Electrostatic Origin of the Red Solvatochromic Shift of DFHBDI in RNA Spinach

Abstract

Interactions with the environment tune the spectral properties of biological chromophores, e.g., fluorescent proteins. Understanding the relative contribution of the various types of noncovalent interactions in the spectral shifts can provide rational design principles toward developing new fluorescent probes. In this work, we investigate the origin of the red shift in the absorption spectra of the difluoro hydroxybenzylidene dimethyl imidazolinone (DFHBDI) chromophore in RNA spinach as compared to the aqueous solution. We systematically decompose the effects of various components of interactions, namely, stacking, hydrogen bonding, and long-range electrostatics, in order to elucidate the relative role of these interactions in the observed spectral behavior. We find that the absorption peak of DFHBDI is red-shifted by ∼0.35 eV in RNA relative to the aqueous solution. Earlier proposals from Huang and co-workers have implicated the stacking interactions between DFHBDI and nucleic acid bases to be the driving force behind the observed red shift. In contrast, our findings reveal that the long-range electrostatic interactions between DFHBDI and negatively charged RNA make the most significant contribution. Moreover, we notice that the opposing electrostatic fields due to the RNA backbone and the polarized water molecules around the RNA give rise to the resultant red shift. Our results emphasize the effect of strong heterogeneity in the various environmental factors that might be competing with each other.

A Multicolor Large Stokes Shift Fluorogen‐Activating RNA Aptamer with Cationic Chromophores

“…This suggests that the Chili RNA exclusively binds the DMHBO + chromophore in its protonated state. The bathochromic shift of 20 nm compared to the free phenol likely originates from a combination of π‐stacking and electrostatic interactions . Excitation of the protonated chromophore‐RNA complex is followed by fast deprotonation, which results in the large apparent Stokes shift of 136 nm.…”

“…The bathochromic shift of 20 nm compared to the free phenol likely originates from ac ombination of p-stacking and electrostatic interactions. [26] Excitation of the protonated chromophore-RNA complex is followed by fast deprotonation, which resultsi nt he large apparent Stokes shift of 136 nm. These results suggest that af unctional group of the RNA near the phenola cts as ap rotons huttle.…”

Data-Driven Modeling of S0 -> S1 Excitation Energy in the BODIPY Chemical Space: High-Throughput Computation, Quantum Machine Learning, and Inverse Design

“…Additionally, CAM-B3LYP's performance is also tested against the SOS-CIS(D) method [104,105] with aug-cc-pVDZ basis set using QCHEM [106]. The latter wavefunction method is known to exhibit good accuracy for excitation energies [107,108] with experimental results. Here, we want to compare its performance with STEOM-DLPNO-CCSD for modeling BODIPY's S 0 → S 1 excitation energy.…”

Prediction of fluorophore brightness in designed mini fluorescence activating proteins

“…Quantum mechanics/molecular mechanics (QM/MM) point calculations from energy minimized structures have suggested that the presence of SPINACH increases the barrier to rotation of the imidazole group primarily through interaction with the MM environment and not through RNA-induced perturbation to the QM energies 8 . A subsequent study highlighted the role of the electrostatic environment in shifting chromophore vertical excitation energies 9 .…”

“…The photophysics of DFHBI bound to SPINACH has been an active area of research 3,7–9 . When exposed to continuous light at the same illumination level, RNA-bound DFHBI exhibited less photobleaching than EGFP or fluorescein 3 .…”