MutS is a DNA repair protein that recognizes unpaired and bulged bases. When it binds to DNA, It bends the double helix. We have developed a novel DNA-based nanomechanlcal device that measures the amount of work that a DNA-bendlng protein can do when it binds to the double helix. The device we report here is a scissors-like device consisting of two double-crossover (DX) molecules connected to each other by a flexible Holliday Junction. The two DX components are connected by a double helix that contains the binding site for MutS; when the binding site duplexiIs bent, the scissors contracts. The two DX molecules are also Joined by sticky ends on an edge adjacent to the binding site; the sticky ends can be disrupted If the protein binds with sufficient free energy. Those sticky ends are flanked by a pair of dyes; when the sticky ends are disrupted, the dyes separate, and the fluorescence resonance energy transfer signal can monitor the disruption. The strength of the sticky ends Is readily varied, so that the ability of the protein to disrupt them can be quantltated. We use this device to measure work in conjunction with a second device that measures the bending angle resulting from protein binding, so as to calibrate the system. Our data are In good agreement with previous measurements of MutS binding, indicating that this device Is able to measure the strength of binding correctly.
ASJC Scopus subject areas
- General Chemistry
- Colloid and Surface Chemistry