNA-conjugated acids and amines by reagent screening and statistically driven optimisation is described. The generality of the method is illustrated by the application to a wide range of examples with unprecedented levels of conversion. The utility of the (N-to-C) coupling of DNA-conjugated acids in DEL synthesis is illustrated by the three cycle synthesis of a fully DNA-encoded compound by two cycles of coupling of an aminoester, with intermediate ester hydrolysis, followed by capping with an amine. This methodology will be of great utility in the synthesis of high fidelity DELs.

Highly efficient forward and reverse on-DNA amide couplings were developed exploiting hydrophobic linkers in combination with the micelle forming surfactant TPGS-750M. The method is highly effective for a wide range of substrates in the synthesis of DNA-encoded libraries.     

FRET detection of Octamer-4 on a protein nanoarray made by size-dependent self-assembly

An alternative approach for fabricating a protein array at nanoscale is suggested with a capability of characterization and/or localization of multiple components on a nanoarray. Fluorescent micro- and nanobeads each conjugated with different antibodies are assembled by size-dependent self-assembly (SDSA) onto nanometer wells that were created on a polymethyl methacrylate (PMMA) substrate by electron beam lithography (EBL). Antibody-conjugated beads of different diameters are added serially and electrostatically attached to corresponding wells through electrostatic attraction between the charged beads (confirmed by zeta potential analysis) and exposed p-doped silicon substrate underneath the PMMA layer. This SDSA method is enhanced by vibrated-wire-guide manipulation of droplets on the PMMA surface containing nanometer wells. Saturation rates of antibody-conjugated beads to the nanometer patterns are up to 97% under one component and 58–70% under two components nanoarrays. High-density arrays (up to 40,000 wells) could be fabricated, which can also be multi-component. Target detection utilizes fluorescence resonance energy transfer (FRET) from fluorescent beads to fluorescent-tagged secondary antibodies to Octamer-4 (Oct4), which eliminates the need for multiple steps of rinsing. The 100 nm green beads are covalently conjugated with anti-Oct4 to capture Oct4 peptides (39 kDa); where the secondary anti-Oct4 and F(ab)₂ fragment of anti-gIgG tagged with phycoerythrin are then added to function as an indicator of Oct4 detection. FRET signals are detected through confocal microscopes, and further confirmed by Fluorolog3 spectrofluorometer. The success rates of detecting Oct4 are 32% and 14% of the beads in right place under one and two component nanoarrays, respectively. Ratiometric FRET is used to quantify the amount of Oct4 peptides per each bead, which is estimated about 2 molecules per bead.     

Sulfonation of polystyrene: Toward the “ideal” polyelectrolyte

Sulfonation of narrow polydispersity polystyrene, PS, standards remains the method of choice for generating polystyrene sulfonate, PSS, samples with defined composition. Although a variety of sulfonation techniques have been described, relatively little is reported on the material obtained, which is used for so many studies on the fundamental behavior of polyelectrolytes. Here, we show that powdered polystyrene treated with concentrated sulfuric acid (96%) at 90 °C without catalyst yields fully sulfonated PSS. Extensive characterization with ¹H and ¹³C NMR as well as size exclusion chromatography coupled with static and dynamic light scattering shows no evidence of sulfone crosslinking or chain degradation under the conditions used. Though mono‐sulfonated as soon as it dissolves in the acid, the PSS contains about 6% meta substitution. Sulfonation kinetics for this heterogeneous reaction depend strongly on particle size, sulfuric acid content and temperature. For preparing perdeuterated PSS from the corresponding PS it is essential to employ D₂SO₄, as about half of the aromatic units undergo H/D exchange during sulfonation. The remaining ortho H/D may be exchanged with extended exposure to the concentrated sulfuric acid, but the meta site is deactivated. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 2416–2624     

Design, Implementation, and Evaluation of Novel Discussion Exercises for First-Year Chemistry Students

In the Fall of 1999, Illinois State University (ISU) piloted a new General Chemistry I course. This course now includes cooperative learning exercises that were developed and implemented in biweekly discussion sections over the past four semesters. We now have discussion exercises all taught by six different tenured and tenure-track faculty members. This study focuses on the effect on student behaviors and learning in General Chemistry I. Data were obtained from student surveys, student interviews, instructor feedback, and examination results. The results obtained in this study show that student interest in chemistry can be maintained or increased by the incorporation of cooperative learning into the general chemistry curriculum. In addition, this cooperative learning approach promoted attendance, was enjoyable for many students, and seemed to have some positive effect on achievement.