In situ monitoring of the influence of water on DNA radiation damage by near-ambient pressure X-ray photoelectron spectroscopy

2D and 3D Micropatterning of Mussel-Inspired Functional Materials by Direct Laser Writing

This work addresses the critical need for multifunctional materials and substrate-independent high-precision surface modification techniques that are essential for advancing microdevices and sensing elements. To overcome existing limitations, the versatility of mussel-inspired materials (MIMs) is combined with state-of-the-art multiphoton direct laser writing (DLW) microfabrication. In this way, 2D and 3D MIM microstructures of complex designs are demonstrated with sub-micron to micron resolution and extensive post-functionalization capabilities. This study includes polydopamine (PDA), mussel-inspired linear, and dendritic polyglycerols (MI-lPG and MI-dPG), allowing their direct microstructure on the substrate of choice with the option to tailor the patterned topography and morphology in a controllable manner. The functionality potential of MIMs is demonstrated by successfully immobilizing and detecting single-stranded DNA on MIM micropattern and nanoarray surfaces. In addition, easy modification of MIM microstructure with silver nanoparticles without the need of any reducing agent is shown. The methodology developed here enables the integration of MIMs in advanced applications where precise surface functionalization is essential.

Interaction of a Dimeric Single-Stranded DNA-Binding Protein (G5P) with DNA Hairpins. A Molecular Beacon Study

Gene-V protein (G5P/GVP) is a single-stranded (ss)DNA-binding protein (SBP) of bacteriophage f1 that is required for DNA synthesis and repair. In solution, it exists as a dimer that binds two antiparallel ssDNA strands with high affinity in a cooperative manner, forming a left-handed helical protein-DNA filament. Here, we report on fluorescence studies of the interaction of G5P with different DNA oligonucleotides having a hairpin structure (molecular beacon, MB) with a seven base-pair stem (dT24-stem7, dT18-stem7), as well as with DNA oligonucleotides (dT38, dT24) without a defined secondary structure. All oligonucleotides were end-labeled with a Cy3-fluorophore and a BHQ2-quencher. In the case of DNA oligonucleotides without a secondary structure, an almost complete quenching of their strong fluorescence (with about 5% residual intensity) was observed upon the binding of G5P. This implies an exact alignment of the ends of the DNA strand(s) in the saturated complex. The interaction of the DNA hairpins with G5P led to the unzipping of the base-paired stem, as revealed by fluorescence measurements, fluorescence microfluidic mixing experiments, and electrophoretic mobility shift assay data. Importantly, the disruption of ssDNA's secondary structure agrees with the behavior of other single-stranded DNA-binding proteins (SBPs). In addition, substantial protein-induced fluorescence enhancement (PIFE) of the Cy3-fluorescence was observed.

Combining the Δ-Self-Consistent-Field and GW Methods for Predicting Core Electron Binding Energies in Periodic Solids

For the computational prediction of core electron binding energies in solids, two distinct kinds of modeling strategies have been pursued: the Δ-Self-Consistent-Field method based on density functional theory (DFT), and the GW method. In this study, we examine the formal relationship between these two approaches and establish a link between them. The link arises from the equivalence, in DFT, between the total energy difference result for the first ionization energy, and the eigenvalue of the highest occupied state, in the limit of infinite supercell size. This link allows us to introduce a new formalism, which highlights how in DFT─even if the total energy difference method is used to calculate core electron binding energies─the accuracy of the results still implicitly depends on the accuracy of the eigenvalue at the valence band maximum in insulators, or at the Fermi level in metals. We examine whether incorporating a quasiparticle correction for this eigenvalue from GW theory improves the accuracy of the calculated core electron binding energies, and find that the inclusion of vertex corrections is required for achieving quantitative agreement with experiment.

Bio-SAXS of single-stranded DNA-binding proteins: radiation protection by the compatible solute ectoine

Small-angle X-ray scattering (SAXS) can be used for structural determination of biological macromolecules and polymers in their native states (e.g. liquid phase). This means that the structural changes of (bio-)polymers, such as proteins and DNA, can be monitored in situ to understand their sensitivity to changes in chemical environments. In an attempt to improve the reliability of such experiments, the reduction of radiation damage occurring from exposure to X-rays is required. One such method, is to use scavenger molecules to protect macromolecules against radicals produced during radiation exposure, such as reactive oxygen species (ROS). In this study we investigate the feasibility of applying the compatible solute, osmolyte and radiation protector Ectoine (THP(B)), as a scavenger molecule during SAXS measurements of the single-stranded DNA-binding protein Gene-V Protein (G5P/GVP). In this case, we monitor the radiation induced changes of G5P during bio-SAXS measurments and the resulting microscopic energy-damage relation was determined from microdosimetric calculations by Monte-Carlo based particle scattering simulations with TOPAS/Geant4 and a custom target-model. This resulted in a median-lethal energy deposit of pure G5P at 4 mg mL^-1 of E_1/2 = 7 ± 5 eV, whereas a threefold increase of energy-deposit was needed under the presence of Ectoine to reach the same level of damage. This indicates that Ectoine increases the possible exposure time before radiation-damage to G5P is observed. Furthermore, the dominant type of damage shifted from aggregation in pure solutions towards a fragmentation for solutions containing Ectoine as a cosolute. These results are interpreted in terms of indirect radiation damage by reactive secondary species, as well as post-irradiation effects, related to preferential-exclusion of the cosolute from the protein surface. Hence, Ectoine is shown to provide a non-disturbing way to improve structure-determination of proteins via bio-SAXS in future studies.

Inclusion of Electron Interactions by Rate Equations in Chemical Models

The concept of treating subranges of the electron energy spectrum as species in chemical models is investigated. This is intended to facilitate simple modification of chemical models by incorporating the electron interactions as additional rate equations. It is anticipated that this embedding of fine details of the energy dependence of the electron interactions into rate equations will yield an improvement in computational efficiency compared to other methods. It will be applicable in situations where the electron density is low enough that the electron interactions with chemical species are significant compared to electron–electron interactions. A target application is the simulation of electron processes in the D-region of the Earth’s atmosphere, but it is anticipated that the method would be useful in other areas, including enhancement of Monte Carlo simulation of electron–liquid interactions and simulations of chemical reactions and radical generation induced by electrons and positrons in biomolecular systems. The aim here is to investigate the accuracy and practicality of the method. In particular, energy must be conserved, while the number of subranges should be small to reduce computation time and their distribution should be logarithmic in order to represent processes over a wide range of electron energies. The method is applied here to the interaction by inelastic and superelastic collisions of electrons with a gas of molecules with only one excited vibrational level. While this is unphysical, it allows the method to be validated by checking for accuracy, energy conservation, maintenance of equilibrium and evolution of a Maxwellian electron spectrum.

Spiers Memorial Lecture: Prospects for photoelectron spectroscopy

An overview is presented of recent advances in photoelectron spectroscopy, focussing on advances in in situ and time-resolved measurements, and in extending the sampling depth of the technique. The future...

Redox-sensitive iodinated polymersomes carrying histone deacetylase inhibitor as a dual-functional nano-radiosensitizer for enhanced radiotherapy of breast cancer

Radiotherapy (RT) is a frequently used means in clinical tumor treatment. The outcome of RT varies, however, to a great extent, due to RT resistance or intolerable dose, which might be resolved by the development of radio-sensitizing strategies. Here, we report redox-sensitive iodinated polymersomes (RIP) carrying histone deacetylase inhibitor, suberoylanilide hydroxamic acid (SAHA, vorinostat), as a new dual-functional nano-radiosensitizer for breast cancer radiotherapy. SAHA-loaded RIP (RIP-SAHA) with a size of about 101 nm exhibited good colloidal stability while the reduction-activated release of SAHA, giving rise to better antitumor effect to 4T1 breast carcinoma cells than free SAHA. Accordingly, RIP-SAHA combined with a 4 Gy dose of X-ray radiation led to significantly enhanced suppression of 4T1 cells compared with SAHA combined 4 Gy of X-ray radiation, as a result of enhanced DNA damage and impeded DNA damage repair. The pharmacokinetics and biodistribution studies by single-photon emission computed tomography (SPECT) with ¹²⁵I-labeled SAHA (¹²⁵I-SAHA) showed a 17.3-fold longer circulation and 237.7-fold better tumor accumulation of RIP-SAHA over SAHA. The systemic administration of RIP-SAHA greatly sensitized radiotherapy of subcutaneous 4T1 breast tumors and brought about significant inhibition of tumor growth, without causing damages to major organs, compared with radiotherapy alone. RIP not only enhanced SAHA delivery but also acted as a radiosensitizer. RIP-SAHA emerges as a smart dual-functional nano-radiosensitizer to effectively enhance tumor radiotherapy.

Low-Energy Electron Damage to Condensed-Phase DNA and Its Constituents

The complex physical and chemical reactions between the large number of low-energy (0-30 eV) electrons (LEEs) released by high energy radiation interacting with genetic material can lead to the formation of various DNA lesions such as crosslinks, single strand breaks, base modifications, and cleavage, as well as double strand breaks and other cluster damages. When crosslinks and cluster damages cannot be repaired by the cell, they can cause genetic loss of information, mutations, apoptosis, and promote genomic instability. Through the efforts of many research groups in the past two decades, the study of the interaction between LEEs and DNA under different experimental conditions has unveiled some of the main mechanisms responsible for these damages. In the present review, we focus on experimental investigations in the condensed phase that range from fundamental DNA constituents to oligonucleotides, synthetic duplex DNA, and bacterial (i.e., plasmid) DNA. These targets were irradiated either with LEEs from a monoenergetic-electron or photoelectron source, as sub-monolayer, monolayer, or multilayer films and within clusters or water solutions. Each type of experiment is briefly described, and the observed DNA damages are reported, along with the proposed mechanisms. Defining the role of LEEs within the sequence of events leading to radiobiological lesions contributes to our understanding of the action of radiation on living organisms, over a wide range of initial radiation energies. Applications of the interaction of LEEs with DNA to radiotherapy are briefly summarized.