Rates of DNA-mediated electron transfer between metallointercalators

Prospects of nano-theranostic approaches against breast and cervical cancer

The bottleneck on therapeutics and diagnostics is removed by an alternate approach known as theranostics which combines both therapeutics and diagnostics within a single platform. Due to this "all in one" nature of theranostics, it is now extensively applied in the medicinal field mainly in cancer treatment over the conventional therapy. Recently, FDA approval of lutetium 177 (177Lu) DOTATATE and 177Lu-PSMA-based radionuclide theranostics are clinically used and very few theranostics specific to breast cancer are in clinical trials. In this review, we are willing to draw special attention to the application of theranostics in the most relevant cancers in women, the breast and the cervical as these cancers affect women harshly but talked very silently due to the social restrictions and discriminations mainly in rural areas of developing and under developing countries. This approach not only combines therapeutics and diagnostics but targeting moieties can also be accommodated for the precise medication. Herein, our main objective is to enlighten the broader aspects of different kinds of theranostic devices based on radioisotopes, nanoparticles, graphene quantum dots, dendrimers and their fruitful application against breast and cervical cancer. The development of synthetic nano-theranostics was reported by accommodating therapeutic drugs, imaging probes and targeting ligands through conjugation or encapsulation. The imaging modalities like optical fluorescence, photosensitizers and radiotracers are used to get the diagnostic images through NIR, PET, MRI and CT/SPECT to detect the progress of cancer non-invasively and also at the same time targeting ligands such as antibodies, proteins and peptides in attachment with the theranostics enhances the therapeutic efficacy in addition to the clarity in diagnostics. The applications of theranostics from the last decade with their present scenario in clinics and future perspectives, as well as the pitfalls with the hurdles that still leave questions to rethink from the root are also been discussed in this review.

A quantum physics layer of epigenetics: a hypothesis deduced from charge transfer and chirality-induced spin selectivity of DNA

BACKGROUND

Epigenetic mechanisms are informational cellular processes instructing normal and diseased phenotypes. They are associated with DNA but without altering the DNA sequence. Whereas chemical processes like DNA methylation or histone modifications are well-accepted epigenetic mechanisms, we herein propose the existence of an additional quantum physics layer of epigenetics.

RESULTS

We base our hypothesis on theoretical and experimental studies showing quantum phenomena to be active in double-stranded DNA, even under ambient conditions. These phenomena include coherent charge transfer along overlapping pi-orbitals of DNA bases and chirality-induced spin selectivity. Charge transfer via quantum tunneling mediated by overlapping orbitals results in charge delocalization along several neighboring bases, which can even be extended by classical (non-quantum) electron hopping. Such charge transfer is interrupted by flipping base(s) out of the double-strand e.g., by DNA modifying enzymes. Charge delocalization can directly alter DNA recognition by proteins or indirectly by DNA structural changes e.g., kinking. Regarding sequence dependency, charge localization, shown to favor guanines, could influence or even direct epigenetic changes, e.g., modification of cytosines in CpG dinucleotides. Chirality-induced spin selectivity filters electrons for their spin along DNA and, thus, is not only an indicator for quantum coherence but can potentially affect DNA binding properties.

CONCLUSIONS

Quantum effects in DNA are prone to triggering and manipulation by external means. By the hypothesis put forward here, we would like to foster research on "Quantum Epigenetics" at the interface of medicine, biology, biochemistry, and physics to investigate the potential epigenetic impact of quantum physical principles on (human) life.

Structural, Optical, and Electrical Characterization of Biological and Bioactive Propolis Films

Natural substances are potential compounds for green electronic devices. So, scientists have to explore and optimize their properties to insert them as active layers in electronic heterostructures. In this study, microstructural, optical, and electrical properties of thin layers of the propolis are investigated. Propolis is a biological organic bioactive material produced by honeybees. A stable, bioactive, green, and low-cost thin layer of this biocompatible material was deposited on different substrates using a propolis alcohol solution. The morphological studies show that the propolis thin film is dense and well covers the substrate surfaces. Transmittance spectra show that propolis film cuts off blue and ultraviolet (UV) radiation, which are responsible for food oxidation, nutrient losses, flavor degradation, and discoloration. Therefore, to prevent food deterioration, a propolis film can be used in food packaging. For red and near-infrared radiation (∼600-2700 nm), a propolis film is transparent. Between near-infrared and mid-infrared radiation (∼2700-3200 nm), a propolis film reveals significant photosensitivity and so can be used as a photosensor. The propolis film reveals an energy gap of 2.88 eV at room temperature, which enables potential optoelectronic applications in the UV and blue ranges. The electrical study shows that the propolis layer has semiconductor behavior and can be a potential active layer in biocompatible temperature sensors. In addition to its medical, pharmaceutical, and food industry applications, in light of this study, propolis presents amazing optical and electrical properties and is a promising candidate for food packaging, optoelectronics, transparent electronics, and bioelectronics.

Spatial Separation of Plasmonic Hot-Electron Generation and a Hydrodehalogenation Reaction Center Using a DNA Wire

Using hot charge carriers far from a plasmonic nanoparticle surface is very attractive for many applications in catalysis and nanomedicine and will lead to a better understanding of plasmon-induced processes, such as hot-charge-carrier- or heat-driven chemical reactions. Herein we show that DNA is able to transfer hot electrons generated by a silver nanoparticle over several nanometers to drive a chemical reaction in a molecule nonadsorbed on the surface. For this we use 8-bromo-adenosine introduced in different positions within a double-stranded DNA oligonucleotide. The DNA is also used to assemble the nanoparticles into nanoparticles ensembles enabling the use of surface-enhanced Raman scattering to track the decomposition reaction. To prove the DNA-mediated transfer, the probe molecule was insulated from the source of charge carriers, which hindered the reaction. The results indicate that DNA can be used to study the transfer of hot electrons and the mechanisms of advanced plasmonic catalysts.

Kinetic Isotope Effects on Electron Transfer Across Self-Assembled Monolayers on Gold

Reactions requiring controlled delivery of protons and electrons are important in storage of energy in small molecules. While control over proton transfer can be achieved by installing appropriate chemical functionality in the catalyst, control of electron-transfer (ET) rates can be achieved by utilizing self-assembled monolayers (SAMs) on electrodes. Thus, a deeper understanding of the ET through SAM to an immobilized or covalently attached redox-active species is desirable. Long-range ET across several SAM-covered Au electrodes to covalently attached ferrocene is investigated using protonated and deuterated thiols (R-SH/R-SD). The rate of tunneling is measured using both chronoamperometry and cyclic voltammetry, and it shows a prominent kinetic isotope effect (KIE). The KIE is ∼2 (normal) for medium-chain-length thiols but ∼0.47 (inverse) for long-chain thiols. These results imply substantial contribution from the classical modes at the Au-(H)SR interface, which shifts substantially upon deuteration of the thiols, to the ET process. The underlying H/D KIE of these exchangeable thiol protons should be considered when analyzing solvent isotope effects in catalysis utilizing SAM.

Effect of cytosine hydroxymethylation on DNA charge transport

DNA hydroxymethylation plays a very important role in some biological processes, such as DNA methylation process. In addition, its presence can also cause some diseases. In this paper, the electrical properties of cytosine hydroxymethylated (Chm) DNA sequences are studied. The density functional theory (DFT) and Landauer-Büttiker framework are used to study the decoherence conductance and transmission of the Chm strands in different configurations, which provides a theoretical basis for the detection of Chm. The results show that the conductance of the hydroxymethylated DNA strand is smaller than that of the native and methylated strands. The length dependence of the Chm strands is also studied. With the length increasing, the conductance becomes larger. This study shows that DNA methylation can be detected electrically.

Multifaceted aspects of charge transfer

Charge transfer and charge transport are by far among the most important processes for sustaining life on Earth and for making our modern ways of living possible. Involving multiple electron-transfer steps, photosynthesis and cellular respiration have been principally responsible for managing the energy flow in the biosphere of our planet since the Great Oxygen Event. It is impossible to imagine living organisms without charge transport mediated by ion channels, or electron and proton transfer mediated by redox enzymes. Concurrently, transfer and transport of electrons and holes drive the functionalities of electronic and photonic devices that are intricate for our lives. While fueling advances in engineering, charge-transfer science has established itself as an important independent field, originating from physical chemistry and chemical physics, focusing on paradigms from biology, and gaining momentum from solar-energy research. Here, we review the fundamental concepts of charge transfer, and outline its core role in a broad range of unrelated fields, such as medicine, environmental science, catalysis, electronics and photonics. The ubiquitous nature of dipoles, for example, sets demands on deepening the understanding of how localized electric fields affect charge transfer. Charge-transfer electrets, thus, prove important for advancing the field and for interfacing fundamental science with engineering. Synergy between the vastly different aspects of charge-transfer science sets the stage for the broad global impacts that the advances in this field have.

Extracellular DNA Promotes Efficient Extracellular Electron Transfer by Pyocyanin in Pseudomonas aeruginosa Biofilms

Redox cycling of extracellular electron shuttles can enable the metabolic activity of subpopulations within multicellular bacterial biofilms that lack direct access to electron acceptors or donors. How these shuttles catalyze extracellular electron transfer (EET) within biofilms without being lost to the environment has been a long-standing question. Here, we show that phenazines mediate efficient EET through interactions with extracellular DNA (eDNA) in Pseudomonas aeruginosa biofilms. Retention of pyocyanin (PYO) and phenazine carboxamide in the biofilm matrix is facilitated by eDNA binding. In vitro, different phenazines can exchange electrons in the presence or absence of DNA and can participate directly in redox reactions through DNA. In vivo, biofilm eDNA can also support rapid electron transfer between redox active intercalators. Together, these results establish that PYO:eDNA interactions support an efficient redox cycle with rapid EET that is faster than the rate of PYO loss from the biofilm.

Unexpected reversible and controllable nuclear uptake and efflux of the DNA “light-switching” Ru(ii)-polypyridyl complex in living cellsviaion-pairing with chlorophenolate counter-anions

An in-depth understanding of the mechanisms of cellular uptake and efflux would facilitate the design of metal complexes with not only better functionality and targeted theranostic efficiency, but also with controlled toxicity.

Electron Transfer in DNA at Electrified Interfaces

The ability of the DNA double helix to transport electrons underlies many life-centered biological processes and bio-electronic applications. However, there is little consensus on how efficiently the base pair π-stacks of DNA mediate electron transport. This minireview scrutinizes the current state-of-the-art knowledge on electron transfer (ET) properties of DNA and its long-range ability to transfer (mediate) electrical signals at electrified interfaces, without being oxidized or reduced. Complex changes an electric field induces in the DNA structure and its electronic properties govern the efficiency of DNA-mediated ET at electrodes and allow addressing the existing phenomenological riddles, while recently discovered rectifying properties of DNA contribute both to our understanding of DNA's ET in living systems and to advances in molecular bioelectronics.

Effective Distance for DNA-Mediated Charge Transport between Repair Proteins

The stacked aromatic base pairs within the DNA double helix facilitate charge transport down its length in the absence of lesions, mismatches, and other stacking perturbations. DNA repair proteins containing [4Fe4S] clusters can take advantage of DNA charge transport (CT) chemistry to scan the genome for mistakes more efficiently. Here we examine the effective length over which charge can be transported along DNA between these repair proteins. We define the effective CT distance as the length of DNA within which two proteins are able to influence their ensemble affinity to the DNA duplex via CT. Endonuclease III, a DNA repair glycosylase containing a [4Fe4S] cluster, was incubated with DNA duplexes of different lengths (1.5-9 kb), and atomic force microscopy was used to quantify the binding of proteins to these duplexes to determine how the relative protein affinity changes with increasing DNA length. A sharp change in binding slope is observed at 3509 base pairs, or about 1.2 μm, that supports the existence of two regimes for protein binding, one within the range for DNA CT, one outside of the range for CT; DNA CT between the redox proteins bound to DNA effectively decreases the ensemble binding affinity of oxidized and reduced proteins to DNA. Utilizing an Endonuclease III mutant Y82A, which is defective in carrying out DNA CT, shows only one regime for protein binding. Decreasing the temperature to 4 °C or including metallointercalators on the duplex, both of which should enhance base stacking and decrease DNA floppiness, leads to extending the effective length for DNA charge transport to ∼5300 bp or 1.8 μm. These results thus support DNA charge transport between repair proteins over kilobase distances. The results furthermore highlight the ability of DNA repair proteins to search the genome quickly and efficiently using DNA charge transport chemistry.

Sensing DNA through DNA Charge Transport

DNA charge transport chemistry involves the migration of charge over long molecular distances through the aromatic base pair stack within the DNA helix. This migration depends upon the intimate coupling of bases stacked one with another, and hence any perturbation in that stacking, through base modifications or protein binding, can be sensed electrically. In this review, we describe the many ways DNA charge transport chemistry has been utilized to sense changes in DNA, including the presence of lesions, mismatches, DNA-binding proteins, protein activity, and even reactions under weak magnetic fields. Charge transport chemistry is remarkable in its ability to sense the integrity of DNA.

Effect on frontier molecular orbitals of substituents in 5-position of uracil base pairs in vacuum and water

The most stable structure of 5-substituted uracil base pairs and metal-mediated-5-substituted uracil complexes are determined. Density functional theory (DFT) method is used in the calculations which are carried out both in vacuum and water. LANL2DZ and 6–311[Formula: see text]G(d,p) basis sets are used for metals and the rest atoms, respectively. Effects on frontier molecular orbitals and energy gaps of substituents in 5-position of uracil base pairs in vacuum and water are found. Conductivity of base pairs or complexes are investigated for single nanowires studied by band theory. It is expected that this study will be an example for future studies that require new nanotechnological applications.

Ultrafast Response in AC-Driven Electrochemiluminescent Cell Using Electrochemically Active DNA/Ru(bpy)32+ Hybrid Film with Mesoscopic Structures

Electrochemiluminescence (ECL) refers to light emission induced by an electrochemical redox reaction. The stability, emission response, and light intensity of the ECL device are known to be improved by using an alternating current (AC) voltage. In this paper, an AC-driven ECL device is fabricated with DNA/Ru(bpy)₃²⁺ hybrid film-modified electrode. The Ru(bpy)₃²⁺ complex exhibits significant electrochemical reactivity in the DNA/Ru(bpy)₃²⁺ hybrid film prepared by electrochemical adsorption. The hybrid film contains unique micrometre-scale aggregates of Ru(bpy)₃²⁺ in DNA matrix. The physicochemical properties of the hybrid film and its AC-driven ECL characteristics in the electrochemical device are studied. Orange-coloured ECL is observed to be emitted from only the aggregated structures in the hybrid film at the high AC frequency of 10 kHz, which corresponds to a response time shorter than 100 μs.

On the origin of multiexponential fluorescence decays from 2-aminopurine-labeled dinucleotides

The fluorescent probe 2-aminopurine (2Ap) has been used for decades to study local conformational fluctuations in DNA. Steady-state and time-resolved measurements of 2Ap fluorescence have been used to predict specific conformational states through suitable modeling of the quenching of the fluorescence of a 2Ap residue incorporated site-specifically into a DNA strand. The success of this approach has been limited by a lack of understanding of the precise factors responsible for the complex, multiexponential decays observed experimentally. In this study, dinucleotides composed of 2Ap and adenine were studied by the time-correlated single-photon counting technique to investigate the causes of heterogeneous emission kinetics. Contrary to previous reports, we argue that emission from 2Ap that is stacked with a neighboring base contributes negligibly to the emission signals recorded more than 50 ps after excitation, which are instead dominated by emission from unstacked 2Ap. We find that the decay kinetics can be modeled using a continuous lifetime distribution, which arises from the inherent distance dependence of electron transfer rates without the need to postulate a small number of discrete states with decay times derived from multiexponential fits. These results offer a new perspective on the quenching of 2Ap fluorescence and expand the information that can be obtained from experiments.

Wire and extended ladder model predict THz oscillations in DNA monomers, dimers and trimers

We call monomer a B-DNA base pair and study, analytically and numerically, electron or hole oscillations in monomers, dimers and trimers. We employ two tight binding (TB) approaches: (I) at the base-pair level, using the on-site energies of the base pairs and the hopping parameters between successive base pairs i.e. a wire model, and (II) at the single-base level, using the on-site energies of the bases and the hopping parameters between neighbouring bases, specifically between (a) two successive bases in the same strand, (b) complementary bases that define a base pair, and (c) diagonally located bases of successive base pairs, i.e. an extended ladder model since it also includes the diagonal hoppings (c). For monomers, with TB II, we predict periodic carrier oscillations with frequency [Formula: see text]-550 THz. For dimers, with TB I, we predict periodic carrier oscillations with [Formula: see text]-100 THz. For trimers made of identical monomers, with TB I, we predict periodic carrier oscillations with [Formula: see text]-33 THz. In other cases, either with TB I or TB II, the oscillations may be not strictly periodic, but Fourier analysis shows similar frequency content. For dimers and trimers, TB I and TB II are successfully compared giving complementary aspects of the oscillations.

DNA Charge Transport: from Chemical Principles to the Cell

The DNA double helix has captured the imagination of many, bringing it to the forefront of biological research. DNA has unique features that extend our interest into areas of chemistry, physics, material science, and engineering. Our laboratory has focused on studies of DNA charge transport (CT), wherein charges can efficiently travel long molecular distances through the DNA helix while maintaining an exquisite sensitivity to base pair π-stacking. Because DNA CT chemistry reports on the integrity of the DNA duplex, this property may be exploited to develop electrochemical devices to detect DNA lesions and DNA-binding proteins. Furthermore, studies now indicate that DNA CT may also be used in the cell by, for example, DNA repair proteins, as a cellular diagnostic, in order to scan the genome to localize efficiently to damage sites. In this review, we describe this evolution of DNA CT chemistry from the discovery of fundamental chemical principles to applications in diagnostic strategies and possible roles in biology.

Redox Signaling through DNA

Biological electron transfer reactions between metal cofactors are critical to many essential processes within the cell. Duplex DNA is, moreover, capable of mediating the transport of charge through its π-stacked nitrogenous bases. Increasingly, [4Fe4S] clusters, generally redox-active cofactors, have been found to be associated with enzymes involved in DNA processing. DNA-binding enzymes containing [4Fe4S] clusters can thus utilize DNA charge transport (DNA CT) for redox signaling to coordinate reactions over long molecular distances. In particular, DNA CT signaling may represent the first step in the search for DNA lesions by proteins containing [4Fe4S] clusters that are involved in DNA repair. Here we describe research carried out to examine the chemical characteristics and biological consequences of DNA CT. We are finding that DNA CT among metalloproteins represents powerful chemistry for redox signaling at long range within the cell.

Unbiased charge oscillations in B-DNA: monomer polymers and dimer polymers

We call monomer a B-DNA base pair and examine, analytically and numerically, electron or hole oscillations in monomer and dimer polymers, i.e., periodic sequences with repetition unit made of one or two monomers. We employ a tight-binding (TB) approach at the base-pair level to readily determine the spatiotemporal evolution of a single extra carrier along a N base-pair B-DNA segment. We study highest occupied molecular orbital and lowest unoccupied molecular orbital eigenspectra as well as the mean over time probabilities to find the carrier at a particular monomer. We use the pure mean transfer rate k to evaluate the easiness of charge transfer. The inverse decay length β for exponential fits k(d), where d is the charge transfer distance, and the exponent η for power-law fits k(N) are computed; generally power-law fits are better. We illustrate that increasing the number of different parameters involved in the TB description, the fall of k(d) or k(N) becomes steeper and show the range covered by β and η. Finally, for both the time-independent and the time-dependent problems, we analyze the palindromicity and the degree of eigenspectrum dependence of the probabilities to find the carrier at a particular monomer.

Solvation-driven charge transfer and localization in metal complexes

In any physicochemical process in liquids, the dynamical response of the solvent to the solutes out of equilibrium plays a crucial role in the rates and products: the solvent molecules react to the changes in volume and electron density of the solutes to minimize the free energy of the solution, thus modulating the activation barriers and stabilizing (or destabilizing) intermediate states. In charge transfer (CT) processes in polar solvents, the response of the solvent always assists the formation of charge separation states by stabilizing the energy of the localized charges. A deep understanding of the solvation mechanisms and time scales is therefore essential for a correct description of any photochemical process in dense phase and for designing molecular devices based on photosensitizers with CT excited states.

In the last two decades, with the advent of ultrafast time-resolved spectroscopies, microscopic models describing the relevant case of polar solvation (where both the solvent and the solute molecules have a permanent electric dipole and the mutual interaction is mainly dipole–dipole) have dramatically progressed. Regardless of the details of each model, they all assume that the effect of the electrostatic fields of the solvent molecules on the internal electronic dynamics of the solute are perturbative and that the solvent–solute coupling is mainly an electrostatic interaction between the constant permanent dipoles of the solute and the solvent molecules. This well-established picture has proven to quantitatively rationalize spectroscopic effects of environmental and electric dynamics (time-resolved Stokes shifts, inhomogeneous broadening, etc.). However, recent computational and experimental studies, including ours, have shown that further improvement is required.

Indeed, in the last years we investigated several molecular complexes exhibiting photoexcited CT states, and we found that the current description of the formation and stabilization of CT states in an important group of molecules such as transition metal complexes is inaccurate. In particular, we proved that the solvent molecules are not just spectators of intramolecular electron density redistribution but significantly modulate it.

Our results solicit further development of quantum mechanics computational methods to treat the solute and (at least) the closest solvent molecules including the nonperturbative treatment of the effects of local electrostatics and direct solvent–solute interactions to describe the dynamical changes of the solute excited states during the solvent response.

Label-free detection of DNA hybridization and single point mutations in a nano-gap biosensor

We describe a conductance-based biosensor that exploits DNA-mediated long-range electron transport for the label-free and direct electrical detection of DNA hybridization. This biosensor platform comprises an array of vertical nano-gap biosensors made of gold and fabricated through standard photolithography combined with focused ion beam lithography. The nano-gap walls are covalently modified with short, anti-symmetric thiolated DNA probes, which are terminated by 19 bases complementary to both the ends of a target DNA strand. The nano-gaps are separated by a distance of 50 nm, which was adjusted to fit the length of the DNA target plus the DNA probes. The hybridization of the target DNA closes the gap circuit in a switch on/off fashion, in such a way that it is readily detected by an increase in the current after nano-gap closure. The nano-biosensor shows high specificity in the discrimination of base-pair mismatching and does not require signal indicators or enhancing molecules. The design of the biosensor platform is applicable for multiplexed detection in a straightforward manner. The platform is well-suited to mass production, point-of-care diagnostics, and wide-scale DNA analysis applications.

Synchrotron ultrafast techniques for photoactive transition metal complexes

In the last decade, the use of time-resolved X-ray techniques has revealed the structure of light-generated transient species for a wide range of samples, from small organic molecules to proteins. Time resolutions of the order of 100 ps are typically reached, allowing one to monitor thermally equilibrated excited states and capture their structure as a function of time. This review aims at providing a general overview of the application of time-resolved X-ray solution scattering (TR-XSS) and time-resolved X-ray absorption spectroscopy (TR-XAS), the two techniques prevalently employed in the investigation of light-triggered structural changes of transition metal complexes. In particular, we herein describe the fundamental physical principles for static XSS and XAS and illustrate the theory of time-resolved XSS and XAS together with data acquisition and analysis strategies. Selected pioneering examples of photoactive transition metal complexes studied by TR-XSS and TR-XAS are discussed in depth.

In-silico assessment of protein-protein electron transfer. a case study: cytochrome c peroxidase--cytochrome c

The fast development of software and hardware is notably helping in closing the gap between macroscopic and microscopic data. Using a novel theoretical strategy combining molecular dynamics simulations, conformational clustering, ab-initio quantum mechanics and electronic coupling calculations, we show how computational methodologies are mature enough to provide accurate atomistic details into the mechanism of electron transfer (ET) processes in complex protein systems, known to be a significant challenge. We performed a quantitative study of the ET between Cytochrome c Peroxidase and its redox partner Cytochrome c. Our results confirm the ET mechanism as hole transfer (HT) through residues Ala194, Ala193, Gly192 and Trp191 of CcP. Furthermore, our findings indicate the fine evolution of the enzyme to approach an elevated turnover rate of 5.47×10⁶ s⁻¹ for the ET between Cytc and CcP through establishment of a localized bridge state in Trp191.

We have developed a protocol capable of describing long-range electron transfer mechanisms at an atomic detailed level. We demonstrate the maturity of the computational techniques in obtaining a quantitative view of the Cytochrome c Peroxidase/Cytochrome c electron transfer process, known to be a significant challenge. In excellent agreement with experimental data, our results allow for the description of the electron transfer pathway, its mechanism and the electron transfer rate at a quantitative level. The overall protocol is free of parameterization and can be applied to any complex electron transfer process. Furthermore, the results reveal the fine enzyme evolution of this protein-protein complex to optimize its electron transfer rate by a localized bridge state.

Label-free electronic probing of nucleic acids and proteins at the nanoscale using the nanoneedle biosensor

Detection of proteins and nucleic acids is dominantly performed using optical fluorescence based techniques, which are more costly and timely than electrical detection due to the need for expensive and bulky optical equipment and the process of fluorescent tagging. In this paper, we discuss our study of the electrical properties of nucleic acids and proteins at the nanoscale using a nanoelectronic probe we have developed, which we refer to as the Nanoneedle biosensor. The nanoneedle consists of four thin film layers: a conductive layer at the bottom acting as an electrode, an oxide layer on top, and another conductive layer on top of that, with a protective oxide above. The presence of proteins and nucleic acids near the tip results in a decrease in impedance across the sensing electrodes. There are three basic mechanisms behind the electrical response of DNA and protein molecules in solution under an applied alternating electrical field. The first change stems from modulation of the relative permittivity at the interface. The second mechanism is the formation and relaxation of the induced dipole moment. The third mechanism is the tunneling of electrons through the biomolecules. The results presented in this paper can be extended to develop low cost point-of-care diagnostic assays for the clinical setting.

Probing charge transport in oxidatively damaged DNA sequences under the influence of structural fluctuations

We present a detailed study of the charge transport characteristics of double-stranded DNA oligomers including the oxidative damage 7,8-dihydro-8-oxoguanine (8-oxoG). The problem is treated by a hybrid methodology combining classical molecular dynamics simulations and semiempirical electronic structure calculations to formulate a coarse-grained charge transport model. The influence of solvent- and DNA-mediated structural fluctuations is encoded in the obtained time series of the electronic charge transfer parameters. Within the Landauer approach to charge transport, we perform a detailed analysis of the conductance and current time series obtained by sampling the electronic structure along the molecular dynamics trajectory, and find that the inclusion of 8-oxoG damages into the DNA sequence can induce a change in the electrical response of the system. However, solvent-induced fluctuations tend to mask the effect, so that a detection of such sequence modifications via electrical transport measurements in a liquid environment seems to be difficult to achieve.

EFFECT OF CATION RADICAL FORMATION ON REACTIVITY AND ACIDITY ENHANCEMENT OF CYTOSINE NUCLEOBASE: NATURAL BOND ORBITAL AND ATOM IN MOLECULE ANALYSIS

The radical cations of DNA constituents generated by the ionizing radiation initiate an alteration of the bases, which is one of the main types of cytotoxic DNA lesions. These cation radical spices are known for their role in producing nucleic acid strand break. In this study, the gas-phase intrinsic chemical properties of the gaseous radical cations of cytosine and its base pair with guanine were examined by employing density functional theory (B3LYP) with the 6-311++G(d,p) basis set. Structures, geometries, adiabatic ionization energies, adiabatic electron affinities, charge distributions, molecular orbital analysis and proton-transfer process of these molecules were investigated. The influence of cation radical formation on acidities of multiple sites in cytosine molecule was investigated. Results of calculations revealed that cytosine radicals formed by deprotonation of cytosine cation radicals can exothermically abstract hydrogen atoms from thiol groups, phenol, and α-positions of amino acid. Furthermore, comparison of acidity value of N–H sites of cytosine cation radical with the known proton affinities (PA) of organic and biological molecules implied that cytosine cation radical can exothermically transfer onto basic sites of amino acids and peptides.

Using metal complex reduced states to monitor the oxidation of DNA

Metallointercalating photooxidants interact intimately with the base stack of double-stranded DNA and exhibit rich photophysical and electrochemical properties, making them ideal probes for the study of DNA-mediated charge transport (CT). The complexes [Rh(phi)(2)(bpy')](3+) (phi = 9,10-phenanthrenequinone diimine; bpy' = 4-methyl-4'-(butyric acid)-2,2'-bipyridine), [Ir(ppy)(2)(dppz')](+) (ppy = 2-phenylpyridine; dppz' = 6-(dipyrido[3,2-a:2',3'-c]phenazin-11-yl)hex-5-ynoic acid), and [Re(CO)(3)(dppz)(py')](+) (dppz = dipyrido[2,3-a:2',3'-c]phenazine; py' = 3-(pyridin-4-yl)-propanoic acid) were each covalently tethered to DNA to compare their photooxidation efficiencies. Biochemical studies show that upon irradiation, the three complexes oxidize guanine by long-range DNA-mediated CT with the efficiency: Rh > Re > Ir. Comparison of spectra obtained by spectroelectrochemistry after bulk reduction of the free metal complexes with those obtained by transient absorption (TA) spectroscopy of the conjugates suggests that the reduced metal states form following excitation of the conjugates at 355 nm. Electrochemical experiments and kinetic analysis of the TA decays indicate that the thermodynamic driving force for CT, variations in the efficiency of back electron transfer, and coupling to DNA are the primary factors responsible for the trend observed in the guanine oxidation yields of the three complexes.

Mapping the surface adsorption forces of nanomaterials in biological systems

The biological surface adsorption index (BSAI) is a novel approach to characterize surface adsorption energy of nanomaterials that is the primary force behind nanoparticle aggregation, protein corona formation, and other complex interactions of nanomaterials within biological systems. Five quantitative nanodescriptors were obtained to represent the surface adsorption forces (hydrophobicity, hydrogen bond, polarity/polarizability, and lone-pair electrons) of the nanomaterial interaction with biological components. We have mapped the surface adsorption forces over 16 different nanomaterials. When the five-dimensional information of the nanodescriptors was reduced to two dimensions, the 16 nanomaterials were classified into distinct clusters according their surface adsorption properties. BSAI nanodescriptors are intrinsic properties of nanomaterials useful for quantitative structure-activity relationship (QSAR) model development. This is the first success in quantitative characterization of the surface adsorption forces of nanomaterials in biological conditions, which could open a quantitative avenue in predictive nanomedicine development, risk assessment, and safety evaluation of nanomaterials.

Luminescent Ir(III) complex exclusively made of polypyridine ligands capable of intercalating into calf-thymus DNA

Efficient intercalation of a luminescent Ir(III) complex exclusively made of polypyridine ligands in natural and synthetic biopolymers is reported for the first time. The emission of the complex is largely enhanced in the presence of [poly(dA-dT)(2)] and strongly quenched in the presence of [poly(dG-dC)(2)]. By comparing the emission decays in DNA and in synthetic polynucleotides, it is proposed that the emission quenching of the title compound by guanine residues in DNA is no longer effective over a distance of four dA-dT base pairs.