Light-induced isomerization dynamics of a cyanine dye in the modulus-controlled regime

Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation

Protein-induced fluorescence enhancement (PIFE) is a popular tool for characterizing protein-DNA interactions. PIFE has been explained by an increase in local viscosity due to the presence of the protein residues. This explanation, however, denies the opposite effect of fluorescence quenching. This work offers a perspective for understanding PIFE mechanism and reports the observation of a phenomenon that we name protein-induced fluorescence quenching (PIFQ), which exhibits an opposite effect to PIFE. A detailed characterization of these two fluorescence modulations reveals that the initial fluorescence state of the labeled mediator (DNA) determines whether this mediator-conjugated dye undergoes PIFE or PIFQ upon protein binding. This key role of the mediator DNA provides a protocol for the experimental design to obtain either PIFQ or PIFE, on-demand. This makes the arbitrary nature of the current experimental design obsolete, allowing for proper integration of both PIFE and PIFQ with existing bulk and single-molecule fluorescence techniques.

Protein-induced fluorescence enhancement (PIFE) is a popular tool for characterizing protein-DNA interactions. Here, authors provide a perspective on understanding the general phenomenon of induced fluorescence modulation

An atomistic view on carbocyanine photophysics in the realm of RNA

Carbocyanine dyes have a long-standing tradition in fluorescence imaging and spectroscopy, due to their photostability and large spectral separation between individual dye species. Herein, we explore the versatility of cyanine dyes to probe the dynamics of nucleic acids and we report on the interrelation of fluorophores, RNA, and metal ions, namely K⁺ and Mg²⁺. Photophysical parameters including the fluorescence lifetime, quantum yield and dynamic anisotropy are monitored as a function of the nucleic acid composition, conformation, and metal ion abundance. Occasional excursions to a non-fluorescent cis-state hint at the remarkable sensitivity of carbocyanines to their local environment. Comparison of time-correlated single photon experiments with all-atom molecular dynamics simulations demonstrate that the propensity of photoisomerization is dictated by sterical constraints imposed on the fluorophore. Structural features in the vicinity of the dye play a crucial role in RNA recognition and have far-reaching implications on the mobility of the fluorescent probe. An atomic level description of the mutual interactions will ultimately benefit the quantitative interpretation of single-molecule FRET measurements on large RNA systems.

Fluorescent pseudorotaxanes of a quinodicarbocyanine dye with gamma cyclodextrin

Spectrophotometric titration of buffered solutions of gamma cyclodextrin (γCD) and 1,1'-diethyl,2,2'-dicarbocyanine (DDI) demonstrates extension of the known 1:2 host:guest complex to form a previously unreported 2:2 complex near the γCD solubility limit. Though DDI is predominantly hosted as a non-fluorescent H-aggregate, both complexes exist in respective equilibria with two secondary complexes hosting unaggregated DDI as 1:1 and 2:1 complexes. The 2:1 complex exhibits significant fluorescence emission, with a quantum yield six times that of DDI in organic solvents, but ten times lower than that of an analogous indodicarbocyanine. Fragment Molecular Orbital calculations suggest that the 2:1 complex has the tail-to-tail conformation, and that solvent access to the dye strongly favors photoisomerization. In the host-guest complex, γCD limits solvent access to the dye and hinders rotation of the quinolyl terminal groups, but nevertheless pairwise rotation of methine carbons within the γCD cavity likely remains as a significant nonradiative relaxation pathway for the excited state.

Photoisomerization mechanism of 1,1'-dimethyl-2,2'-pyridocyanine in the gas phase and in solution

The trans→cis and cis→trans photoisomerization mechanisms of 1,1'-dimethyl-2,2'-pyridocyanine have been investigated theoretically in the gas phase and in methanol. Two-dimensional potential energy surfaces were computed for the ground and first excited singlet states of the isolated molecule using complete active space self-consistent field method. Our computations suggest that the torsion around the central C-C bonds with carbon-out-of-plane motion is the preferred photoisomerization mechanism. In the gas phase, conical intersections were found near the minima of excited state. The excited-state decay follows a barrierless minimum-energy pathway before the molecule moves to the excited-state global minimum (minS1) and the system relaxes to the ground state through a conical intersection. In methanol, the system would first reach a stationary structure of C2 symmetry after the trans form is electronically excited. Solvent polarity effects were investigated in chloroform, dichloromethane, 1-propanol, ethanol, methanol, and water. There is a significant barrier between the stationary structure of C2 symmetry and minS1 in the excited state in high polarity solvents. Thus, Me-1122P has a much longer lifetime of the excited state in solvents of high polarity.