A mutate-and-map protocol for inferring base pairs in structured RNA

Chemical mapping is a widespread technique for structural analysis of nucleic acids in which a molecule's reactivity to different probes is quantified at single-nucleotide resolution and used to constrain structural modeling. This experimental framework has been extensively revisited in the past decade with new strategies for high-throughput read-outs, chemical modification, and rapid data analysis. Recently, we have coupled the technique to high-throughput mutagenesis. Point mutations of a base-paired nucleotide can lead to exposure of not only that nucleotide but also its interaction partner. Carrying out the mutation and mapping for the entire system gives an experimental approximation of the molecules contact map. Here, we give our in-house protocol for this mutate-and-map strategy, based on 96-well capillary electrophoresis, and we provide practical tips on interpreting the data to infer nucleic acid structure.Comment: 22 pages, 5 figure

Combined macro-/mesoporous microelectrode arrays for low-noise extracellular recording of neural networks

Microelectrode arrays (MEAs) are appealing tools to probe large neural ensembles and build neural prostheses. Microelectronics microfabrication technologies now allow building high-density MEAs containing several hundreds of microelectrodes. However, several major problems become limiting factors when the size of the microelectrodes decreases. In particular, regarding recording of neural activity, the intrinsic noise level of a microelectrode dramatically increases when the size becomes small (typically below 20-?m diameter). Here, we propose to overcome this limitation using a template-based, single-scale meso- or two-scale macro-/mesoporous modification of the microelectrodes, combining the advantages of an overall small geometric surface and an active surface increased by several orders of magnitude. For this purpose, standard platinum MEAs were covered with a highly porous platinum overlayer obtained by lyotropic liquid crystal templating possibly in combination with a microsphere templating approach. These porous coatings were mechanically more robust than Pt-black coating and avoid potential toxicity issues. They had a highly increased active surface, resulting in a noise level ?3 times smaller than that of conventional flat electrodes. This approach can thus be used to build highly dense arrays of small-size microelectrodes for sensitive neural signal detection