Keeping it together (or not) with molecular glue

Gary Boas

Spontaneous hybridization of complementary DNA drives a range of biological functions and can be exploited to build DNA-based materials and nanoarchitectures. Researchers, therefore, have devoted considerable time and effort to controlling hybridization.

In recent years, a team with Osaka University in Ibaraki, Japan, has developed a series of synthetic small molecules — called mismatch binding ligands — that bind to two DNA strands that do not hybridize with one another spontaneously, thereby inducing hybridization. They recently reported a photoswitchable molecular glue that enables reversible hybridization using these molecules.

The researchers previously had achieved pseudo-bidirectional control of DNA hybridization using a thermally degradable molecular glue that could be refilled after each use. In the present study, they achieved true bidirectional control by incorporating a photoresponsive unit (naphthyridine carbamate dimer) into the ligands.

They showed that they could alter the relative orientations and positions of the naphthyridine moieties through stimulation with an external light source (from trans to cis form and back again), switching on and off the glue’s ability to hold the strands together, thus facilitating hybridization and dehybridization of the DNA.

Researchers have reported a photoswitchable “molecular glue” that binds to two DNA strands that do not otherwise hybridize spontaneously, facilitating improved control of a variety of biological events as well as construction of DNA-based materials and nanoarchitectures. Irradiation with 360-nm light induces binding, leading to hybridization of the DNA. Subsequent irradiation with 430-nm light causes dehybridization.

They confirmed binding of the photoswitchable molecular glue and the DNA with cold-spray ionization time-of-flight mass spectrometry, using an AccuTof system made by Jeol Ltd. of Tokyo. When the glue was in its trans form, the only detectable peaks were ions corresponding to the DNA. However, after irradiation with 360-nm light, the measurements revealed both the glue in its cis form and the DNA. These results agreed with previously characterized complexes of the naphthyridine carbamate dimer binding to the particular sequence.

The most difficult part of the study, said principal investigator Kazuhiko Nakatani, was how to visually demonstrate the reversibility of DNA hybridization. To this end, they performed surface plasmon resonance imaging using a system made by Toyobo Co. Ltd. of Osaka, Japan.

A solution containing DNA and the glue in the trans form circulated between a photoreaction cell and a surface plasmon resonance cell with a gold coating upon which another DNA strand had been immobilized. To isomerize the glue from the trans to the cis form, they irradiated the solution in the photoreaction cell with 360-nm light. Surface plasmon resonance signals began to emerge at the sites of hybridization almost immediately, and the intensity of the signals increased as irradiation continued.

Subsequent irradiation with 430-nm light caused the surface plasmon resonance signals to disappear, indicating that photoisomerization of the glue enabled hybridization and dehybridization of DNA complexes.

The researchers are exploring whether they can apply the technique to control both biologically and nonbiologically important events. The target events include protein expression, transmembrane signal transduction and construction of DNA nanostructures.

Journal of the American Chemical Society, Sept. 12, 2007, pp. 11898-11899.