Photoswitch controls DNA duplex creation, separation

FEBRUARY 18, 2009--Researchers at Riken, one of Japan's largest research organizations, have developed a light-controlled switch to regulate the formation and separation of DNA duplexes. Their creation may have implications for numerous biological processes, including gene regulation. The photoswitch, a photochromic nucleoside (PCN), can be easily incorporated into a DNA strand and its physical conformation can be altered reversibly when irradiated by an external light source.

FEBRUARY 18, 2009--Researchers at Riken, one of Japan's largest research organizations, have developed a light-controlled switch to regulate the formation and separation of DNA duplexes. Their creation may have implications for numerous biological processes, including gene regulation.

Formation of nucleic acid complexes underlies many biological events. And hybridization of the nucleic acids, through base pairing, produces the intricate complexes responsible for the creation of DNA duplexes. The ability to control hybridization, and consequently biological events, has been a key goal for scientists. Shinzi Ogasawara and Mizuo Maeda of Riken's Advanced Science Institute (Wako, Japan) have described how the switch directs the formation and destabilization of a series of DNA duplexes in a paper published by Angewandte Chemie International Edition.

They designed the photoswitch, a photochromic nucleoside (PCN), with several fundamental properties and benefits. The switch can be easily incorporated into a DNA strand and its physical conformation can be altered reversibly when irradiated by an external light source. Change of the physical conformation, by isomerization, disrupts and destabilizes the hybridization of two DNA strands.

Another benefit of the PCN switch is that installing it into DNA has little influence on the structure of the duplex when it forms. Further, the PCN can be used as molecular trace label because it is fluorescent. This PCN photoswitch is therefore easy to track in the body and could be used in living cells without disruption.

The researchers irradiated a series of reaction mixtures containing PCN-modified DNA duplexes, which were fluorescent, with light at 370 nm for 5 minutes. After this time, only a slight fluorescence was seen. The PCN fragments had isomerized and the duplex broken. They then irradiated the mixtures at 254 nm for 2 minutes and the fluorescence returned, indicating a change back in conformation of the PCNs and importantly, hybridization to re-form the duplexes (Fig. 1). This switching showed good reversibility over two cycles.

Surprisingly, this easy switching system also works below room temperature. "There were no particular problems we had to overcome," says Ogasawara. However, the synthesis of the PCNs was not as straightforward as they would have liked.

Ogasawara and Maeda now want to build on the results of this current study. "We plan to apply this technology to gene regulation such as antigene, antisense and siRNA," says Ogasawara. "We think that this light-switching technique can be applied to nanotechnology, for example [using] light [to] control DNA nanomachines and architectures."

More information:
See the paper, Straightforward and reversible photoregulation of hybridization by using a photochromic nucleoside, in Angewandte Chemie International.

Posted by Barbara G. Goode, barbarag@pennwell.com, for BioOptics World.

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