“By combining single-molecule fluorescence resonance energy transfer and an optical trap, we now have a technique that can detect subtle conformational changes of a biomolecule at an extremely low applied force,” said U. of I. physics professor Taekjip Ha, the corresponding author of a paper to appear in the Oct. 12 issue of the journal Science
The hybrid technique, demonstrated in the Science paper on the dynamics of Holliday junctions, is also applicable to other nucleic acid systems and their interaction with proteins and enzymes.
The Holliday junction is a four-stranded DNA structure that forms during homologous recombination – for example, when damaged DNA is repaired. The junction is named after geneticist Robin Holliday, who proposed the model of DNA-strand exchange in 1964.
To better understand the mechanisms and functions of proteins that interact with the Holliday junction, researchers must first understand the structural and dynamic properties of the junction itself.
But purely mechanical measurement techniques can not detect the tiny changes that occur in biomolecules in the regime of weak forces. Ha and colleagues have solved this problem by combining the exquisite force control of an optical trap and the precise measurement capabilities of single-molecule fluorescence resonance energy transfer.
With this latest work, the researchers have deduced the pathway of the conformational flipping of the Holliday junction, and determined the intermediate structure is similar to that of a Holliday junction bound to its own processing enzyme.
“The next challenge is to obtain a timeline of movement by force, for example, due to the action of DNA processing enzymes, and correlate it with the enzyme conformational changes simultaneously measured by fluorescence,” Ha said.