Holographic molecular binding assays

Insights from Fragment Hit Binding Assays by Molecular Simulations

Novel bioactive molecules can be rationally designed by growing and linking small fragments. Because fragments are fast and promiscuous, it is common to have contradictory hit results between different experimental screening techniques. Here, we simultaneously determine fragment binding poses, affinities, and kinetics on a focused library of 42 fragments against the serine protease factor Xa us...

Correction to Insights from Fragment Hit Binding Assays by Molecular Simulations.

High-Throughput Electrophoretic Mobility Shift Assays for Quantitative Analysis of Molecular Binding Reactions

We describe a platform for high-throughput electrophoretic mobility shift assays (EMSAs) for identification and characterization of molecular binding reactions. A photopatterned free-standing polyacrylamide gel array comprised of 8 mm-scale polyacrylamide gel strips acts as a chassis for 96 concurrent EMSAs. The high-throughput EMSAs was employed to assess binding of the Vc2 cyclic-di-GMP ribos...

Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays

WRKY transcription factors constitute a large protein family in plants that is involved in the regulation of developmental processes and responses to biotic or abiotic stimuli. The question arises how stimulus-specific responses are mediated given that the highly conserved WRKY DNA-binding domain (DBD) exclusively recognizes the 'TTGACY' W-box consensus. We speculated that the W-box consensus m...

Miniaturized ligand-binding assays: theoretical considerations

Markus F. Templin Dieter Stoll Monika Schrenk Petra C. Traub Christian F. Vöhringer and Thomas O. Joos* NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany. *e-mail: [email protected] The fundamental principles of miniaturized and parallelized microspot ligand-binding assays were described more than a decade ago. In the ‘ambient analy...