Mechanism of homology recognition in DNA recombination from dual-molecule experiments.

In E. coli homologous recombination, a filament of RecA protein formed on DNA searches and pairs a homologous sequence within a second DNA molecule with remarkable speed and fidelity. Here, we directly probe the strength of the two-molecule interactions involved in homology search and recognition using dual-molecule manipulation, combining magnetic and optical tweezers. We find that the filament's secondary DNA-binding site interacts with a single strand of the incoming double-stranded DNA during homology sampling. Recognition requires opening of the helix and is strongly promoted by unwinding torsional stress. Recognition is achieved upon binding of both strands of the incoming dsDNA to each of two ssDNA-binding sites in the filament. The data indicate a physical picture for homology recognition in which the fidelity of the search process is governed by the distance between the DNA-binding sites.

Quantifying self-absorption losses in luminescent solar concentrators.

Analytical equations quantifying self-absorption losses in circular luminescent solar concentrators (LSCs) are presented that can easily be solved numerically by commercial math software packages. With the quantum efficiency, the absorption and emission spectra of a luminescent material, the LSC dimensions, and the refractive index as the only input parameters, the model gives an accurate account of the decrease of LSC efficiency due to self-absorption as a function of LSC radius, thickness, and luminescence quantum efficiency. Results give insight into how many times light is reabsorbed and reemitted, the red shift of the emission spectrum, and on how multiple reabsorptions and reemissions are distributed over the LSC. As an example case the equations were solved for a circular LSC containing a Lumogen F Red 305 dye with 80% luminescence quantum efficiency, and it follows that for an LSC with a 50 cm radius the self-absorption reduces the number of photons reaching the LSC edge by a factor of four compared to the case when there would be no self-absorption. The equations can just as well be solved for any material for which the optical properties are known like type I and type II quantum dots.

Scanning a DNA molecule for bound proteins using hybrid magnetic and optical tweezers.

The functional state of the genome is determined by its interactions with proteins that bind, modify, and move along the DNA. To determine the positions and binding strength of proteins localized on DNA we have developed a combined magnetic and optical tweezers apparatus that allows for both sensitive and label-free detection. A DNA loop, that acts as a scanning probe, is created by looping an optically trapped DNA tether around a DNA molecule that is held with magnetic tweezers. Upon scanning the loop along the λ-DNA molecule, EcoRI proteins were detected with ~17 nm spatial resolution. An offset of 33 ± 5 nm for the detected protein positions was found between back and forwards scans, corresponding to the size of the DNA loop and in agreement with theoretical estimates. At higher applied stretching forces, the scanning loop was able to remove bound proteins from the DNA, showing that the method is in principle also capable of measuring the binding strength of proteins to DNA with a force resolution of 0.1 pN/[Formula: see text]. The use of magnetic tweezers in this assay allows the facile preparation of many single-molecule tethers, which can be scanned one after the other, while it also allows for direct control of the supercoiling state of the DNA molecule, making it uniquely suitable to address the effects of torque on protein-DNA interactions.