MOLECULAR BIOLOGY: New approach enables trapping of even the smallest fluorescently tagged molecules

Scientists have used anti-Brownian electrokinetic (ABEL) traps to study the dynamics of protein complexes and DNA chains in solution, but have been limited to larger molecules.

Scientists have used anti-Brownian electrokinetic (ABEL) traps to study the dynamics of protein complexes and DNA chains in solution, but have been limited to larger molecules. But small molecules, combined with their relative dimness and tendency to diffuse light more quickly, has enabled them to elude observation. Now, a new advance could allow the trapping and manipulation of any soluble molecule that can be fluorescently labeled.

In a recent paper, Harvard University researchers describe a feedback-based ABEL that compensates classical thermal noise to the maximal extent allowed by quantum measurement noise. The feedback is provided by a field programmable gate array (FPGA), which executes a custom-designed algorithm many thousands of times per second. This enabled them to trap single fluorophores with a molecular weight of < 1 kDa and a hydrodynamic radius of 6.7 Å for longer than one second, in aqueous buffer at room temperature—an achievement that represents the ability to trap objects with 800 times less mass than before.1

“We studied the binding of unlabeled RecA to fluorescently labeled single-stranded DNA,” the researchers report. “Binding of RecA induced changes in the DNA diffusion coefficient, electrophoretic mobility, and brightness, all of which were measured simultaneously and on a molecule-by-molecule basis.” This device extends the size range of molecules that can be studied by room temperature feedback trapping, and could lead to further studies of the binding of unmodified proteins to DNA in free solution.

1. A.P. Fields and A.E. Cohen, PNAS 108 (22), 8937–8942 (2011).

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