Covalent Incorporation of Methyl Red Dyes into Double‐Stranded DNA for Their Ordered Clustering

Abstract

An ordered dye cluster of Methyl Reds was formed in double-stranded DNA by hybridizing two complementary DNA-dye conjugates, each involving a Methyl Red moiety on a threoninol linker and a 1,3-propanediol spacer arranged alternately in the middle of the DNA sequence. In the duplex, Methyl Reds from each strand were axially stacked antiparallel to each other, as determined from NMR analysis. This clustering of Methyl Reds induced distinct changes in both UV/Vis and CD spectra. Single-stranded DNA-Methyl Red conjugates on D-threoninol linkers and (1,3-propanediol) spacers exhibited broad absorption spectra with lambda(max) at around 480 nm, and almost no CD was observed at around the absorption maximum of Methyl Red. However, as Methyl Reds were clustered by hybridization, lambda(max) shifted towards shorter wavelengths with respect to its monomeric transition. This hypsochromic shift increased as the number of Methyl Red molecules increased. Furthermore, a positive couplet was also strongly induced here. These dye clusters are H-aggregates, in which molecular excitons are coupled. The positive couplet demonstrates that the clusters on D-threoninol form a right-handed helix. In contrast, the induced CD became much weaker with Methyl Red on L-threoninol, which intrinsically prefers counterclockwise winding. Thus, mutual orientation of the stacked dye molecules was controlled by the chirality of the linker.

Visible‐Light Photoresponsivity of a 4‐(Dimethylamino)azobenzene Unit Incorporated into Single‐Stranded DNA: Demonstration of a Large Spectral Change Accompanying Isomerization in DMSO and Detection of Rapid (Z)‐to‐(E) Isomerization in Aqueous Solution

“…With a conventional spectrophotometer we were unable to detect changes in the spectral profile of 6 in an aqueous solution after irradiation with visible light (420 nm) [Figure 3 (a), solid and dotted lines], consistent with previous reports, [11,13] so we attempted to detect (E)/(Z) isomerization by laser flash photolysis. [17] Figure 3 (b) shows the changes in absorbance at 460 nm after a laser (λ = 532 nm) photoflash.…”

“…[11,13] We speculated that, in aqueous solutions, the dimethylamino group of the 4-DMAzo moiety in 6 undergoes protonation, similarly to the parent 4-DMAzo or 4Ј-carboxy-4-DMAzo, [18] so that no significant spectral change in 6 is detectable with a conventional spectrophotometer due to the rapid thermal (Z)-to-(E) transition. For this reason we attempted to observe changes in the absorption spectra with a conventional spectrophotometer by conducting measurements in DMSO, an aprotic solvent that should suppress protonation of the dimethylamino group.…”

“…Synthetic oligonucleotides conjugated with methyl red [4Ј-carboxy-4-(dimethylamino)azobenzene] [9][10][11][12] have been shown to absorb visible light, and it has been suggested that methyl red conjugated oligonucleotides could be useful as DNA beacons thanks to their unique H-aggregation and stacking properties. When these oligonucleotides were irradiated with visible light in aqueous solution, however, no photoresponsivity of the oligonucleotides could be detected with a conventional spectrophotometer, [11,13] so little is currently known about the visible-light photoresponsivity of oligonucleotides incorporating tethered azobenzene derivatives with a dimethylamino group at the 4Ј-position, either in aqueous or in organic solutions.…”

Studies on sildenafil citrate (Viagra) interaction with DNA using electrochemical DNA biosensor

“…These spectra clearly showed that the λ max shifted towards a shorter wavelength (hypsochromic effect) with the addition of salmon sperm DNA. The spectral shift of the absorption maxima (hypochromic or hypsochromic effect) of the drug or DNA binding molecules on binding to DNA is a typical characteristic of DNA intercalation (Chen et al, 2005;Erdem et al, 2001;Ibrahim, 2001;Kashida et al, 2006;Sehgal et al, 1988). These spectral characteristics are attributed to the strong interaction of the drug chromophore with DNA bases.…”

TTF‐Modified DNA

“…[34][35][36][37] They were explored as hairpin replacements, [38][39][40][41][42][43][44] as units for conformational control in DNA, [45][46][47] or as replacements of the natural nucleotides maintaining helical organization. [48][49][50] Further efforts are aimed at the development of advanced functional building blocks with a high level of structural organization. Interest in TTF-oligonucleotide conjugates is documented in patents describing the use of redox-active labels for the development of oligonucleotide-based sensors.…”