Measuring the density of DNA films using ultraviolet-visible interferometry

Proton relative biological effectiveness for the induction of DNA double strand breaks based on Geant4

Uncertainties in the relative biological effectiveness (RBE) of proton remains a major barrier to the biological optimization of proton therapy. A large amount of experimental data suggest that proton RBE is variable. As an evolving Monte Carlo code toolkit, Geant4-DNA is able to simulate the initial DNA damage caused by particle beams through physical and chemical interactions at the nanometer scale over a short period of time. This contributes to evaluating the radiobiological effects induced by ionizing radiation. Based on the Geant4-DNA toolkit, this study constructed a DNA geometric model containing 6.32Gbp, simulated the relationship between radiochemical yields (G-values) and their corresponding chemical constructors, and calculated a detailed calculation of the sources of damage and the complexity of damage in DNA strand breaks. The damage model constructed in this study can simulate the relative biological effectiveness (RBE) in the proton Bragg peak region. The results indicate that: (1) When the electron energy is below 400 keV, the yield of OH·account for 18.1% to 25.3% of the total water radiolysis yields. (2) Under the influence of histone clearance function, the yield of indirect damage account for over 72.93% of the yield of DNA strand breaks (SBs). When linear energy transfer (LET) increased from 29.79 (keV/μm) to 64.29 (keV/μm), the yield of double strand breaks (DSB) increased from 17.27% to 32.65%. (3) By investigating the effect of proton Bragg peak depth on the yield of direct DSB (DSBdirect) and total DSB (DSBtotal), theRBEDSBtotandRBEDSBdirlevels of cells show that the RBE value of protons reaches 2.2 in the Bragg peak region.

The Effects of Particle LET and Fluence on the Complexity and Frequency of Clustered DNA Damage

Motivation

Clustered DNA-lesions are predominantly induced by ionizing radiation, particularly by high-LET particles, and considered as lethal damage. Quantification of this specific type of damage as a function of radiation parameters such as LET, dose rate, dose, and particle type can be informative for the prediction of biological outcome in radiobiological studies. This study investigated the induction and complexity of clustered DNA damage for three different types of particles at an LET range of 0.5-250 keV/μm.

Methods

Nanometric volumes (36.0 nm3) of 15 base-pair DNA with its hydration shell was modeled. Electron, proton, and alpha particles at various energies were simulated to irradiate the nanometric volumes. The number of ionization events, low-energy electron spectra, and chemical yields for the formation of °OH, H°, e aq - , and H2O2 were calculated for each particle as a function of LET. Single- and double-strand breaks (SSB and DSB), base release, and clustered DNA-lesions were computed from the Monte-Carlo based quantification of the reactive species and measured yields of the species responsible for the DNA lesion formation.

Results

The total amount of DNA damage depends on particle type and LET. The number of ionization events underestimates the quantity of DNA damage at LETs higher than 10 keV/μm. Minimum LETs of 9.4 and 11.5 keV/μm are required to induce clustered damage by a single track of proton and alpha particles, respectively. For a given radiation dose, an increase in LET reduces the number of particle tracks, leading to more complex clustered DNA damage, but a smaller number of separated clustered damage sites.

Conclusions

The dependency of the number and the complexity of clustered DNA damage on LET and fluence suggests that the quantification of this damage can be a useful method for the estimation of the biological effectiveness of radiation. These results also suggest that medium-LET particles are more appropriate for the treatment of bulk targets, whereas high-LET particles can be more effective for small targets.

DNA damage by radiation as a function of electron energy and interaction at the atomic level with Monte Carlo simulation

In radiotherapy, X-ray or heavy ion beams target tumors to cause damage to their cell DNA. This damage is mainly induced by secondary low energy electrons. In this paper, we report the DNA molecular breaks at the atomic level as a function of electron energy and types of electron interactions using of Monte Carlo simulation. The number of DNA single and double strand breaks are compared to those from experimental results based on electron energies. In recent years, DNA atomistic models were introduced but still the simulations consider energy deposition in volumes of DNA or water equivalent material. We simulated a model of atomistic B-DNA in vacuum, forming 1122 base pairs of 30 nm in length. Each atom has been represented by a sphere whose radius equals the radius of van der Waals. We repeatedly simulated 10 million electrons for each energy from 4 eV to 500 eV and counted each interaction type with its position x, y, z in the volume of DNA. Based on the number and types of interactions at the atomic level, the number of DNA single and double strand breaks were calculated. We found that the dissociative electron attachment has the dominant effect on DNA strand breaks at energies below 10 eV compared to excitation and ionization. In addition, it is straightforward with our simulation to discriminate the strand and base breaks as a function of radiation interaction type and energy. In conclusion, the knowledge of DNA damage at the atomic level helps design direct internal therapeutic agents of cancer treatment.

Low-Energy Electron Damage to Plasmid DNA in Thin Films: Dependence on Substrates, Surface Density, Charging, Environment, and Uniformity

The interaction of low-energy electrons (LEEs) with DNA plays a significant role in the mechanisms leading to biological damage induced by ionizing radiation, particularly in radiotherapy, and its sensitization by chemotherapeutic drugs and nanoparticles. Plasmids constitute the form of DNA found in mitochondria and appear as a suitable model of genomic DNA. In a search for the best LEE targets, damage was induced to plasmids, in thin films in vacuum, by 6, 10, and 100 eV electrons under single collision conditions. The yields of single- and double-strand breaks, other cluster damage, isolated base lesions, and crosslinks were measured by electrophoresis and enzyme treatment. The films were deposited on oriented graphite or polycrystalline tantalum, with or without DNA autoassembly via diaminopropane (Dap) intercalation. Yields were correlated with the influence of vacuum, film uniformity, surface density, substrates, and the DNA environment. Aided by surface potential measurements and scanning electron microscopy and atomic force microscopy images, the lyophilized Dap-DNA films were found to be the most practical high-quality targets. These studies pave the way to the fabrication of LEE target-films composed of plasmids intercalated with biomolecules that could mimic the cellular environment; for example, as a first step, by replacing Dap with an amino acid.

Clinical Feasibility Study of Gold Nanoparticles as Theragnostic Agents for Precision Radiotherapy

Background: Gold nanoparticles (AuNP) may be useful in precision radiotherapy and disease monitoring as theragnostic agents. In diagnostics, they can be detected by computerized tomography (CT) because of their higher atomic number. AuNP may also improve the treatment results in radiotherapy due to a higher cross-section, locally improving the physically absorbed dose. Methods: Key parameters values involved in the use of AuNP were imposed to be optimal in the clinical scenario. Mass concentration of AuNP as an efficient contrast agent in clinical CT was found and implemented in a Monte Carlo simulation method for dose calculation under different proposed therapeutic beams. The radiosensitization effect was determined in irradiated cells with AuNP. Results: an AuNP concentration was found for a proper contrast level and enhanced therapeutic effect under a beam typically used for image-guided therapy and monitoring. This lower energetic proposed beam showed potential use for treatment monitoring in addition to absorbed dose enhancement and higher radiosensitization at the cellular level. Conclusion: the results obtained show the use of AuNP concentration around 20 mg Au·mL⁻¹ as an efficient tool for diagnosis, treatment planning, and monitoring treatment. Simultaneously, the delivered prescription dose provides a higher radiobiological effect on the cancer cell for achieving precision radiotherapy.

Tailored Nucleic Acid Architectures at Gold Surfaces for Controlled Therapeutic Release

Nucleic acids are versatile materials capable of forming smart nanocarriers with highly controllable therapeutic delivery. DNA-gated release is a mechanism by which DNA oligonucleotides physically block the release of encapsulated drugs from porous nanoparticles. We extend this mechanism to be used with drugs bound to the surface of DNA-capped gold nanoparticles (AuNPs). We investigated DNA monolayers of different thicknesses and hybridization states to determine how DNA surface architecture can affect the release of a template drug bound to the gold surface. DNA layers are investigated on the planar gold surface via quartz crystal microbalance with dissipation and on AuNPs via dynamic light scattering. The resultant layer architectures were studied for their effect on the release rate of drugs. We observed that varying DNA architectures on AuNPs result in different release rates of the drug. The rate of drug release can be slowed using either folded or randomly coiled DNA sequences, which act as a physical barrier to diffusion. DNA monolayers with upright orientation release drugs more quickly. When the longer single-stranded DNA is used, the drug release is slowed even further. However, even upright DNA layers provide a barrier to drug diffusion at longer sequence lengths. We hypothesize that it is the architecture of the DNA layer, influenced by the folded or upright orientation of individual DNA molecules, that affects the free diffusion of the drug away from the AuNP surface. This mechanism may improve the biological availability of many surface-bound drugs on solid, DNA-capped nanoparticles.

Long term conservation of DNA at ambient temperature. Implications for DNA data storage

DNA conservation is central to many applications. This leads to an ever-increasing number of samples which are more and more difficult and costly to store or transport. A way to alleviate this problem is to develop procedures for storing samples at room temperature while maintaining their stability. A variety of commercial systems have been proposed but they fail to completely protect DNA from deleterious factors, mainly water. On the other side, Imagene company has developed a procedure for long-term conservation of biospecimen at room temperature based on the confinement of the samples under an anhydrous and anoxic atmosphere maintained inside hermetic capsules. The procedure has been validated by us and others for purified RNA, and for DNA in buffy coat or white blood cells lysates, but a precise determination of purified DNA stability is still lacking. We used the Arrhenius law to determine the DNA degradation rate at room temperature. We found that extrapolation to 25°C gave a degradation rate constant equivalent to about 1 cut/century/100 000 nucleotides, a stability several orders of magnitude larger than the current commercialized processes. Such a stability is fundamental for many applications such as the preservation of very large DNA molecules (particularly interesting in the context of genome sequencing) or oligonucleotides for DNA data storage. Capsules are also well suited for this latter application because of their high capacity. One can calculate that the 64 zettabytes of data produced in 2020 could be stored, standalone, for centuries, in about 20 kg of capsules.

Multi-scale Monte Carlo simulations of gold nanoparticle-induced DNA damages for kilovoltage X-ray irradiation in a xenograft mouse model using TOPAS-nBio

Background

Gold nanoparticles (AuNPs) are considered as promising agents to increase the radiosensitivity of tumor cells. However, the biological mechanisms of radiation enhancement effects of AuNPs are still not well understood. We present a multi-scale Monte Carlo simulation framework within TOPAS-nBio to investigate the increase of DNA damage due to the presence of AuNPs in mouse tumor models.

Methods

A tumor was placed inside a voxel mouse model and irradiated with either 100 kVp or 200 kVp x-ray beams. Phase spaces were employed to transfer particles from the macroscopic (voxel) scale to the microscopic scale, which consists of a cell geometry including a detailed mouse DNA model. Radiosensitizing effects were calculated in the presence and absence of hybrid nanoparticles with a Fe2O3 core surrounded by a gold layer (AuFeNPs). To simulate DNA damage even for very small energy tracks, Geant4-DNA physics and chemistry models were used on microscopic scale.

Results

An AuFeNP induced enhancement of both dose and DNA strand breaks has been established for different scenarios. Produced chemical radicals including hydroxyl molecules, which were assumed to be responsible for DNA damage through chemical reactions, were found to be significantly increased. We further observed a dependency of the results on the location of the cells within the tumor for 200 kVp x-ray beams.

Conclusions

Our multi-scale approach allows to study irradiation induced physical and chemical effects on cells. We showed a potential increase in cell radiosensitization caused by relatively small concentrations of AuFeNPs. Our new methodology allows the individual adjustment of parameters in each simulation step and therefore can be used for other studies investigating the radiosensitizing effects of AuFeNPs or AuNPs in living cells.

Towards the characterization of neutron carcinogenesis through direct action simulations of clustered DNA damage

Neutron exposure poses a unique radiation protection concern because neutrons have a large, energy-dependent relative biological effectiveness (RBE) for stochastic effects. Recent computational studies on the microdosimetric properties of neutron dose deposition have implicated clustered DNA damage as a likely contributor to this marked energy dependence. So far, publications have focused solely on neutron RBE for inducing clusters of DNA damage containing two or more DNA double strand breaks (DSBs). In this study, we have conducted a novel assessment of neutron RBE for inducing all types of clustered DNA damage that contain two or more lesions, stratified by whether the clusters contain DSBs (complex DSB clusters) or not (non-DSB clusters). This assessment was conducted for eighteen initial neutron energies between 1 eV and 10 MeV as well as a reference radiation of 250 keV x-rays. We also examined the energy dependence of cluster length and cluster complexity because these factors are believed to impact the DNA repair process. To carry out our investigation, we developed a user-friendly TOPAS-nBio application that includes a custom nuclear DNA model and a novel algorithm for recording clustered DNA damage. We found that neutron RBE for inducing complex DSB clusters exhibited similar energy dependence to the canonical neutron RBE for stochastic radiobiological effects, at multiple depths in human tissue. Qualitatively similar results were obtained for non-DSB clusters, although the quantitative agreement was lower. Additionally we identified a significant neutron energy dependence in the average length and complexity of clustered lesions. These results support the idea that many types of clustered DNA damage contribute to the energy dependence of neutron RBE for stochastic radiobiological effects and imply that the size and constituent lesions of individual clusters should be taken into account when modeling DNA repair. Our results were qualitatively consistent for (i) multiple radiation doses (including a low-dose 0.1 Gy irradiation), (ii) variations in the maximal lesion separation distance used to define a cluster, and (iii) two distinct collections of physics models used to govern particle transport. Our complete TOPAS-nBio application has been released under an open-source license to enable others to independently validate our work and to expand upon it.

Cellular Response to Proton Irradiation: A Simulation Study with TOPAS-nBio

The cellular response to ionizing radiation continues to be of significant research interest in cancer radiotherapy, and DNA is recognized as the critical target for most of the biologic effects of radiation. Incident particles can cause initial DNA damages through physical and chemical interactions within a short time scale. Initial DNA damages can undergo repair via different pathways available at different stages of the cell cycle. The misrepair of DNA damage results in genomic rearrangement and causes mutations and chromosome aberrations, which are drivers of cell death. This work presents an integrated study of simulating cell response after proton irradiation with energies of 0.5-500 MeV (LET of 60-0.2 keV/µm). A model of a whole nucleus with fractal DNA geometry was implemented in TOPAS-nBio for initial DNA damage simulations. The default physics and chemistry models in TOPAS-nBio were used to describe interactions of primary particles, secondary particles, and radiolysis products within the nucleus. The initial DNA double-strand break (DSB) yield was found to increase from 6.5 DSB/Gy/Gbp at low-linear energy transfer (LET) of 0.2 keV/µm to 21.2 DSB/Gy/Gbp at high LET of 60 keV/µm. A mechanistic repair model was applied to predict the characteristics of DNA damage repair and dose response of chromosome aberrations. It was found that more than 95% of the DSBs are repaired within the first 24 h and the misrepaired DSB fraction increases rapidly with LET and reaches 15.8% at 60 keV/µm with an estimated chromosome aberration detection threshold of 3 Mbp. The dicentric and acentric fragment yields and the dose response of micronuclei formation after proton irradiation were calculated and compared with experimental results.

Effect of static magnetic field on DNA synthesis: The interplay between DNA chirality and magnetic field left-right asymmetry

Interactions between magnetic fields (MFs) and living cells may stimulate a large variety of cellular responses to a MF, while the underlying intracellular mechanisms still remain a great puzzle. On a fundamental level, the MF - cell interaction is affected by the two broken symmetries: (a) left-right (LR) asymmetry of the MF and (b) chirality of DNA molecules carrying electric charges and subjected to the Lorentz force when moving in a MF. Here we report on the chirality-driven effect of static magnetic fields (SMFs) on DNA synthesis. This newly discovered effect reveals how the interplay between two fundamental features of symmetry in living and inanimate nature-DNA chirality and the inherent features of MFs to distinguish the left and right-manifests itself in different DNA synthesis rates in the upward and downward SMFs, consequently resulting in unequal cell proliferation for the two directions of the field. The interplay between DNA chirality and MF LR asymmetry will provide fundamental knowledge for many MF-induced biological phenotypes.

Clinically relevant nanodosimetric simulation of DNA damage complexity from photons and protons

Relative Biological Effectiveness (RBE), the ratio of doses between radiation modalities to produce the same biological endpoint, is a controversial and important topic in proton therapy. A number of phenomenological models incorporate variable RBE as a function of Linear Energy Transfer (LET), though a lack of mechanistic description limits their applicability. In this work we take a different approach, using a track structure model employing fundamental physics and chemistry to make predictions of proton and photon induced DNA damage, the first step in the mechanism of radiation-induced cell death. We apply this model to a proton therapy clinical case showing, for the first time, predictions of DNA damage on a patient treatment plan. Our model predictions are for an idealised cell and are applied to an ependymoma case, at this stage without any cell specific parameters. By comparing to similar predictions for photons, we present a voxel-wise RBE of DNA damage complexity. This RBE of damage complexity shows similar trends to the expected RBE for cell kill, implying that damage complexity is an important factor in DNA repair and therefore biological effect.

Relative Biological Effectiveness (RBE) is a controversial and important topic in proton therapy. This work uses Monte Carlo simulations of DNA damage for protons and photons to probe this phenomenon, providing a plausible mechanistic understanding.

Absolute cross section for DNA damage induced by low-energy (10 eV) electrons: Experimental refinements and sample characterization by AFM

This work describes multiple experimental improvements for measuring absolute cross sections of DNA damage induced by low-energy electrons in nanometer-thick films in vacuum. Measurements of such cross sections are particularly sensitive to film thickness and uniformity. Using atomic force microscopy in 70% ethanol, we present a novel and effective method to determine plasmid DNA film thickness and uniformity that combines height histograms and force-distance curves. We also investigate film deposition with DNA intercalated with 1,3-diaminopropane (Dap) on tantalum-coated substrates as a convenient and cost-effective alternative to the previously-used graphite substrate. The tantalum substrate permits deposition of films very similar to those formed on graphite. Using these refinements and further optimizations of the experimental procedure, we measure an absolute cross section of (7.4 ± 2.3) × 10^-18 cm² per nucleotide for conformational damage to a 3197 base-pair plasmid, induced by 10 eV electrons, which we believe should be considered as a reference value.

Optical dispersion control in surfactant-free DNA thin films by vitamin B2 doping

A new route to systematically control the optical dispersion properties of surfactant-free deoxyribonucleic acid (DNA) thin solid films was developed by doping them with vitamin B2, also known as riboflavin. Surfactant-free DNA solid films of high optical quality were successfully deposited on various types of substrates by spin coating of aqueous solutions without additional chemical processes, with thicknesses ranging from 18 to 100 nm. Optical properties of the DNA films were investigated by measuring UV-visible-NIR transmission, and their refractive indices were measured using variable-angle spectroscopic ellipsometry. By doping DNA solid films with riboflavin, the refractive index was consistently increased with an index difference Δn ≥ 0.015 in the spectral range from 500 to 900 nm, which is sufficiently large to make an all-DNA optical waveguide. Detailed correlation between the optical dispersion and riboflavin concentration was experimentally investigated and thermo-optic coefficients of the DNA-riboflavin thin solid films were also experimentally measured in the temperature range from 20 to 85 °C, opening the potential to new bio-thermal sensing applications.

Biomass density-function relationships in suspended growth biological processes - A critical review

Good settling performance in suspended growth biomass systems, for example in activated sludge (AS) process, leads to efficient wastewater and sludge treatment. Factors that cause the differences in settleablility of AS include the morphology of bacteria, microbial community structure, and the density of bacteria and flocs. Density of AS at three levels, namely, cell, floc, and process, have been discussed here to explain the variations in AS settleability. Dense materials, inside or outside the cell, significantly increase density of AS bacteria or flocs. Functional bacteria, defined as those performing N and P removal and recovery such as phosphate accumulating organisms, nitrifiers, and anammox contain cellular inclusions that increase their density, and consequently a dense and well-settling biomass results at the process level in those systems. A density based selector of AS can be used to enrich functional bacteria in the process through the wasting and sludge age control operations in AS process. This paper critically reviews the latest literature to elucidate mechanisms of density enhancement from cell to process level, and identifies needs/strategies to improve the AS process through a biomass density selector.

Gold nanoparticles for cancer radiotherapy: a review

Radiotherapy is currently used in around 50% of cancer treatments and relies on the deposition of energy directly into tumour tissue. Although it is generally effective, some of the deposited energy can adversely affect healthy tissue outside the tumour volume, especially in the case of photon radiation (gamma and X-rays). Improved radiotherapy outcomes can be achieved by employing ion beams due to the characteristic energy deposition curve which culminates in a localised, high radiation dose (in form of a Bragg peak). In addition to ion radiotherapy, novel sensitisers, such as nanoparticles, have shown to locally increase the damaging effect of both photon and ion radiation, when both are applied to the tumour area. Amongst the available nanoparticle systems, gold nanoparticles have become particularly popular due to several advantages: biocompatibility, well-established methods for synthesis in a wide range of sizes, and the possibility of coating of their surface with a large number of different molecules to provide partial control of, for example, surface charge or interaction with serum proteins. This gives a full range of options for design parameter combinations, in which the optimal choice is not always clear, partially due to a lack of understanding of many processes that take place upon irradiation of such complicated systems. In this review, we summarise the mechanisms of action of radiation therapy with photons and ions in the presence and absence of nanoparticles, as well as the influence of some of the core and coating design parameters of nanoparticles on their radiosensitisation capabilities.

Investigation of various fluorescent protein–DNA binding peptides for effectively visualizing large DNA molecules

Single-molecule DNA visualization with fluorescent protein DNA binding peptides.

Water versus DNA: new insights into proton track-structure modelling in radiobiology and radiotherapy

Water is a common surrogate of DNA for modelling the charged particle-induced ionizing processes in living tissue exposed to radiations. The present study aims at scrutinizing the validity of this approximation and then revealing new insights into proton-induced energy transfers by a comparative analysis between water and realistic biological medium. In this context, a self-consistent quantum mechanical modelling of the ionization and electron capture processes is reported within the continuum distorted wave-eikonal initial state framework for both isolated water molecules and DNA components impacted by proton beams. Their respective probability of occurrence-expressed in terms of total cross sections-as well as their energetic signature (potential and kinetic) are assessed in order to clearly emphasize the differences existing between realistic building blocks of living matter and the controverted water-medium surrogate. Consequences in radiobiology and radiotherapy will be discussed in particular in view of treatment planning refinement aiming at better radiotherapy strategies.

Proton-induced direct and indirect damage of plasmid DNA

Clustered DNA damage induced by 10, 20 and 30 MeV protons in pBR322 plasmid DNA was investigated. Besides determination of strand breaks, additional lesions were detected using base excision repair enzymes. The plasmid was irradiated in dry form, where indirect radiation effects were almost fully suppressed, and in water solution containing only minimal residual radical scavenger. Simultaneous irradiation of the plasmid DNA in the dry form and in the solution demonstrated the contribution of the indirect effect as prevalent. The damage composition slightly differed when comparing the results for liquid and dry samples. The obtained data were also subjected to analysis concerning different methodological approaches, particularly the influence of irradiation geometry, models used for calculation of strand break yields and interpretation of the strand breaks detected with the enzymes. It was shown that these parameters strongly affect the results.