All organisms store the information necessary to maintain life in their DNA. Any process that damages DNA, causing a loss or corruption of that information, jeopardizes the viability of the organism. One-electron oxidation is such a process. In this Account, we address three of the central features of one-electron oxidation of DNA: (i) the migration of the radical cation away from the site of its formation; (ii) the electronic and structural factors that determine the nucleobases at which irreversible reactions most readily occur; (iii) the mechanism of reaction for nucleobase radical cations. The loss of an electron (ionization) from DNA generates an electron "hole" (a radical cation), located most often on its nucleobases, that migrates reversibly through duplex DNA by hopping until it is trapped in an irreversible chemical reaction. The particular sequence of nucleobases in a DNA oligomer determines both the efficiency of hopping and the specific location and nature of the damaging chemical reaction. In aqueous solution, DNA is a polyanion because of the negative charge carried by its phosphate groups. Counterions to the phosphate groups (typically Na(+)) play an important role in facilitating both hopping and the eventual reaction of the radical cation with H(2)O. Irreversible reaction of a radical cation with H(2)O in duplex DNA occurs preferentially at the most reactive site. In normal DNA, comprising the four common DNA nucleobases G, C, A, and T, reaction occurs most commonly at a guanine, resulting in its conversion primarily to 8-oxo-7,8-dihydroguanine (8-OxoG). Both electronic and steric effects control the outcome of this process. If the DNA oligomer does not contain a suitable guanine, then reaction of the radical cation occurs at the thymine of a TT step, primarily by a tandem process. The oxidative damage of DNA is a complex process, influenced by charge transport and reactions that are controlled by a combination of enthalpic, entropic, steric, and compositional factors. These processes occur over a broad distribution of energies, times, and spatial scales. The emergence of a complete picture of DNA oxidation will require additional exploration of the structural, kinetic, and dynamic properties of DNA, but this Account offers insight into key elements of this challenge.
Although luminescence spectroscopy has been a promising sensing technology with widespread applications in point-of-care diagnostics and chem-bio detection, it fundamentally suffers from low signal collection efficiency, considerable background noise, poor photostability, and intrinsic omnidirectional emission properties. In this regard, surface plasmon-coupled emission, a versatile plasmon-enhanced detection platform with >50% signal collection efficiency, high directionality, and polarization has previously been explored to amplify the limit of detection of desired analytes. However, high Ohmic loss in metal-dependent plasmonic platforms has remained an inevitable challenge. Here, we develop a hybrid nanocavity interface on a template-free and loss-less photonic crystal-coupled emission (PCCE) platform by the quintessential integration of high refractive index dielectric Nd2O3 “Huygens sources” and sharp-edged silver nanoprisms (NPrs). While efficient forward light scattering characteristics of Nd2O3 nanorods (NRs) present 460-fold emission enhancements in PCCE, the tunable localized plasmon resonances of NPrs display high electromagnetic field confinement at sharp nanotips and protrusions, boosting the enhancements 947-fold. The judicious use of silver NPr (AgNPr) metal-Nd2O3 dielectric hybrid resonances in conjugation with surface-trapped Bloch surface waves of the one-dimensional photonic crystal (1DPhC) displayed unprecedented >1300-fold enhancements. The experimental results are validated by excellent correlations with numerical calculations. The multifold hotspots generated by zero and nonzero nanogaps between the coassembly of NPrs, NRs, and 1DPhCs are used for (i) determination of hyper and hypothyroidism levels through monitoring the concentration of iodide (I–) ions and (ii) single-molecule detection (zeptomolar) of the stress hormone, cortisol, through the synthesized cortisol-rhodamine B conjugate obtained using a simple esterification reaction.
An experimental investigation and theoretical study of the duplex DNA sequences d(5′-GAGG-3′)‚ d(3′-CTCC-5′) and d(5′-GTGG-3′)‚d(3′-CACC-5′) was carried out. The experiments show that the efficiency of radical cation transport, revealed by strand cleavage after treatment with piperidine, is the same in both sequences. Density functional theory (DFT) calculations reveal essentially identical ionization potentials and hole distributions for these sequences when they are properly hydrated. The effect of hydration on the electronic properties of these sequences was examined theoretically. Calculations on dry DNA (i.e., having no water molecules) gives "phantom" electronic transitions to orbitals associated with the sodium counterions. However, these transitions vanish even with a minimal level of hydration. Meaningful theoretical results for DNA are obtained only when the counterions and hydrating water molecules are properly considered.
cyano-1-p-nitrophenyl-4-phenylbuta-1Z,3E-diene (6), and 1-cyano-1-phenyl-4-pnitrophenylbuta-1Z,3E-diene (7), have been synthesized and their absorption and fluorescence properties in organic solvents, water-dioxane, and SDS, CTAB, and Triton-X-100 micelles have been investigated. The fluorescence behavior of these dienes has also been examined in ethanol-methanol (1:1) matrix at 298 and 77 K. The dienes with nitro substituents on the aromatic ring are capable of exhibiting dramatically redshifted fluorescence emission due to twisted intramolecular charge-transfer excited states. The fluorescence properties of nitro-substituted dienes 3, and 5-7 have been utilized to probe the microenvironment of SDS and CTAB micelles in terms of dielectric constant of water-micelle interface, location of the probe molecules in the micelles, and the cmc values. This study has brought out interesting features of the excited state structure and potential energy surface of diphenylpolyenes. It further provides new directions for the development of fluorescence probes as sensors and reporters of microenvironments of organized assemblies.
The escalating concern about ohmic losses in metal-dependent plasmonics demands more effective material fabrication for the development of biosensing frameworks. The omnidirectionality and low signal collection efficiency of a conventional fluorescence-based detection platform make it challenging to realize better sensitivity for real-time point-of-care diagnostics. In an attempt to address these demands, recently a photonic crystal-coupled emission (PCCE) platform has been demonstrated to outperform the well-established surface plasmon-coupled emission platform for biophysicochemical sensing applications. The effects of the different numbers of bilayers (BLs) of a one-dimensional photonic crystal (1DPhC) on the electric field intensity of Bloch surface waves and internal optical modes (IOMs) are extensively studied in this work to improve the performance of the PCCE platform rationally. Specifically, the 1DPhC with 10 BLs presented 55-fold PCCE enhancements because of the strong field confinement by the IOMs and small losses. In addition, the critical role of nanoengineering graphene oxide π-plasmon and silver nanowires on the PCCE platform has been explored to yield an unprecedented >1300-fold increase in fluorescence intensity. The amplified PCCE enhancements obtained with the first experimental evidence of the synergism among dielectric plasmons (1DPhC), graphene oxide plasmons, and metal plasmons (from silver nanowires) have been utilized to sense cholesterol at the single-molecule limit of detection. The photoplasmonic sensor presented here exhibits potential utility in academia and industry and provides a perspective for combining materials at nanoregimes for the desired applications.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.