Nucleobase-Specific Quenching of Fluorescent Dyes. 1. Nucleobase One-Electron Redox Potentials and Their Correlation with Static and Dynamic Quenching Efficiencies

Interaction of solid lipid nanoparticles with bovine serum albumin: physicochemical mechanistic insights

This study investigates the interaction of solid lipid nanoparticles (SLNs) with the transport protein bovine serum albumin (BSA) in terms of thermodynamic signatures, employing both spectroscopic and calorimetric techniques. When nanoparticles are exposed to biological media, proteins are adsorbed on their surfaces, leading to protein corona formation. Therefore, controlling the formation of the protein corona is essential for in vivo therapeutic efficacy. Although SLNs have previously been explored solely as potential nano-carriers for drug delivery, no prior efforts have been made to study their interactions with biomolecules from a biophysical and mechanistic perspective. SLNs are colloidal dispersions of the solid lipid in an aqueous solution stabilized by surfactants. Herein, a hot emulsification methodology was employed to formulate SLNs, and their interactions with BSA were analyzed. The SLNs were characterized using transmission electron microscopy (TEM) and dynamic light scattering (DLS) techniques to obtain information on their size, zeta potential, and shape. Fluorescence data suggested the presence of weak interactions between the SLNs and BSA. Static quenching is confirmed using time-correlated single-photon counting (TCSPC) experiments. Differential scanning calorimetric (DSC) and fluorescence spectroscopic experiments suggest the thermal stabilization of BSA by the SLNs. This stabilization results from the enhancement of the secondary structure of the protein without significantly altering the tertiary structure. Isothermal calorimetry (ITC) results suggest weak interactions between the SLNs and BSA, although not in a site-specific manner. Overall, mechanistic insights into lipid nanoparticle-protein interactions obtained from such studies efficiently overcome the hurdles associated with targeted drug delivery.

NEIL1: The second DNA glycosylase involved in action-at-a-distance mutations induced by 8-oxo-7,8-dihydroguanine

8-Oxo-7,8-dihydroguanine (GO, 8-hydroxyguanine), an oxidatively damaged base, induces mutations and is involved in cancer initiation. In addition to G:C→T:A transversions at the damaged site, it causes untargeted base substitution (action-at-a-distance) mutations at the G bases of 5'-GpA-3' sites in human cells. Paradoxically, OGG1, a DNA glycosylase involved in the base excision repair (BER) pathway, enhances the action-at-a-distance mutations by GO. In this study, other DNA glycosylases, potential repair enzymes for the GO base, were knocked down, and their effects on the untargeted mutations were examined using the supF reporter gene. The knockdown of NEIL1 decreased such mutations, while those of NTH1, NEIL2, and NEIL3 had no effects. The double knockdown of OGG1 and NEIL1 additively affected the mutation frequency. These results indicated that NEIL1 is another BER protein involved in the action-at-a-distance mutations triggered by the oxidized guanine base.

5'-Amino-Formyl-Thieno[3,2-b]thiophene End-Label for On-Strand Synthesis of Far-Red Fluorescent Molecular Rotors and pH-Responsive Probes

The ability to label synthetic oligonucleotides with fluorescent probes has greatly expanded their nanotechnological applications. To continue this expansion, it is essential to develop approachable, modular, and tunable fluorescent platforms. In this study, we present the synthesis and incorporation of an amino-formyl-thieno[3,2-b]thiophene (AFTh2) handle at the 5'-position of DNA oligonucleotides. The 5'-AFTh2 end-label participates in both on-strand Knoevenagel and heterocyclization reactions, yielding far-red hemicyanines and pH-responsive probes with pKa values in the biological regime. The Knoevenagel products, designated 5'-ATh2Btz and 5'-ATh2Ind, demonstrate excitation maxima beyond 640 nm with brightness up to ∼50,000 M-1 cm-1. Notably, 5'-ATh2Btz demonstrates strong topology sensitivity, allowing it to probe transitions from duplex- to single-strand (SS)/G-quadruplex (GQ) topologies with an ∼9-fold increase in fluorescence in the absence of quenchers. In contrast, the heterocyclization product, 5'-ATh2BIM, displays visible excitation and emission and is weakly fluorescent in basic solution. Upon lowering the pH from ∼8 to 5, this probe undergoes an unprecedented 400-fold light-up. Additionally, attaching 5'-ATh2BIM to a polymorphic GQ allows for a shift in pKa by ∼1.5 pH units simply by changing topology. The performance of the probes has been demonstrated in various contexts, including GQs, i-motifs, duplexes, and SS oligonucleotides. Their performance should facilitate the development of new DNA-based sensing platforms.

The Hidden Mechanism: Excited-State Proton-Electron Pair Transfer in Metal Nanocluster Emission

Comprehending the underlying factors that govern photoluminescence (PL) in metal nanoclusters (NCs) under physiological conditions remains a highly intriguing and unresolved challenge, particularly for their biomedical applications. In this study, we evaluate the critical role of excited-state proton-coupled electron transfer in the emission of metal NCs. Our findings demonstrate that hydronium ion (H3O+) binding can trigger a nonlinear, pH-dependent excited-state concerted electron proton transfer (CEPT) reaction. This involves simultaneous electron transfer from the Au(0) core to the Au(I)-ATT (ATT denotes 6-aza-2-thiothymidine) surface and proton transfer from H3O+ to the ATT ligand in a single step, greatly promoting vibrations and rotations of the Au(I)-ATT surface, resulting in substantial PL quenching of Au10(ATT)6 NCs. Further analyses show that the unique CEPT dynamics are strongly influenced by the opposing effects of increased reorganization energy and a larger pre-exponential factor on the electron transfer rate. Moreover, the proposed excited-state CEPT process is found to be prevalent in core-shell relaxation metal NCs, such as Au25(SR)18 (SR denotes thiolate) NCs, and serves as an important factor in limiting their PL emission. By simply controlling the pKa of the ligands, the emission performance of Au25(SR)18 can be easily regulated in physiological environments.

Quencher-Free Fluorescence Monitoring of G-Quadruplex Folding

Guanine-rich sequences exhibit a high degree of polymorphism and can form single-stranded, Watson-Crick duplex, and four-stranded G-quadruplex structures. These sequences have found a wide range of uses in synthetic biology applications, arising in part from their structural plasticity. High-throughput, low-cost tools for monitoring the folding and unfolding transitions of G-rich sequences would provide an enabling technology for accelerating the prototyping of synthetic biological systems and for accelerating design-build-test cycles. Here, we show that unfolding transitions of a range of G-quadruplex-forming DNA sequences can be monitored in a FRET-like format using DNA sequences that possess only a single dye label, with no quencher. These quencher-free assays can be performed at low cost, with both cost and lead times ca. 1 order of magnitude lower than FRET-labeled strands. Thus, quencher-free secondary structure monitoring promises to be a valuable tool for the testing and development of synthetic biology systems employing G-quadruplexes.

Elucidation of a distinct photoreduction pathway in class II Arabidopsis thaliana photolyase

Class II photolyases (PLs) are a distant subclade in the photolyase/cryptochrome superfamily, displaying a unique Trp-Tyr tetrad for photoreduction and exhibiting a lower quantum yield (QY) of DNA repair (49%) than class I photolyases (82%) [M. Zhang, L. Wang, S. Shu, A. Sancar, D. Zhong, Science 354, 209-213 (2016)]. Using layer-by-layer mutant design and femtosecond spectroscopy, we have successfully determined the rates of electron transfer and proton transfer, driving force, and reorganization energy for nine elementary steps involved in the initial photoreduction of class II Arabidopsis thaliana photolyase (AtPL), thereby constructing the photoreduction network specific to class II PLs. Several dynamic features have been revealed including a slow-rise (172 ps) and fast-decay (26 ps) kinetics between the excited lumiflavin and adenine groups within the flavin adenine dinucleotide cofactor, a slower electron transfer (ET) (22 ps) between the excited lumiflavin and the nearest Trp in the Trp triad (Wa) as compared to reported class I PL (0.8 ps), and a rapid deprotonation of the distal Trp in the Trp triad (Wc). Most strikingly, we captured a slightly energetically unfavorable ET step between Wa and the center Trp (Wb), as opposed to the decreasing reduction potential observed in class I PL that drives the electron flow unidirectionally. Such an energetically uphill ET step leads to a lower photoreduction quantum yield (~34%) in class II AtPL compared to that of class I PL (~45%), raising an important question on the evolutionary implications of various photoreduction networks in photolyases and cryptochromes.

Hole Transfer and the Resulting DNA Damage

In this review, we focus on the one-electron oxidation of DNA, which is a multipart event controlled by several competing factors. We will discuss the oxidation free energies of the four nucleobases and the electron detachment from DNA, influenced by specific interactions like hydrogen bonding and stacking interactions with neighboring sites in the double strand. The formation of a radical cation (hole) which can migrate through DNA (hole transport), depending on the sequence-specific effects and the allocation of the final oxidative damage, is also addressed. Particular attention is given to the one-electron oxidation of ds-ODN containing G:C pairs, including the complex mechanism of the deprotonation vs. hydration steps of a G:C•+ pair, as well as to the modes of formation of the two guanyl radical tautomers after deprotonation. Among the reactive oxygen species (ROS) generated in aerobic organisms by cellular metabolisms, several oxidants react with DNA. The mechanism of stable product formation and their use as biomarkers of guanine oxidation in DNA damage are also addressed.

Ultrafast Cycloreversion of Thymine-Toluene [2 + 2] Cycloadducts by DNA Photolyase

DNA photolyases use blue light and fully reduced flavin cofactor to repair UV-induced cyclobutane pyrimidine dimers (CPD) formed between two adjacent thymine bases in DNA. Thymine can form [2 + 2] cyclobutane adducts with its biological isosteres like toluene upon UV irradiation, resulting in chemically different analogues of CPD. Here, we investigated the cycloreversion reactions of two such adducts formed between thymine and toluene, T<>Tol, catalyzed by a class-I CPD photolyase. The photolyase can bind to the T<>Tol adducts efficiently and restore the constituent bases upon excitation. Using femtosecond spectroscopy, we systematically characterized all the elementary steps involved in the enzymatic cycloreversion of the T<>Tol adducts and comprehensively analyzed the key intermolecular electron-transfer (ET) reactions and cyclobutane bond splitting steps. The initial electron injection to the bound adducts happens primarily through a two-step electron hopping mechanism, unlike in CPD repair where direct electron tunneling is dominant. After electron injection and ultrafast first-bond splitting, the delicate competition between the second bond splitting and a futile back ET dictates the overall reaction quantum yields of the adducts, influenced by the stability of adduct intermediates and steric crowding around the constituent bases. The final electron return for the cycloreversion reactions adopts a different pathway compared to CPD repair. The photolyase utilizes its conserved photorepair mechanism and allows ET pathway flexibility to reverse the [2 + 2] cycloaddition reaction of non-natural analogues of CPD.

2D Titanium Carbide MXene and Single-Molecule Fluorescence: Distance-Dependent Nonradiative Energy Transfer and Leaflet-Resolved Dye Sensing in Lipid Bilayers

Despite their growing popularity, many fundamental properties and applications of MXene materials remain underexplored. Here, the nonradiative energy transfer properties of 2D titanium carbide MXene are investigated and their application in single-molecule biosensing is explored for the first time. DNA origami positioners are used for single dye placement immobilized by a specific chemistry based on glycine-MXene interactions, allowing precise control of their orientation on the surface. Each DNA origami structure carries a single dye molecule at predetermined heights. Single-molecule fluorescence confocal microscopy reveals that energy transfer of an organic emitter (ATTO 542) on transparent thin films made of spincast Ti3C2Tx flakes follows a cubic distance dependence, where 50% of energy transfer efficiency is reached at 2.7 nm (d0). MXenes are applied as short-distance spectroscopic nanorulers, determining z distances of dye-labeled supported lipid bilayers fused on MXene's hydrophilic surface. Hydration layer (2.1 nm) and lipid bilayer thickness (4.5 nm) values that agree with the literature are obtained. These results highlight titanium carbide MXenes as promising substrates for single-molecule biosensing of ultrathin assemblies, owing to their sensitivity near the interface, a distance regime that is typically inaccessible to other energy transfer tools.

Quantum Chemical Insights into DNA Nucleobase Oxidation: Bridging Theory and Experiment

The oxidation free energies of DNA nucleobases in aqueous solution are still matter of extensive discussion because of the contrasting results reported so far. With the aim of settling a longstanding debate about the oxidation potentials of DNA constituents, herein we report the results of state-of-the-art DFT-based molecular dynamics simulations, in which the whole solvent environment is modeled at the atomistic level, by using DFT supercell calculations, with periodic boundary conditions. Calculated vertical ionization energies are very close to those observed by photoelectron spectroscopy both in the gas phase and in solution. One-electron oxidation free energies in aqueous solution agree well with the results of differential pulse voltammetry measurements and with those inferred by photoelectron spectroscopy with the aid of theoretical computations to estimate vibrational relaxation.

Binding of a Tricationic meso-Substituted Porphyrin to poly(A)⋅poly(U): an Experimental Study

The porphyrins are macrocyclic compounds widely used as photosensitizers in anticancer photodynamic therapy. The binding of a tricationic meso-tris(N-methylpyridinium)-porphyrin, TMPyP3+, to poly(A)⋅poly(U) polynucleotide has been studied in neutral buffered solution, pH6.9, of low and near-physiological ionic strength in a wide range of molar phosphate-to-dye ratios (P/D). Effective TMPyP3+ binding to the biopolymer was established using absorption spectroscopy, polarized fluorescence, fluorimetric titration and resonance light scattering. We propose a model in which TMPyP3+ binds to the polynucleotide in two competitive binding modes: at low P/D ratios (< 4) external binding of the porphyrin to polynucleotide backbone without self-stacking dominates, and at higher P/D (> 30) the partially stacked porphyrin J-dimers are embedded into the polymer groove. Enhancement of the porphyrin emission was observed upon binding in all P/D range, contrasting the binding of this porphyrin to poly(G)⋅poly(C) with significant quenching of the porphyrin fluorescence at low P/D ratios. This observation indicates that TMPyP3+ can discriminate between poly(A)⋅poly(U) and poly(G)⋅poly(C) polynucleotides at low P/D ratios. Formation of highly scattering extended porphyrin aggregates was observed near the stoichiometric in charge binding ratio, P/D = 3. It was revealed that the efficiency of the porphyrin external binding and aggregation is reduced in the solution of near-physiological ionic strength.

Exploiting G-Quadruplex-DNA Damage as a Tool to Quantify Singlet Oxygen Production

G-Quadruplexes (G4s) are highly dynamic and polymorphic nucleic acid structures that can adopt a variety of conformations. When exposed to oxidative conditions, more specifically singlet oxygen, the guanosine nucleobases can be oxidized, which in turn can affect the conformation and folding of the G4. Based on this peculiar phenomenon, it is rationalized that G4s can serve as quantification sensors for the production of singlet oxygen. Here, a method for determining the quantum yield of singlet oxygen generation for visible as well as UV-light excited photosensitizers, using a short G4 DNA sequence, readily available from common DNA companies, as a biological and water-soluble probe, is presented.

Live-Cell Imaging of MicroRNA Expression via Photoinduced Electron Transfer Controlled by Catalytic Hairpin Assembly

MicroRNAs (miRNAs) serve as emerging biomarkers for a range of diseases, and their quantitative analysis draws increasing attention. Yet, current invasive methods limit continuous tracking within living cells. To overcome this, a nonenzymatic DNA-based nanoprobe is developed for dynamic, noninvasive miRNA tracking via live-cell imaging. This probe features a unique hairpin DNA structure with five guanines that act as internal quenchers, suppressing fluorescence from an attached fluorophore via photoinduced electron transfer. Target miRNA initiates toehold-mediated strand displacement, restoring, and amplifying the fluorescence signal. Additionally, by introducing a single mismatch to the hairpin DNA, the nanoprobe's sensitivity is significantly enhanced, lowering the detection limit to about 60 pM without compromising specificity. To optimize intracellular delivery for prolonged monitoring, the nanoprobe is encapsulated within multilamellar lipid nanovesicles, fluorescently labeled for dual-wavelength ratiometric analysis. The proposed nanoprobe demonstrates a significant advance in live-cell miRNA detection, promising enhanced in situ analysis for a better understanding of miRNAs' pathophysiological function.

Dark times: iminothioindoxyl-C-nucleoside fluorescence quenchers with defined location and minimal perturbation in DNA

Fluorescence quenchers for application in DNA - like the BHQ family - tend to be large molecules which need to be attached, often post-synthetically, via long linkers. In this study, we present two new iminothioindoxyl-C-nucleosidic quenchers which are very compact, feature a native backbone and can be introduced into DNA via regular solid-phase synthesis. Especially with dT as juxtaposed nucleobase, they have a defined location and orientation in a DNA duplex with minimal perturbation of the structure and hence interaction capabilities. Depending on the nature of the fluorophore, they can be used for orientation-(un)specific FRET studies. Their Förster radius is smaller than the one of BHQ-2. This makes these quenchers ideal for sophisticated studies using conditional quenching in the range between 470 and 670 nm in DNA.

Generic Reporter Sets for Colorimetric Multiplex dPCR Demonstrated with 6-Plex SNP Quantification Panels

Digital PCR (dPCR) is a powerful method for highly sensitive and precise quantification of nucleic acids. However, designing and optimizing new multiplex dPCR assays using target sequence specific probes remains cumbersome, since fluorescent signals must be optimized for every new target panel. As a solution, we established a generic fluorogenic 6-plex reporter set, based on mediator probe technology, that decouples target detection from signal generation. This generic reporter set is compatible with different target panels and thus provides already optimized fluorescence signals from the start of new assay development. Generic reporters showed high population separability in a colorimetric 6-plex mediator probe dPCR, due to their tailored fluorophore and quencher selection. These reporters were further tested using different KRAS, NRAS and BRAF single-nucleotide polymorphisms (SNP), which are frequent point mutation targets in liquid biopsy. We specifically quantified SNP targets in our multiplex approach down to 0.4 copies per microliter (cp/µL) reaction mix, equaling 10 copies per reaction, on a wild-type background of 400 cp/µL for each, equaling 0.1% variant allele frequencies. We also demonstrated the design of an alternative generic reporter set from scratch in order to give detailed step-by-step guidance on how to systematically establish and optimize novel generic reporter sets. Those generic reporter sets can be customized for various digital PCR platforms or target panels with different degrees of multiplexing.

Single-molecule fluorescence multiplexing by multi-parameter spectroscopic detection of nanostructured FRET labels

Multiplexed, real-time fluorescence detection at the single-molecule level can reveal the stoichiometry, dynamics and interactions of multiple molecular species in mixtures and other complex samples. However, fluorescence-based sensing is typically limited to the detection of just 3-4 colours at a time due to low signal-to-noise ratio, high spectral overlap and the need to maintain the chemical compatibility of dyes. Here we engineered a palette of several dozen composite fluorescent labels, called FRETfluors, for multiplexed spectroscopic measurements at the single-molecule level. FRETfluors are compact nanostructures constructed from three chemical components (DNA, Cy3 and Cy5) with tunable spectroscopic properties due to variations in geometry, fluorophore attachment chemistry and DNA sequence. We demonstrate FRETfluor labelling and detection for low-concentration (<100 fM) mixtures of mRNA, dsDNA and proteins using an anti-Brownian electrokinetic trap. In addition to identifying the unique spectroscopic signature of each FRETfluor, this trap differentiates FRETfluors attached to a target from unbound FRETfluors, enabling wash-free sensing. Although usually considered an undesirable complication of fluorescence, here the inherent sensitivity of fluorophores to the local physicochemical environment provides a new design axis complementary to changing the FRET efficiency. As a result, the number of distinguishable FRETfluor labels can be combinatorically increased while chemical compatibility is maintained, expanding prospects for spectroscopic multiplexing at the single-molecule level using a minimal set of chemical building blocks.

Charge Transfer Mechanism in Guanine-Based Self-Assembled Monolayers on a Gold Surface

In this work, we have theoretically determined the one-electron oxidation potentials and charge transfer mechanisms in complex systems based on a self-assembled monolayer of guanine molecules adsorbed on a gold surface through different organic linkers. Classical molecular dynamics simulations were carried out to sample the conformational space of both the neutral and the cationic species. Thus, the redox potentials were determined for the ensembles of geometries through multiscale quantum-mechanics/molecular-mechanics/continuum solvation model calculations in the framework of the Marcus theory and in combination with an additive scheme previously developed. In this context, conformational sampling, description of the environment, and effects caused by the linker have been considered. Applying this methodology, we unravel the phenomena of electric current transport by evaluating the different stages in which charge transfer could occur. The results revealed how the positive charge migrates from the organic layer to the gold surface. Specifically, the transport mechanism seems to take place mainly along a single ligand and driven with the help of the electrostatic interactions of the surrounding molecules. Aside, several self-assembled monolayers with different linkers have been analyzed to understand how the nature of that moiety can tune the redox properties and the efficiency of the transport. We have found that the conjugation between the guanine and the linker, at the same time conjugated to the gold surface, gives rise to a more efficient transport. In conclusion, the established computational protocol sheds light on the mechanism behind charge transport in electrochemical DNA-based biosensor nanodevices.

Molecular Insights into the Conformational and Binding Behaviors of Human Serum Albumin Induced by Surface-Active Ionic Liquids

Extensive research has been carried out to investigate the stability and function of human serum albumin (HSA) when exposed to surface-active ionic liquids (SAILs) with different head groups (imidazolium, morpholinium, and pyridinium) and alkyl chain lengths (ranging from decyl to tetradecyl). Analysis of the protein fluorescence spectra indicates noticeable changes in the secondary structure of HSA with varying concentrations of all SAILs tested. Helicity calculations based on the Fourier transform infrared (FTIR) data show that HSA becomes more organized at the micellar concentration of SAILs, leading to an increased protein activity at this level. Small-angle neutron scattering (SANS) data confirm the formation of a bead-necklace structure between the SAILs and HSA. Atomistic molecular dynamics (MD) simulation results identify several hotspots on the protein surface for interaction with SAIL, which results in the modulation of protein conformational fluctuation and stability. Furthermore, fluorescence resonance energy transfer (FRET) experiments with the intramolecular charge transfer (ICT) probe trans-ethyl p-(dimethylamino) cinnamate (EDAC) demonstrate that higher alkyl chain lengths and SAIL concentrations result in a significantly increased energy transfer efficiency. The findings of this study provide a detailed molecular-level understanding of how the protein structure and function are affected by the presence of SAILs, with potential implications for a wide range of applications involving protein-SAIL composite systems.

Modeling One-Electron Oxidation Potentials and Hole Delocalization in Double-Stranded DNA by Multilayer and Dynamic Approaches

The number of innovative applications for DNA nowadays is growing quickly. Its use as a nanowire or electrochemical biosensor leads to the need for a deep understanding of the charge-transfer process along the strand, as well as its redox properties. These features are computationally simulated and analyzed in detail throughout this work by combining molecular dynamics, multilayer schemes, and the Marcus theory. One-electron oxidation potential and hole delocalization have been analyzed for six DNA double strands that cover all possible binary combinations of nucleotides. The results have revealed that the one-electron oxidation potential decreases with respect to the single-stranded DNA, giving evidence that the greater rigidity of a double helix induces an increase in the capacity of storing the positive charge generated upon oxidation. In addition, the hole is mainly stored in nucleobases with large reducer character, i.e., purines, especially when those are arranged in a stacked configuration in the same strand. From the computational point of view, the sampling needed to describe biological systems implies a significant computational cost. Here, we show that a small number of representative conformations generated by clustering analysis provides accurate results when compared with those obtained from sampling, reducing considerably the computational cost.

Unveiling the Antioxidative Potential of Galangin: Complete and Detailed Mechanistic Insights through Density Functional Theory Studies

A comprehensive quantum mechanical investigation delved into the antioxidative activity of galangin (Glg). Thermochemical and kinetic data were used to assess antiradical, chelating, and renewal potential under physiological conditions. A brief comparison with reference antioxidants and other flavonoids characterized Glg as a moderate antioxidative agent. The substance showed significantly lower performance in lipid compared to aqueous solvent─the reaction rates for scavenging •OOH in both media were established at 3.77 × 103 M-1 s-1 and 6.21 × 104 M-1 s-1, respectively, accounting for the molar fraction of both interacting molecules at the given pH. The impact of pH value on the kinetics was assessed. Although efficient at chelating Cu(II) ions, the formed complexes can still undergo the Fenton reaction. On the other hand, they persistently scavenge •OH in statu nascendi. The flavonoid effectively repairs oxidatively damaged biomolecules except model lipid acids. All Glg radicals are readily restored by physiologically prevailing O2•-. Given this, the polyphenol is expected to participate in antiradical and regenerating activities multiple times, amplifying its antioxidative potential.

Exploring enzyme inhibition and comprehensive mechanisms of antioxidant/prooxidative activity of natural furanocoumarin derivatives: A comparative kinetic DFT study

This study aimed to explore the antioxidant and prooxidative activity of two natural furanocoumarin derivatives, Bergaptol (4-Hydroxy-7H-furo [3,2-g] [1]benzopyran-7-one, BER) and Xanthotoxol (9-Hydroxy-7H-furo [3,2-g] [1]benzopyran-7-one, XAN). The collected thermodynamic and kinetic data demonstrate that both compounds possess substantial antiradical activity against HO• and CCl3OO• radicals in physiological conditions. BER exhibited better antiradical activity in comparison to XAN, which can be attributed to the enhanced deprotonation caused by the positioning of the -OH group on the psoralen ring. In contrast to highly reactive radical species, newly formed radical species BER• and XAN• exhibited negligible reactivity towards the chosen constitutive elements of macromolecules (fatty acids, amino acids, nucleobases). Furthermore, in the presence of O2•─, the ability to regenerate newly formed radicals BER• and XAN• was observed. Conversely, in physiological conditions in the presence of Cu(II) ions, both compounds exhibit prooxidative activity. Nevertheless, the prooxidative activity of both compounds is less prominent than their antioxidant activity. Furthermore, it has been demonstrated that anionic species can engage in the creation of a chelate complex, which restricts the reduction of metal ions when reducing agents are present (O2•─ and Asc─). Moreover, studies have demonstrated that these chelating complexes can be coupled with other radical species, hence enhancing their ability to inactivate radicals. Both compounds exhibited substantial inhibitory effects against enzymes involved in the direct or indirect generation of ROS: Xanthine Oxidase (XOD), Lipoxygenase (LOX), Myeloperoxidase (MPO), NADPH oxidase (NOX).

Recognition of 8-Oxo-2'-deoxyguanosine in DNA Using the Triphosphate of 2'-Deoxycytidine Connecting the 1,3-Diazaphenoxazine Unit, dCdapTP

DNA is constantly damaged by various external and internal factors. In particular, oxidative damage occurs in a steady state, and 8-oxo-2'-deoxyguanosine (oxodG) is known as the main oxidative damage. OxodG is a strong genotoxic nucleoside and is thought to be involved in the pathogenesis of cancer and neurological diseases. However, a breakthrough method to detect the position of oxodG in DNA has not yet been developed. Therefore, we attempted to develop a novel method to detect oxodG in DNA using artificial nucleosides. Recently, we have succeeded in the recognition of oxodG in DNA by a single nucleotide elongation reaction using nucleoside derivatives based on a purine skeleton with a 1,3-diazaphenoxazine unit. In this study, we developed a new nucleoside derivative with a pyrimidine skeleton in order to further improve the recognition ability and enzymatic reaction efficiency. We, therefore, designed and synthesized 2'-deoxycytidine-1,3-diazaphenoxazine (Cdap) and its triphosphate derivatives. The results showed that it was incorporated into the primer strand relative to the dG template because of its cytidine skeleton, but it was more effective at the complementary position of the oxodG template. These results indicate that the new nucleoside derivative can be considered as one of the new candidates for the detection of oxodG in DNA.

A Two-color Single-molecule Sequencing Platform and Its Clinical Applications

DNA sequencers have become increasingly important research and diagnostic tools over the past 20 years. In this study, we developed a single-molecule desktop sequencer, GenoCare 1600 (GenoCare), which utilizes amplification-free library preparation and two-color sequencing-by-synthesis chemistry, making it more user-friendly compared with previous single-molecule sequencing platforms for clinical use. Using the GenoCare platform, we sequenced an Escherichia coli standard sample and achieved a consensus accuracy exceeding 99.99%. We also evaluated the sequencing performance of this platform in microbial mixtures and coronavirus disease 2019 (COVID-19) samples from throat swabs. Our findings indicate that the GenoCare platform allows for microbial quantitation, sensitive identification of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, and accurate detection of virus mutations, as confirmed by Sanger sequencing, demonstrating its remarkable potential in clinical application.

Chemical Repair of Radical Damage to the GC Base Pair by DNA-Bound Bisbenzimidazoles

The migration of an electron-loss center (hole) in calf thymus DNA to bisbenzimidazole ligands bound in the minor groove is followed by pulse radiolysis combined with time-resolved spectrophotometry. The initially observed absorption spectrum upon oxidation of DNA by the selenite radical is consistent with spin on cytosine (C), as the GC• pair neutral radical, followed by the spectra of oxidized ligands. The rate of oxidation of bound ligands increased with an increase in the ratio (r) ligands per base pair from 0.005 to 0.04. Both the rate of ligand oxidation and the estimated range of hole transfer (up to 30 DNA base pairs) decrease with the decrease in one-electron reduction potential between the GC• pair neutral radical of ca. 1.54 V and that of the ligand radicals (E0', 0.90-0.99 V). Linear plots of log of the rate of hole transfer versus r give a common intercept at r = 0 and a free energy change of 12.2 ± 0.3 kcal mol-1, ascribed to the GC• pair neutral radical undergoing a structural change, which is in competition to the observed hole transfer along DNA. The rate of hole transfer to the ligands at distance, R, from the GC• pair radical, k2, is described by the relationship k2 = k0 exp(constant/R), where k0 includes the rate constant for surmounting a small barrier.

Iridium(III)-based minor groove binding complexes as DNA photocleavage agents

Transition metal complexes containing the qtpy ligand (2':4,4'':4',4'''-quaterpyridyl) are known to be DNA intercalators or minor groove binders. In this study, new tricationic iridium(III) complexes of qtpy are reported. Both [Ir(bpy)2(qtpy)]3+1 and [Ir(phen)2(qtpy)]3+2 display good water solubility as chloride salts. The complexes possess high-energy excited states, which are quenched in the presence of duplex DNA and even by the mononucleotides guanosine monophosphate and adenosine monophosphate. Further studies reveal that although the complexes bind to quadruplex DNA, they display a preference for duplex structures, which are bound with an order of magnitude higher affinities than their isostructural dicationic RuII-analogues. Detailed molecular dynamics simulations confirm that the complexes are groove binders through the insertion of, predominantly, the qtpy ligand into the minor groove. Photoirradiation of 1 in the presence of plasmid DNA confirms that this class of complexes can function as synthetic photonucleases by cleaving DNA.

Oxidative DNA damage on the VEGF G-quadruplex forming promoter is repaired via long-patch BER

In response to oxidative damage, base excision repair (BER) enzymes perturb the structural equilibrium of the VEGF promoter between B-form and G4 DNA conformations, resulting in epigenetic-like modifications of gene expression. However, the mechanistic details remain enigmatic, including the activity and coordination of BER enzymes on the damaged G4 promoter. To address this, we investigated the ability of each BER factor to conduct its repair activity on VEGF promoter G4 DNA substrates by employing pre-steady-state kinetics assays and in vitro coupled BER assays. OGG1 was able to initiate BER on double-stranded VEGF promoter G4 DNA substrates. Moreover, pre-steady-state kinetics revealed that compared to B-form DNA, APE1 repair activity on the G4 was decreased ~two-fold and is the result of slower product release as opposed to inefficient strand cleavage. Interestingly, Pol β performs multiple insertions on G4 substrates via strand displacement DNA synthesis in contrast to a single insertion on B-form DNA. The multiple insertions inhibit ligation of the Pol β products, and hence BER is not completed on the VEGF G4 promoter substrates through canonical short-patch BER. Instead, repair requires the long-patch BER flap-endonuclease activity of FEN1 in response to the multiple insertions by Pol β prior to ligation. Because the BER proteins and their repair activities are a key part of the VEGF transcriptional enhancement in response to oxidative DNA damage of the G4 VEGF promoter, the new insights reported here on BER activity in the context of this promoter are relevant toward understanding the mechanism of transcriptional regulation.

Spectroscopic view on the interaction between the psoralen derivative amotosalen and DNA

Psoralens are eponymous for PUVA (psoralen plus UV-A radiation) therapy, which inter alia can be used to treat various skin diseases. Based on the same underlying mechanism of action, the synthetic psoralen amotosalen (AMO) is utilized in the pathogen reduction technology of the INTERCEPT® Blood System to inactivate pathogens in plasma and platelet components. The photophysical behavior of AMO in the absence of DNA is remarkably similar to that of the recently studied psoralen 4'-aminomethyl-4,5',8-trimethylpsoralen (AMT). By means of steady-state and time-resolved spectroscopy, intercalation and photochemistry of AMO and synthetic DNA were studied. AMO intercalates with a higher affinity into A,T-only DNA (KD = 8.9 × 10-5 M) than into G,C-only DNA (KD = 6.9 × 10-4 M). AMO covalently photobinds to A,T-only DNA with a reaction quantum yield of ΦR = 0.11. Like AMT, it does not photoreact following intercalation into G,C-only DNA. Femto- and nanosecond transient absorption spectroscopy reveals the characteristic pattern of photobinding to A,T-only DNA. For AMO and G,C-only DNA, signatures of a photoinduced electron transfer are recorded.

Ultrafast spectroscopy study of DNA photophysics after proflavine intercalation

Proflavine (PF), an acridine DNA intercalating agent, has been widespread applied as an anti-microbial and topical antiseptic agent due to its ability to suppress DNA replication. On the other hand, various studies show that PF intercalation to DNA can increase photogenotoxicity and has potential chances to induce carcinomas of skin appendages. However, the effects of PF intercalation on the photophysical and photochemical properties of DNA have not been sufficiently explored. In this study, the excited state dynamics of the PF intercalated d(GC)9 • d(GC)9 and d(AT)9 • d(AT)9 DNA duplex are investigated in an aqueous buffer solution. Under 267 nm excitation, we observed ultrafast charge transfer (CT) between PF and d(GC)9 • d(GC)9 duplex, generating a CT state with an order of magnitude longer lifetime compared to that of the intrinsic excited state reported for the d(GC)9 • d(GC)9 duplex. In contrast, no excited state interaction was detected between PF and d(AT)9 • d(AT)9. Nevertheless, a localized triplet state with a lifetime over 5 µs was identified in the PF-d(AT)9 • d(AT)9 duplex.

Mechanistic Aspects of Photodegradation of Deoxynucleosides Induced by Triplet State of Effluent Organic Matter

Excited triplet states of wastewater effluent organic matter (3EfOM*) are known as important photo-oxidants in the degradation of extracellular antibiotic resistance genes (eArGs) in sunlit waters. In this work, we further found that 3EfOM* showed highly selective reactivity toward 2'-deoxyguanosine (dG) sites within eArGs in irradiated EfOM solutions at pH 7.0, while it showed no photosensitizing capacity toward 2'-deoxyadenosine, 2'-deoxythymidine, and 2'-deoxycytidine (the basic structures of eArGs). The 3EfOM* contributed to the photooxidation of dG primarily via one-electron transfer mechanism, with second-order reaction rate constants of (1.58-1.74) × 108 M-1 s-1, forming the oxidation intermediates of dG (dG(-H)•). The formed dG(-H)• could play a significant role in hole hopping and damage throughout eArGs. Using the four deoxynucleosides as probes, the upper limit for the reduction potential of 3EfOM* is estimated to be between 1.47 and 1.94 VNHE. Compared to EfOM, the role of the triplet state of terrestrially natural organic matter (3NOM*) in dG photooxidation was minor (∼15%) mainly due to the rapid reverse reactions of dG(-H)• by the antioxidant moieties of NOM. This study advances our understanding of the difference in the photosensitizing capacity and electron donating capacity between NOM and EfOM and the photodegradation mechanism of eArGs induced by 3EfOM*.

Exploring the impact of novel thiazole-pyrazole fused benzo-coumarin derivatives on human serum albumin: Synthesis, photophysical properties, anti-cholinergic activity, and interaction studies

Derivatives of thiazole-pyrazole fused benzo-coumarin compounds were successfully synthesized and characterized, followed by a comprehensive spectroscopic investigation on various photophysical properties in different media. The multipronged approach using steady state and time resolved fluorescence spectroscopy pointed out the impact of substitution in the estimated spectroscopic and other physicochemical properties of the systems. Further, the evaluation of anti-acetylcholinesterase (anti-AChE) activity yielded significant insight into the therapeutic potential of the synthesized coumarinyl compounds for the treatment of Alzheimer's disease (AD). The findings revealed a non-competitive mode of inhibition mechanism, with an estimated IC50 value of 67.72 ± 2.00 nM observed for one of the investigated systems as AChE inhibitor. Notably, this value is even lower than that of an FDA-approved AD drug Donepezil (DON), indicating the enhanced potency of the coumarin derivatives in inhibiting AChE. Interestingly, significant diminution in inhibition was observed in presence of human serum albumin (HSA) as evidenced by the relative increase in IC50 value by 8 ∼ 39 % in different cases, which emphasized the role of albumin proteins to control therapeutic efficacies of potential medications. In-depth spectroscopic and in-silico analysis quantified the nature of interactions of the investigated systems with HSA and AChE. Overall, the outcomes of this study provide significant understanding into the biophysical characteristics of novel thiazole-pyrazole fused benzo-coumarin systems, which could aid in the development of new cholinergic agents for the treatment of AD and materials based on coumarin motifs.

Endoplasmic Reticulum-Targeting Quinazolinone-Based Lipophilic Probe for Specific Photoinduced Ferroptosis and Its Induced Lipid Dynamic Regulation

Lethal lipid peroxidation caused by reactive oxygen species occurs in different types of programmed cell death, especially in ferroptosis. Ferroptosis inducers, which serve as small-molecule probes, can provide insight into the mechanism of ferroptosis and facilitate drug discovery. The classical ferroptosis inducers indirectly lead to lipid peroxidation; thus, it is difficult to explore lipid regulation during the ferroptotic process. In this study, we designed two quinazolinone-based lipophilic probes BODIQPy-TPA and QPy-TPA, which proved to directly induce lipid peroxidation by light irradiation in vitro. The probe BODIQPy-TPA, which was mainly distributed in the endoplasmic reticulum (ER), specifically triggered ferroptosis in B16 and HepG2 cells upon light irradiation. As a comparison, the probe QPy-TPA, which was mainly distributed in lipid droplets (LDs), induced cell death by a nonferroptotic pathway. Further lipidomic analysis revealed that these two probes caused different patterns of lipid regulation and lipid peroxidation, suggesting that ferroptosis might activate distinct lipid regulation.

Action-at-a-distance mutations induced by 8-oxo-7,8-dihydroguanine are dependent on APOBEC3

DNA oxidation is a serious threat to genome integrity and is involved in mutations and cancer initiation. The G base is most frequently damaged, and 8-oxo-7,8-dihydroguanine (GO, 8-hydroxyguanine) is one of the predominant damaged bases. In human cells, GO causes a G:C→T:A transversion mutation at the modified site, and also induces untargeted substitution mutations at the G bases of 5'-GpA-3' dinucleotides (action-at-a-distance mutations). The 5'-GpA-3' sequences are complementary to the 5'-TpC-3' sequences, the preferred substrates for apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3 (APOBEC3) cytosine deaminases, and thus their contribution to mutagenesis has been considered. In this study, APOBEC3B, the most abundant APOBEC3 protein in human U2OS cells, was knocked down in human U2OS cells, and a GO-shuttle plasmid was then transfected into the cells. The action-at-a-distance mutations were reduced to ~25% by the knockdown, indicating that GO-induced action-at-a-distance mutations are highly dependent on APOBEC3B in this cell line.

Inhibition of Uracil DNA Glycosylase Alters Frequency and Spectrum of Action-at-a-Distance Mutations Induced by 8-Oxo-7,8-dihydroguanine

The generation of DNA damage causes mutations and consequently cancer. Reactive oxygen species are important sources of DNA damage and some mutation signatures found in human cancers. 8-Oxo-7,8-dihydroguanine (GO, 8-hydroxyguanine) is one of the most abundant oxidized bases and induces a G→T transversion mutation at the modified site. The damaged G base also causes untargeted base substitution mutations at the G bases of 5'-GpA-3' dinucleotides (action-at-a-distance mutations) in human cells, and the cytosine deaminase apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3 (APOBEC3) is involved in the mutation process. The deaminated cytosine, i.e., uracil, bases are expected to be removed by uracil DNA glycosylase. Most of the substitution mutations at the G bases of 5'-GpA-3' might be caused by abasic sites formed by the glycosylase. In this study, we expressed the uracil DNA glycosylase inhibitor from Bacillus subtilis bacteriophage PBS2 in human U2OS cells and examined the effects on the GO-induced action-at-a-distance mutations. The inhibition of uracil DNA glycosylase increased the mutation frequency, and in particular, the frequency of G→A transitions. These results indicated that uracil DNA glycosylase, in addition to APOBEC3, is involved in the untargeted mutation process induced by GO.

Chimeric GFP-uracil based molecular rotor fluorophores

Uracil has been modified at the 5-position to derive a small library of nucleobase-chromophores which were inspired by green fluorescent protein (GFP). The key steps in the syntheses were Erlenmeyer azlactone synthesis followed by amination by use of hexamethyl disilazane (HMDS) to produce the imidazolinone derivatives. The uracil analogues displayed emission in the green region of visible spectrum and exhibited microenvironmental sensitivity exemplified by polarity-based solvatochromism and viscosity-dependent emission enhancement. Solid-state quantum yields of approximately 0.2 and solvent dependent emission wavelengths beyond 500 nm were observed. Select analogues were incorporated into peptide nucleic acid (PNA) strands which upon duplex formation with DNA showed good response ranging from a turn-off of fluorescence in presence of an opposing mismatched residue to a greater than 3-fold turn-on of fluorescence upon binding to fully complementary DNA strand.

Time-resolved crystallography captures light-driven DNA repair

Photolyase is an enzyme that uses light to catalyze DNA repair. To capture the reaction intermediates involved in the enzyme's catalytic cycle, we conducted a time-resolved crystallography experiment. We found that photolyase traps the excited state of the active cofactor, flavin adenine dinucleotide (FAD), in a highly bent geometry. This excited state performs electron transfer to damaged DNA, inducing repair. We show that the repair reaction, which involves the lysis of two covalent bonds, occurs through a single-bond intermediate. The transformation of the substrate into product crowds the active site and disrupts hydrogen bonds with the enzyme, resulting in stepwise product release, with the 3' thymine ejected first, followed by the 5' base.

Fluorescence Quenching Dynamics of 2-Amino-7-methyl-1,8-naphthyridine in Abasic-Site-Containing DNA Duplexes for Nucleobase Recognition

Dramatic fluorescence quenching of small heterocyclic ligands trapped in the abasic site (AP) of DNA has been implemented as an unprecedented strategy recognizing single-base mutations in sequence analysis of cancer genes. However, the key mechanisms governing selective nucleobase recognition remain to be disentangled. Herein, we perform fluorescence quenching dynamics studies for 2-amino-7-methyl-1,8-naphthyridine (AMND) in well-designed AP-containing DNA single/double strands. The primary mechanism is discovered, showing that AMND only targets cytosine to form a pseudo-base pair, and therefore, fluorescence quenching of AMND arises through the DNA-mediated electron transfer (ET) between excited state AMND* and flanking nucleobases, most favorably with flanking guanines. Subtle dynamic conformational variations induced by different flanking nucleobases are revealed and found to modulate efficiencies of electron transfer and fluorescence quenching. These findings provide critical mechanistic insights for guiding the design of photoinduced electron transfer (PET)-based fluorescent ligands as sensitive single-base recognition reporters.

Redox-Based Defect Detection in Packed DNA: Insights from Hybrid Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations

The impact of an 8-oxoguanine (8oxoG) defect on the redox properties of DNA within the nucleosome core particle (NCP) was investigated employing hybrid quantum mechanical/molecular mechanics (QM/MM) molecular dynamics simulations of native and 8oxoG-containing NCP systems with an explicit representation of a biologically relevant environment. Two distinct NCP positions with varying solvent accessibility were considered for 8oxoG insertion. In both cases, it is found that the presence of 8oxoG drastically decreases the redox free energy of oxidation by roughly 1 eV, which is very similar to what was recently reported for free native and 8oxoG-containing DNA. In contrast, the effect of 8oxoG on the reorganization free energy is even smaller for packed DNA (decrease of 0.13 and 0.01 eV for defect-free and defect-containing systems, respectively) compared to the one for free DNA (0.25 eV), consistent with the increased rigidity of the NCP as compared to free DNA. Furthermore, the presence of an 8oxoG defect does not yield any significant changes in the packed DNA structure. Such a conclusion favors the idea that in the case of chromatin, defect-induced changes in DNA redox chemistry can also be exploited to detect damaged bases via DNA-mediated hole transfer.

One-Electron Oxidation Potentials and Hole Delocalization in Heterogeneous Single-Stranded DNA

The study of DNA processes is essential to understand not only its intrinsic biological functions but also its role in many innovative applications. The use of DNA as a nanowire or electrochemical biosensor leads to the need for a deep investigation of the charge transfer process along the strand as well as of the redox properties. In this contribution, the one-electron oxidation potential and the charge delocalization of the hole formed after oxidation are computationally investigated for different heterogeneous single-stranded DNA strands. We have established a two-step protocol: (i) molecular dynamics simulations in the frame of quantum mechanics/molecular mechanics (QM/MM) were performed to sample the conformational space; (ii) energetic properties were then obtained within a QM1/QM2/continuum approach in combination with the Marcus theory over an ensemble of selected geometries. The results reveal that the one-electron oxidation potential in the heterogeneous strands can be seen as a linear combination of that property within the homogeneous strands. In addition, the hole delocalization between different nucleobases is, in general, small, supporting the conclusion of a hopping mechanism for charge transport along the strands. However, charge delocalization becomes more important, and so does the tunneling mechanism contribution, when the reducing power of the nucleobases forming the strand is similar. Moreover, charge delocalization is slightly enhanced when there is a correlation between pairs of some of the interbase coordinates of the strand: twist/shift, twist/slide, shift/slide, and rise/tilt. However, the internal structure of the strand is not the predominant factor for hole delocalization but the specific sequence of nucleotides that compose the strand.

Pursuing excitonic energy transfer with programmable DNA-based optical breadboards

DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.

A Photochemical Study of Photo-Induced Electron Transfer from DNAs to a Cationic Phthalocyanine Derivative

Water-soluble cationic gallium(III)-Pc complex (GaPc) is capable of photogenerating ROSs but does not exhibit photocytotoxicity in vivo. GaPc binds selectively, through a π-π stacking interaction, to the 5'-terminal G-quartet of a G-quadruplex DNA. The photo-excited state of GaPc of the complex is effectively quenched through electron transfer (ET) from the ground state of DNA guanine (G) bases to the photo-excited state of GaPc (ET(G-GaPc)). Hence the loss of the photocytotoxicity of GaPc in vivo is most likely to be due to the effective quenching of its photo-excited state through ET(G-GaPc). In this study, we investigated the photochemical properties of GaPc in the presence of duplex DNAs formed from a series of sequences to elucidate the nature of ET(G-GaPc). We found that ET(G-GaPc) is allowed in electrostatic complexes between GaPc and G-containing duplex DNAs and that the rate of ET(G-GaPc) (kET(G-GaPc)) can be reasonably interpreted in terms of the distance between Pc moiety of GaPc and DNA G base in the complex. We also found that the quantum yields of singlet oxygen (1O2) generation (ΦΔs) determined for the GaPc-duplex DNA complexes were similar to the value reported for free GaPc (Fujishiro R, Sonoyama H, Ide Y, et al (2019) J Inorg Biochem 192:7-16), indicating that ET(G-GaPc) in the complex is rather limited. These results clearly demonstrated that photocytotoxicity of GaPc is crucially affected by ET(G-GaPc). Thus elucidation of interaction of a photosensitizer with biomolecules, i.e., an initial process in PDT, would be helpful to understand its subsequent photochemical processes.

Synthesis of tertiary alkylphosphonate oligonucleotides through light-driven radical-polar crossover reactions

Chemical modification of nucleotides can improve the metabolic stability and target specificity of oligonucleotide therapeutics, and alkylphosphonates have been employed as charge-neutral replacements for naturally-occurring phosphodiester backbones in these compounds. However, at present, the alkyl moieties that can be attached to phosphorus atoms in these compounds are limited to methyl groups or primary/secondary alkyls, and such alkylphosphonate moieties can degrade during oligonucleotide synthesis. The present work demonstrates the tertiary alkylation of the phosphorus atoms of phosphites bearing two 2'-deoxynuclosides. This process utilizes a carbocation generated via a light-driven radical-polar crossover mechanism. This protocol provides tertiary alkylphosphonate structures that are difficult to synthesize using existing methods. The conversion of these species to oligonucleotides having charge-neutral alkylphosphonate linkages through a phosphoramidite-based approach was also confirmed in this study.

Exciton delocalization in a fully synthetic DNA-templated bacteriochlorin dimer

A bacteriochlorophyll a (Bchla) dimer is a basic functional unit in the LH1 and LH2 photosynthetic pigment-protein antenna complexes of purple bacteria, where an ordered, close arrangement of Bchla pigments-secured by noncovalent bonding to a protein template-enables exciton delocalization at room temperature. Stable and tunable synthetic analogs of this key photosynthetic subunit could lead to facile engineering of exciton-based systems such as in artificial photosynthesis, organic optoelectronics, and molecular quantum computing. Here, using a combination of synthesis and theory, we demonstrate that exciton delocalization can be achieved in a dimer of a synthetic bacteriochlorin (BC) featuring stability, high structural modularity, and spectral properties advantageous for exciton-based devices. The BC dimer was covalently templated by DNA, a stable and highly programmable scaffold. To achieve exciton delocalization in the absence of pigment-protein interactions critical for the Bchla dimer, we relied on the strong transition dipole moment in BC enabled by two auxochromes along the Qy transition, and omitting the central metal and isocyclic ring. The spectral properties of the synthetic "free" BC closely resembled those of Bchla in an organic solvent. Applying spectroscopic modeling, the exciton delocalization in the DNA-templated BC dimer was evaluated by extracting the excitonic hopping parameter, J to be 214 cm-1 (26.6 meV). For comparison, the same method applied to the natural protein-templated Bchla dimer yielded J of 286 cm-1 (35.5 meV). The smaller value of J in the BC dimer likely arose from the partial bacteriochlorin intercalation and the difference in medium effect between DNA and protein.

Endogenous Photosensitizers in Human Skin

Endogenous photosensitizers play a critical role in both beneficial and harmful light-induced transformations in biological systems. Understanding their mode of action is essential for advancing fields such as photomedicine, photoredox catalysis, environmental science, and the development of sun care products. This review offers a comprehensive analysis of endogenous photosensitizers in human skin, investigating the connections between their electronic excitation and the subsequent activation or damage of organic biomolecules. We gather the physicochemical and photochemical properties of key endogenous photosensitizers and examine the relationships between their chemical reactivity, location within the skin, and the primary biochemical events following solar radiation exposure, along with their influence on skin physiology and pathology. An important take-home message of this review is that photosensitization allows visible light and UV-A radiation to have large effects on skin. The analysis presented here unveils potential causes for the continuous increase in global skin cancer cases and emphasizes the limitations of current sun protection approaches.

Probing of DNA Photochemistry with C-Nucleosides of Xanthones and Triphenylene as Photosensitizers To Study the Formation of Cyclobutane Pyrimidine Dimers

The direct and sequence-dependent investigation of photochemical processes in DNA on the way to cyclobutane pyrimidine dimers (CPDs) as DNA damage requires the probing by photochemically different photosensitizers. The C-nucleosides of xanthone, thioxanthone, 3-methoxyxanthone, and triphenylene as photosensitizers were synthesized by Heck couplings and incorporated into ternary photoactive DNA architectures. This structural approach allows the site-selective excitation of the DNA by UV light. Together with a single defined site for T-T dimerization, not only the direct CPD formation but also the distance-dependent CPD formation in DNA as well as the possibility for energy transport processes could be investigated. Direct CPD formation was observed with xanthone, 3-methoxyxanthone, and triphenylene as sensitizers but not with thioxanthone. Only xanthone was able to induce CPDs remotely by a triplet energy transfer over up to six intervening A-T base pairs. Taken together, more precise information on the sequence dependence of the DNA triplet photochemistry was obtained.

Synthesis and Evaluation of Diguanosine Cap Analogs Modified at the C8-Position by Suzuki-Miyaura Cross-Coupling: Discovery of 7-Methylguanosine-Based Molecular Rotors

Chemical modifications of the mRNA cap structure can enhance the stability, translational properties, and half-life of mRNAs, thereby altering the therapeutic properties of synthetic mRNA. However, cap structure modification is challenging because of the instability of the 5'-5'-triphosphate bridge and N7-methylguanosine. The Suzuki-Miyaura cross-coupling reaction between boronic acid and halogen compound is a mild, convenient, and potentially applicable approach for modifying biomolecules. Herein, we describe two methods to synthesize C8-modified cap structures using the Suzuki-Miyaura cross-coupling reaction. Both methods employed phosphorimidazolide chemistry to form the 5',5'-triphosphate bridge. However, in the first method, the introduction of the modification via the Suzuki-Miyaura cross-coupling reaction at the C8 position occurs postsynthetically, at the dinucleotide level, whereas in the second method, the modification was introduced at the level of the nucleoside 5'-monophosphate, and later, the triphosphate bridge was formed. Both methods were successfully applied to incorporate six different groups (methyl, cyclopropyl, phenyl, 4-dimethylaminophenyl, 4-cyanophenyl, and 1-pyrene) into either the m⁷G or G moieties of the cap structure. Aromatic substituents at the C8-position of guanosine form a push-pull system that exhibits environment-sensitive fluorescence. We demonstrated that this phenomenon can be harnessed to study the interaction with cap-binding proteins, e.g., eIF4E, DcpS, Nudt16, and snurportin.

A Photoredox Reaction for the Selective Modification of 5-Carboxycytosine in DNA

Covalent epigenetic modifications contribute to the regulation of important cellular processes during development and differentiation, and changes in their genomic distribution and frequency are linked to the emergence of genetic disease states. Chemical and enzymatic methods that selectively target the orthogonal chemical functionality of epigenetic markers are central to the study of their distribution and function, and considerable research effort has been focused on the development of nondestructive sequencing approaches which preserve valuable DNA samples. Photoredox catalysis enables transformations with tunable chemoselectivity under mild, biocompatible reaction conditions. We report the reductive decarboxylation of 5-carboxycytosine via a novel iridium-based treatment, which represents the first application of visible-light photochemistry to epigenetic sequencing via direct base conversion. We propose that the reaction involves an oxidative quenching cycle beginning with single-electron reduction of the nucleobase by the photocatalyst, followed by hydrogen atom transfer from a thiol. The saturation of the C5-C6 backbone permits decarboxylation of the nonaromatic intermediate, and hydrolysis of the N4-amine constitutes a conversion from a cytosine derivative to a T-like base. This conversion demonstrates selectivity for 5-carboxycytosine over other canonical or modified nucleoside monomers, and is thereby applied to the sequencing of 5-carboxycytosine within modified oligonucleotides. The photochemistry explored in this study can also be used in conjunction with enzymatic oxidation by TET to profile 5-methylcytosine at single-base resolution. Compared to other base-conversion treatments, the rapid photochemical reaction takes place within minutes, which could provide advantages for high-throughput detection and diagnostic applications.

Intramolecular and intermolecular hole delocalization rules the reducer character of isolated nucleobases and homogeneous single-stranded DNA

The use of DNA strands as nanowires or electrochemical biosensors requires a deep understanding of charge transfer processes along the strand, as well as of the redox properties. These properties are computationally assessed in detail throughout this study. By applying molecular dynamics and hybrid QM/continuum and QM/QM/continuum schemes, the vertical ionization energies, adiabatic ionization energies, vertical attachment energies, one-electron oxidation potentials, and delocalization of the hole generated upon oxidation have been determined for nucleobases in their free form and as part of a pure single-stranded DNA. We show that the reducer ability of the isolated nucleobases is explained by the intramolecular delocalization of the positively charged hole, while the enhancement of the reducer character when going from aqueous solution to the strand correlates very well with the intermolecular hole delocalization. Our simulations suggest that the redox properties of DNA strands can be tuned by playing with the balance between intramolecular and intermolecular charge delocalization.

Triplet Photochemistry of Effluent Organic Matter in Degradation of Extracellular Antibiotic Resistance Genes

Wastewater effluent is a major source of extracellular antibiotic resistance genes (eArGs) in the aquatic environment, a threat to human health and biosecurity. However, little is known about the extent to which organic matter in the wastewater effluent (EfOM) might contribute to photosensitized oxidation of eArGs. Triplet states of EfOM were found to dominate the degradation of eArGs (accounting for up to 85%). Photo-oxidation proceeded mainly via proton-coupled electron transfer reactions. They broke plasmid strands and damaged bases. O₂^•- was also involved, and it coupled with the reactions' intermediate radicals of eArGs. The second-order reaction rates of bla_TEM-1 and tet-A segments (209-216 bps) with the triplet state of 4-carboxybenzophenone were calculated to be (2.61-2.75) × 10⁸ M^-1 s^-1. Besides as photosensitizers, the antioxidant moieties in EfOM also acted as quenchers to revert intermediate radicals back to their original forms, reducing the rate of photodegradation. However, the terrestrial origin natural organic matter was unable to photosensitize because it formed less triplets, especially high-energy triplets, so its inhibitory effects predominated. This study advances our understanding of the role of EfOM in the photo-oxidation of eArGs and the difference between EfOM and terrestrial-origin natural organic matter.

Supramolecular Recognition of Cytidine Phosphate in Nucleotides and RNA Sequences

Supramolecular recognition of nucleotides would enable manipulating crucial biochemical pathways like transcription and translation directly and with high precision. Therefore, it offers great promise in medicinal applications, not least in treating cancer or viral infections. This work presents a universal supramolecular approach to target nucleoside phosphates in nucleotides and RNA. The artificial active site in new receptors simultaneously realizes several binding and sensing mechanisms: encapsulation of a nucleobase via dispersion and hydrogen bonding interactions, recognition of the phosphate residue, and a self-reporting feature-"turn-on" fluorescence. Key to the high selectivity is the conscious separation of phosphate- and nucleobase-binding sites by introducing specific spacers in the receptor structure. We have tuned the spacers to achieve high binding affinity and selectivity for cytidine 5' triphosphate coupled to a record 60-fold fluorescence enhancement. The resulting structures are also the first functional models of poly(rC)-binding protein coordinating specifically to C-rich RNA oligomers, e.g., the 5'-AUCCC(C/U) sequence present in poliovirus type 1 and the human transcriptome. The receptors bind to RNA in human ovarian cells A2780, causing strong cytotoxicity at 800 nM. The performance, self-reporting property, and tunability of our approach open up a promising and unique avenue for sequence-specific RNA binding in cells by using low-molecular-weight artificial receptors.