Fluorescent bursts reveal how biomolecules fold

To gather clues about the structure of a protein, DNA, or other chain-like biomolecule, researchers can tag it with two fluorescent dyes. In what’s known as fluorescence resonance energy transfer (FRET), the excitation of one dye, the donor, can cause a nearby partner, the acceptor, to also fluoresce. The resulting two-color burst of photons hints at the biomolecule’s shape: The larger the contribution of the acceptor to the total fluorescence, the closer the dyes. Now, two groups have paired single-molecule-resolution FRET with microfluidics to shed light on complex biophysical phenomena. Ashok Deniz (Scripps Research Institute, La Jolla, California), Alex Groisman (University of California, San Diego), and colleagues used a novel microfluidic design to quickly initiate folding of a tagged protein and then track the time evolution of the donor–acceptor distances. Their experiment revealed the three-step process, illustrated here, by which the protein α-synuclein folds from its intrinsic disordered state into an extended helix. Another group of researchers led by Shimon Weiss (UCLA) and Stephen Quake (Stanford University) devised a microscale network of flow channels, valves, and pumps to facilitate high-throughput FRET experiments. The team used the device to investigate effects of chemical environment on bacterial RNA transcription, which could be detected as changes in fluorescence when tagged DNA strands hybridized with matching RNA strands. (Y. Gambin et al., Nat. Methods 8, 239, 2011 ; S. Kim et al., Nat. Methods 8, 242, 2011 .)—Ashley G. Smart