Effect of the ortho modification of azobenzene on the photoregulatory efficiency of DNA hybridization and the thermal stability of its cis form.

We synthesized various azobenzenes methylated at their ortho positions with respect to the azo bond for more effective photoregulation of DNA hybridization. Photoregulatory efficiency, evaluated from the change of T(m) (DeltaT(m)) induced by trans-cis isomerization, was significantly improved for all ortho-modified azobenzenes compared with non-modified azobenzene due to the more stabilized trans form and the more destabilized cis form. Among the synthesized azobenzenes, 4-carboxy-2',6'-dimethylazobenzene (2',6'-Me-Azo), in which two ortho positions of the distal benzene ring with respect to carboxyl group were methylated, exhibited the largest DeltaT(m), whereas the newly synthesized 2,6-Me-Azo (4-carboxy-2,6-dimethylazobenzene), which possesses two methyl groups on the two ortho positions of the other benzene ring, showed moderate improvement of DeltaT(m). Both NMR spectroscopic analysis and computer modeling revealed that the two methyl groups on 2',6'-Me-Azo were located near the imino protons of adjacent base pairs; these stabilized the DNA duplex by stacking interactions in the trans form and destabilized the DNA duplex by steric hindrance in the cis form. In addition, the thermal stability of cis-2',6'-Me-Azo was also greatly improved, but not that of cis-2,6-Me-Azo. Solvent effects on the half-life of the cis form demonstrated that cis-to-trans isomerization of all the modified azobenzenes proceeded through an inversion route. Improved thermal stability of 2',6'-Me-Azo but not 2,6-Me-Azo in the cis form was attributed to the retardation of the inversion process due to steric hindrance between lone pair electrons of the pi orbital of the nitrogen atom and the methyl group on the distal benzene ring.

[1]  H. Ono,et al.  Kinetic study of thermal Z to E isomerization reactions of azobenzene and 4-dimethylamino-4'-nitroazobenzene in ionic liquids [1-R-3-methylimidazolium bis(trifluoromethylsulfonyl)imide with R = butyl, pentyl, and hexyl]. , 2006, Chemistry.

[2]  M. Komiyama,et al.  Spiropyran as a Regulator of DNA Hybridization with Reversed Switching Mode to That of Azobenzene , 2001 .

[3]  M. Komiyama,et al.  NMR study on the photoresponsive DNA tethering an azobenzene. Assignment of the absolute configuration of two diastereomers and structure determination of their duplexes in the trans-form. , 2003, Journal of the American Chemical Society.

[4]  P. Haberfield,et al.  Enthalpies of solvent transfer of the transition states in the cis-trans isomerization of azo compounds. Rotation vs. the nitrogen inversion mechanism , 1975 .

[5]  R. Weiss,et al.  Liquid crystalline solvents as mechanistic probes. 11. The syn .fwdarw. anti thermal isomerization mechanism of some low-bipolarity azobenzenes , 1983 .

[6]  Shunzo Yamamoto,et al.  Thermal Cis-to-Trans Isomerization of Substituted Azobenzenes II. Substituent and Solvent Effects , 1976 .

[7]  Günter Mayer,et al.  Biologically active molecules with a "light switch". , 2006, Angewandte Chemie.

[8]  S. Yagai,et al.  Recent advances in photoresponsive supramolecular self-assemblies. , 2008, Chemical Society reviews.

[9]  Noriyuki Kurita,et al.  Mechanism of Cis-to-Trans Isomerization of Azobenzene: Direct MD Study , 2003 .

[10]  Ruojie Sha,et al.  A DNA-based nanomechanical device with three robust states , 2008, Proceedings of the National Academy of Sciences.

[11]  Hiroyuki Asanuma,et al.  Azobenzene-tethered T7 promoter for efficient photoregulation of transcription. , 2006, Journal of the American Chemical Society.

[12]  Synthesis and characterisation of novel 3'-O- and 5'-O- modified azobenzene-thymidine phosphoramidites and their oligonucleotide conjugates as colorimeter DNA probes and FRET quenchers , 2003 .

[13]  M. Komiyama,et al.  Photoregulation of RNA digestion by RNase H with azobenzene-tethered DNA. , 2004, Journal of the American Chemical Society.

[14]  H. Asanuma,et al.  Rational Design of Functional DNA with a Non-Ribose Acyclic Scaffold , 2009 .

[15]  C. Leumann,et al.  2-Phenanthrenyl-DNA: synthesis, pairing, and fluorescence properties. , 2009, Chemistry.

[16]  Xingguo Liang,et al.  A DNA Nanomachine Powered by Light Irradiation , 2008, Chembiochem : a European journal of chemical biology.

[17]  N. Bunce,et al.  Sterically hindered azobenzenes: isolation of cis isomers and kinetics of thermal cis .fwdarw. trans isomerization , 1987 .

[18]  M. Braun,et al.  Excited-State Dynamics of trans- and cis-Azobenzene after UV Excitation in the ππ* Band , 2004 .

[19]  Xingguo Liang,et al.  Synthesis of azobenzene-tethered DNA for reversible photo-regulation of DNA functions: hybridization and transcription , 2007, Nature Protocols.

[20]  Yoshihiro Ito,et al.  DNA as a 'nanomaterial' , 2004 .

[21]  E. Kool,et al.  Synthesis and properties of size-expanded DNAs: toward designed, functional genetic systems. , 2007, Accounts of chemical research.

[22]  M. Garavelli,et al.  The different photoisomerization efficiency of azobenzene in the lowest n pi* and pi pi* singlets: the role of a phantom state. , 2008, Journal of the American Chemical Society.

[23]  H. Asanuma,et al.  Molecular design for reversing the photoswitching mode of turning ON and OFF DNA hybridization. , 2008, Chemistry, an Asian journal.

[24]  C. Renner,et al.  Azobenzene as Conformational Switch in Model Peptides , 2006, Chembiochem : a European journal of chemical biology.

[25]  M. Hara,et al.  Self-assembly of long-lived cis-azobenzenes into crystalline nanoparticles , 2007 .

[26]  H. Lusic,et al.  Gene Silencing in Mammalian Cells with Light‐Activated Antisense Agents , 2008, Chembiochem : a European journal of chemical biology.

[27]  Z. Xi,et al.  A thermostable azo-linker for reversible photoregulation of DNA replication , 2008 .

[28]  C. Leumann.  DNA analogues: from supramolecular principles to biological properties. , 2002, Bioorganic & medicinal chemistry.

[29]  R. Petersen.  The Linear Relationship between Enthalpy and Entropy of Activation , 1964 .

[30]  Hiroyuki Asanuma,et al.  Clear-cut photo-regulation of the formation and dissociation of the DNA duplex by modified oligonucleotide involving multiple azobenzenes. , 2005, Nucleic acids symposium series.

[31]  J. Robertson.  47. Crystal structure and configuration of the isomeric azobenzenes , 1939 .

[32]  T. Asano,et al.  Further kinetic evidence for the competitive rotational and inversional Z―E isomerization of substituted azobenzenes , 1986 .

[33]  H. Powell,et al.  The electronic effect of the phenylazo and t-butylazo groups , 1988 .

[34]  G. Mayer,et al.  Biologisch aktive Moleküle mit “Lichtschalter” , 2006 .

[35]  Joakim Andréasson,et al.  Photoswitched DNA-binding of a photochromic spiropyran. , 2008, Journal of the American Chemical Society.

[36]  A. Fujishima,et al.  Kinetic studies on the thermal cis-trans isomerization of an azo compound in the assembled monolayer film , 1992 .

[37]  J. Barton,et al.  Ru(phen)(2)dppz(2+) Luminescence: Dependence on DNA Sequences and Groove-Binding Agents. , 1998, Inorganic chemistry.

[38]  H. Asanuma,et al.  2',6'-Dimethylazobenzene as an efficient and thermo-stable photo-regulator for the photoregulation of DNA hybridization. , 2007, Chemical communications.