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Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

Single-molecule observation of enzymes and DNA structural changes in the DNA nanostructures

Direct observation of the movement of biomolecules including enzymes and DNAs should be one of the ultimate goals for investigating the detailed mechanical behavior of the molecules during the reactions. We designed various DNA nanostructures using DNA origami method for the preparation of single-molecule observation scaffolds. Using the designed DNA scaffold and high-speed atomic force microscopy (AFM), the single-molecule behaviors of the DNA modifying enzymes, repair enzymes, and recombinases were observed in the target double-stranded DNAs (dsDNAs) placed in the DNA frame structure (Endo et al. 2010). DNA structural changes including G-quadruplex formation (Sannohe etal. 2010) and B-Z DNA conformational change (Rajendran et al. 2013) were also visualized. Using this system, we observed the photo-induced DNA hybridization and dissociation by detecting the global structural changes of the incorporated two dsDNAs in the DNA frame structure (Endo et al. 2012). A pair of azobenzene-modified oligonucleotides (ODNs) was employed, which forms duplex in the trans-form and dissociates in the cis-form. During UV-irradiation, hybridized azobenzene-modified ODNs at the center dissociated, and the subsequent visible-light irradiation induced the hybridization of the photoresponsive ODNs, meaning that the reversed switching behavior such as the hybridization and dissociation was directly visualized at the single-molecule level. These photoresponsive ODNs were also used for controlling assembly and disassembly of the hexagonal DNA origami structures with photoirradiation (Yang et a. 2012). The combination of the designed DNA scaffold modified with target DNA strands and high-speed AFM is valuable for visualizing and analyzing the single enzymatic and chemical reactions.

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Figure 1. Single-molecule observation of the behavior of enzymes and their reactions and DNA structural changes in the DNA frame structure. (A) DNA frame nanostructure. (B) Two-dsDNA-attached DNA frame. (C) AFM image of DNA frame with two dsDNAs. (D) EcoRI methyltransferase binding on the dsDNA. (E) Observation of G-quadruplex formation in the DNA frame. G-quaduplex forming DNA strands are attached to the middle of two dsDNAs. (F) High-speed AFM images of G-quadruplex formation in the presence of KCl.

References

    M. Endo, Y. Katsuda, K. Hidaka, H. Sugiyama, J. Am. Chem. Soc. 132, 1592–1597 (2010).

    M. Endo, Y. Katsuda, K. Hidaka, H. Sugiyama, Angew. Chem. Int. Ed. 49, 9412-9416 (2010).

    Y. Sannohe, M. Endo, Y. Katsuda, K. Hidaka, H. Sugiyama, J. Am. Chem. Soc. 132, 16311–16313 (2010).

    A. Rajendran, M. Endo, K. Hidaka, H. Sugiyama, J. Am. Chem. Soc. 135, 1117-1123 (2013).

    M. Endo, Y. Yang, Y. Suzuki, K. Hidaka, H. Sugiyama, Angew. Chem. Int. Ed. 51, 10518-10522 (2012).

    Y. Yang, M. Endo, K. Hidaka, H. Sugiyama, J. Am. Chem. Soc. 134, 20645-20653 (2012).

Hiroshi Sugiyama*
Masayuki Endo

Institute for Integrated Cell-Material Sciences (WPI-iCeMS)
Department of Chemistry
Graduate School of Science
Kyoto University,
Yoshida-ushinomiyacho
Sakyo-ku, Kyoto 606-8501, Japan

Phone: +81-75-753-4002
Fax: +81-75-753-3670
hs@ kuchem.kyoto-u.ac.jp