Abstract
A phosphoramidite monomer bearing an azobenzene is synthesized from D-threoninol. Using this monomer, azobenzene moieties can be introduced into oligodeoxyribonucleotide (DNA) at any position on a conventional DNA synthesizer. With this azobenzene-tethered DNA, formation and dissociation of a DNA duplex can be reversibly photo-regulated by cis–trans isomerization of the azobenzene. When the azobenzene takes a trans-form, a stable duplex is formed. After isomerization of the trans-azobenzene to its cis-form by UV-light irradiation (300 nm < λ < 400 nm), the duplex can be dissociated into two strands. The duplex is reformed on photo-induced cis–trans isomerization (λ > 400 nm). The introduction of azobenzenes into the T7 promoter at specific positions also efficiently and reversibly photo-regulates transcription by T7-RNA polymerase. The reversible regulation can be repeated many times without causing damage to the DNA or the azobenzene moiety. These procedures take approximately 10 d to complete.
NOTE: In Figure 4 of the version of this article originally published online, the base sequence of the oligonucleotide was incorrect. The figure has been replaced in all versions of the article.
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01 March 2007
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References
Braasch, D.A. & Corey, D.R. Novel antisense and peptide nucleic acid strategies for controlling gene expression. Biochemistry 41, 4503–4510 (2002).
Schmitz, K. & Schepers, U. Polyamides as artificial transcription factors: novel tools for molecular medicine? Angew. Chem. Int. Ed. 43, 2472–2475 (2004).
Benenson, Y., Gil, B., Ben-Dor, U., Adar, R. & Shapiro, E. An autonomous molecular computer for logical control of gene expression. Nature 429, 423–429 (2004).
Dittmer, W.U. & Simmel, F.C. Transcriptional control of DNA-based nanomachines. Nano Lett. 4, 689–691 (2004).
Murata, M., Kaku, W., Anada, T., Soh, N., Katayama, Y. & Maeda, M. Thermo responsive DNA/polymer conjugate for intelligent antisense strategy. Chem. Lett. 32, 266–267 (2003).
Kobatake, E., Suzuki, S. & Aizawa, M. Assembling of recombinant calmodulin with modulating function on solid surface. Sens. Actuators B Chem. 94, 165–168 (2003).
Wada, T., Minamimoto, N., Inaki, Y. & Inoue, Y. Peptide ribonucleic acids (PRNA) 2. A novel strategy for active control of DNA recognition through borate ester formation. J. Am. Chem. Soc. 122, 6900–6910 (2000).
Asanuma, H., Takarada, T., Yoshida, T., Liang, X. & Komiyama, M. Enantioselective incorporation of azobenzenes into oligodeoxyribonucleotide for the effective photo-regulation of duplex formation. Angew. Chem. Int. Ed. 40, 2671–2673 (2001).
Takarada, T., Tamaru, D., Liang, X., Asanuma, H. & Komiyama, M. l-threoninol as a chiral linker of azobenzene for the effective photo-regulation of DNA triplex formation. Chem. Lett. 732–733 (2001).
Liang, X., Asanuma, H. & Komiyama, M. Phenylazonaphthalene as a superb photo-regulator for DNA-triplex formation. Tetrahedron Lett. 42, 6723–6725 (2001).
Asanuma, H., Liang, X., Yoshida, T. & Komiyama, M. Photo-control of DNA-duplex formation by use of oligonucleotide carrying an azobenzene. Chembiochem 2, 39–44 (2001).
Liang, X., Asanuma, H. & Komiyama, M. Photo-regulation of DNA-triplex formation by azobenzene. J. Am. Chem. Soc. 124, 1877–1883 (2002).
Asanuma, H., Matsunaga, D. & Komiyama, M. Clear-cut photo-regulation of the formation and dissociation of the DNA duplex by modified oligonucleotide involving multiple azobenzenes. Nucleic Acids Symp. Ser. 49, 35–36 (2005).
Asanuma, H., Tamaru, D., Yamazawa, A., Liu, M. & Komiyama, M. Photo-regulation of transcription reaction by T7 RNA polymerase by tethering an azobenzene in the promoter. Chembiochem 3, 786–789 (2002).
Liu, M., Tamaru, D., Asanuma, H. & Komiyama, M. Synergistic effect of the two azobenzenes in the promoter on the photo-regulation of transcription reaction with SP6 RNA polymerase. Chem. Lett. 32, 1174–1175 (2003).
Liu, M., Asanuma, H. & Komiyama, M. Azobenzene-tethered T7 promoter for efficient photoregulation of transcription. J. Am. Chem. Soc. 128, 1009–1015 (2006).
Liang, X. et al. NMR study on the photo-responsive DNA tethering an azobenzene. Assignment of the absolute configuration of two diastereomers and structure determination of their duplexes in the trans-form. J. Am. Chem. Soc. 125, 16408–16415 (2003).
Glen Research. Users Guide to DNA Purification (2006).
Matsunaga, D., Asanuma, H. & Komiyama, M. Photo-regulation of RNA digestion by RNase H with azobenzene-tethered DNA. J. Am. Chem. Soc. 126, 11452–11453 (2004).
Acknowledgements
This work was supported by Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST). Partial support through a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan, and The Mitsubishi Foundation (for H.A.) is also acknowledged.
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Asanuma, H., Liang, X., Nishioka, H. et al. Synthesis of azobenzene-tethered DNA for reversible photo-regulation of DNA functions: hybridization and transcription. Nat Protoc 2, 203–212 (2007). https://doi.org/10.1038/nprot.2006.465
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DOI: https://doi.org/10.1038/nprot.2006.465
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