Light responsive nucleic acid for biomedical application

Nucleic acids are widely used in biomedical applications because of their programmability and biocompatibility. The light responsive nucleic acids have attracted wide attention due to their remote control and high spatiotemporal resolution. In this review, we summarized the latest developments in biomedicine of light responsive molecules. The molecules which confer light responsive properties to nucleic acids were summarized. The binding sites of molecules to nucleic acids, the induced structural changes, and functional regulation of nucleic acids were reviewed. Then, the biomedical applications of light responsive nucleic acids were listed, such as drug delivery, biosensing, optogenetics, gene editing, etc. Finally, the challenges were discussed and possible future directions of light-responsive nucleic acids were proposed.

Photoresponsive Control of G-Quadruplex DNA Systems

G-quadruplex (G4) oligonucleotide secondary structures have recently attracted significant attention as therapeutic targets owing to their occurrence in human oncogene promoter sequences and the genome of pathogenic organisms. G4s also demonstrate interesting catalytic activities in their own right, as well as the ability to act as scaffolds for the development of DNA-based materials and nanodevices. Owing to this diverse range of opportunities to exploit G4 in a variety of applications, several strategies to control G4 structure and function have emerged. Interrogating the role of G4s in biology requires the delivery of small-molecule ligands that promote its formation under physiological conditions, while exploiting G4 in the development of responsive nanodevices is normally achieved by the addition and sequestration of the metal ions required for the stabilization of the folded structure. Although these strategies prove successful, neither allows the system in question to be controlled externally. Meanwhile, light has proven to be an attractive means for the control of DNA-based systems as it is noninvasive, can be delivered with high spatiotemporal precision, and is orthogonal to many chemical and biological processes. A plethora of photoresponsive DNA systems have been reported to date; however, the vast majority deploy photoreactive moieties to control the stability and assembly of duplex DNA hybrids. Despite the unique opportunities afforded by the regulation of G-quadruplex formation in biology, catalysis, and nanotechnology, comparatively little attention has been devoted to the design of photoresponsive G4-based systems. In this Perspective, we consider the potential of photoresponsive G4 assemblies and examine the strategies that may be used to engineer these systems toward a variety of applications. Through an overview of the main developments in the field to date, we highlight recent progress made toward this exciting goal and the emerging opportunities that remain ripe for further exploration in the coming years.

Enhanced Rigidity Changes Ultraviolet Absorption: Effect of a Merocyanine Binder on G-Quadruplex Photophysics

The urge to discover selective fluorescent binders to G-quadruplexes (G4s) for rapid diagnosis must be linked to understand the effect that those have on the DNA photophysics. Herein, we report on the electronic excited states of a bound merocyanine dye to c-Myc G4 using extensive multiscale quantum mechanics/molecular mechanics calculations. We find that the absorption spectra of c-Myc G4, both without and with the intercalated dye, are mainly composed of exciton states and mixed local/charge-transfer states. The presence of merocyanine hardly affects the energy range of the guanine absorption or the number of guanines excited. However, it triggers a substantial amount (16%) of detrimental pure charge-transfer states involving oxidized guanines. We identify the rigidity introduced by the probe in G4, reducing the overlap among guanines, as the one responsible for the changes in the exciton and charge-transfer states, ultimately leading to a redshift of the absorption maximum.

Nonadiabatic Dynamics Simulations on Early-Time Photochemistry of Spirobenzopyran

Photoinduced ring-opening, decay, and isomerization of spirobenzopyran have been explored by the OM2/MRCI nonadiabatic dynamics simulations based on Tully's fewest-switches surface hopping scheme. The efficient S₁ to S₀ internal conversion as observed in experiments is attributed to the existence of two efficient excited-state decay pathways. The first one is related to the C-N dissociation, and the second one is done to the C-O dissociation. The C-O dissociation pathway is dominant, and more than 90% trajectories decay to the S₀ state via the C-O bond-fission related S₁/S₀ conical intersections. Near these regions in the S₀ state, trajectories can either return to spirobenzopyran or proceed to various intermediates including merocyanine via a series of bond rotations. Our nonadiabatic dynamics simulations also demonstrate that the hydrogen-out-of-plane (HOOP) motion is important for efficient and ultrafast excited-state deactivation. On the other hand, we have also found that the replacement of methyl groups by hydrogen atoms in spirobenzopyran can artificially introduce different intramolecular hydrogen transfers leading to hydrogen-transferred intermediates. This finding is important for the community and demonstrates that such a kind of structural truncation, sometimes, could be problematic, leading to incorrect photodynamics. Our present work provides valuable insights into the photodynamics of spirobenzopyran, which could be helpful for the design of spiropyran-based photochromic materials.