Sequencing

RNA fitness landscapes

Pitt and Ferré-D'Amaré describe an approach to generate fitness landscapes for catalytic RNAs. They incubated a pool of ribozymes with a substrate RNA immobilized on beads; after allowing the RNAs to react, they isolated and deep-sequenced the ribozymes that bound the beads, identifying the fittest variants. The resulting high-resolution map, which yields insights into the fittest genotypes for a particular phenotype, contains 107 unique RNA genotypes.

Pitt, J.N. & Ferré-D'Amaré, A.R. Science 330, 376–379 (2010).

Chemistry

Capturing G-quadruplexes

G-quadruplex motifs are four-stranded nucleic acid structures found in genomic DNA that are thought to be associated with telomere maintenance and gene expression, though much remains to be discovered about G-quadruplex function. Müller et al. designed a small molecule that selectively binds G-quadruplexes in human cells, so that they can be isolated for further analysis. The small molecule contains a biotin moiety that serves as a handle for capturing G-quadruplexes on streptavidin-coated beads.

Müller, S. et al. Nat. Chem. advance online publication 10 October 2010.

Sensors and probes

Dual-color protein interaction probes

Protein-protein interactions can be detected via protein fragment complementation, whereby two pieces of a split fluorescent or bioluminescent protein are reunited and produce a signal when their fusion partners bind. Villalobos et al. describe several pairs of reversible, dual-color complementation fragments based on firefly and click beetle luciferases that use a single substrate, D-luciferin, to produce a bioluminescent signal, allowing dynamic analysis of multiple protein interactions in living cells.

Villalobos, V. et al. Chem. Biol. 17, 1018–1029 (2010).

Neuroscience

Mapping microcircuitry in the fly brain

The complex patterns of synaptic connections in the brain, known as microcircuitry, form the basis of behavior. Mapping microcircuits across whole brains has been a technical challenge because it requires analyzing complete series of thin sections by transmission electron microscopy (TEM). Cardona et al. applied a software package called TrakEM2 to comprehensively reconstruct the neuronal microcircuitry from serial TEM sections of the larval brain of the fly Drosophila melanogaster.

Cardona, A. et al. PLoS Biol. 8, e1000502 (2010).

Biochemistry

Microscale thermophoresis

The term thermophoresis refers to the directed motion of molecules in solution as a result of temperature gradients; thermophoretic behavior depends on properties such as mass, size and charge. Wienken et al. exploited this phenomenon to develop a method to detect protein-protein and protein–small molecule interactions in vitro without immobilization. An infrared laser locally heats a solution containing a fluorescently labeled protein of interest; the thermophoretic behavior of the protein changes upon binding, as monitored by fluorescence.

Wienken, C.J. et al. Nat. Commun. advance online publication 19 October 2010.