Analysis of Coherent Heteroclustering of Different Dyes by Use of Threoninol Nucleotides for Comparison with the Molecular Exciton Theory

Abstract

To test the molecular exciton theory for heterodimeric chromophores, various heterodimers and clusters, in which two different dyes were stacked alternately, were prepared by hybridizing two oligodeoxyribonucleotides (ODNs), each of which tethered a different dye on D-threoninol at the center of the strand. NMR analyses revealed that two different dyes from each strand were stacked antiparallel to each other in the duplex, and were located adjacent to the 5'-side of a natural nucleobase. The spectroscopic behavior of these heterodimers was systematically examined as a function of the difference in the wavelength of the dye absorption maxima (Delta lambda(max)). We found that the absorption spectrum of the heterodimer was significantly different from that of the simple sum of each monomeric dye in the single strand. When azobenzene and Methyl Red, which have lambda(max) at 336 and 480 nm, respectively, in the single strand (Delta lambda(max) = 144 nm), were assembled on ODNs, the band derived from azobenzene exhibited a small hyperchromism, whereas the band from Methyl Red showed hypochromism and both bands shifted to a longer wavelength (bathochromism). These hyper- and hypochromisms were further enhanced in a heterodimer derived from 4'-methylthioazobenzene and Methyl Red, which had a much smaller Delta lambda(max) (82 nm; lambda(max) = 398 and 480 nm in the single-strand, respectively). With a combination of 4'-dimethylamino-2-nitroazobenzene and Methyl Red, which had an even smaller Delta lambda(max) (33 nm), a single sharp absorption band that was apparently different from the sum of the single-stranded spectra was observed. These changes in the intensity of the absorption band could be explained by the molecular exciton theory, which has been mainly applied to the spectral behavior of H- and/or J-aggregates composed of homo dyes. However, the bathochromic band shifts observed at shorter wavelengths did not agree with the hypsochromism predicted by the theory. Thus, these data experimentally verify the molecular exciton theory of heterodimerization. This coherent coupling among the heterodimers could also partly explain the bathochromicity and hypochromicity that were observed when the dyes were intercalated into the duplex.

Femtosecond photoisomerization of azobenzene-derivative binding to DNA

“…This result suggests that the AzD is the much more efficient T-to-C photoisomerization molecule as a photoregulator compared to the already-reported Az 9 and its derivatives [3][4][5][6], with the advantage of the pump wavelength without damaging the living cell [7,8]. S -to-I T T C kinetic rate hardly changes.…”

“…[7]. The AzD solution in dimethylsulfoxide (DMSO, spectroscopic grade) was at the concentration of 4.0 mM or 8.0 mM.…”

“…Furthermore, a new azobenzene derivative, 4'-methylthioazobenzene (we call AzD), without giving the optical damage to the living cell, has been demonstrated, where trans (T) to cis (C) photoisomerization occurs by CW-lamp irradiation at the longer wavelength than 400 nm (S 2 excitation) and C-to-T photoisomerization occurs at around 520 nm (S 1 excitation) [7,8]. However, we have no knowledge of ultrafast electronic excited-state dynamics of the AzD binding to DNA (AzD-DNA) as well as the AzD, though for Az related compounds extensive studies on photoisomerization mechanisms such as rotation, inversion and concerted inversion processes have been carried out to clarify the relation between these processes and the excitation bands [9][10][11].…”

Development of Pseudo Base-Pairs on d-Threoninol which Exhibit Various Functions

“…17 Although azobenzene derivatives are much larger than natural bases, they are stacked in antiparallel manner without disturbing natural base pairs ( Figure 2B). Thus, we concluded that surprisingly high stability of M-M pairs is caused by strong intermolecular stacking interactions between M residues.…”

Anthracene-modified oligonucleotides as fluorescent DNA mismatch sensors: discrimination between various base-pair mismatches

“…Although these isomers could be separated, the linker stereochemistry was difficult to assign with complete certainty. We therefore turned our attention towards a threoninol linker (Figure 1b), which has previously been successfully used in other studies on functionalised oligonucleotides 6,21,[24][25][26] and as an enantiopure starting material, removes the problem of generating diastereomers.…”