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The formation and structure of the 5′–G[8–5]U–3′ intrastrand cross-link are studied using density functional theory and molecular dynamics simulations due to the potential role of this lesion in the activity of 5-halouracils in antitumor therapies. Upon UV irradiation of 5-halouracil-containing DNA, a guanine radical cation reacts with the uracil radical to form the cross-link, which involves phosphorescence or an intersystem crossing and a rate-determining step of bond formation. Following ionizing radiation, guanine and the uracil radical react, with a rate-limiting step involving hydrogen atom removal. Although cross-link formation from UV radiation is favored, comparison of calculated reaction thermokinetics with that for related experimentally observed purine–pyrimidine cross-links suggests this lesion is also likely to form from ionizing radiation. For the first time, the structure of 5′–G[8–5]U–3′ within DNA is identified by molecular dynamics simulations. Furthermore, three conformations of cross-linked DNA are revealed, which differ in the configuration of the complementary bases. Distortions, such as unwinding, are localized to the cross-linked dinucleotide and complementary nucleotides, with minimal changes to the flanking bases. Global changes to the helix, such as bending and groove alterations, parallel cisplatin-induced distortions, which indicate 5′–G[8–5]U–3′, may contribute to the cytotoxicity of halouracils in tumor cell DNA using similar mechanisms. [ABSTRACT FROM AUTHOR]

Bulky DNA addition products (adducts) formed through attack at the C8 site of guanine can adopt the synorientation about the glycosidic bond due to changes in conformational stability or hydrogen-bonding preferences directly arising from the bulky group. Indeed, the bulky substituent may improve the stability of (non-native) Hoogsteen pairs. Therefore, such adducts often result in mutations upon DNA replication. This work examines the hydrogen-bonded pairs between the Watson−Crick and Hoogsteen faces of the orthoor paraC8-phenoxyl-2′-deoxyguanosine adduct and each natural (undamaged) nucleobase with the goal to clarify the conformational preference of this type of damage, as well as provide insight into the likelihood of subsequent mutation events. B3LYP/6-311(2df,p)//B3LYP/6-31G(d) hydrogen-bond strengths were determined using both nucleobase and nucleoside models for adduct pairs, as well as the corresponding complexes involving natural 2′-deoxyguanosine. In addition to the magnitude of the binding strengths, the R(C1′···C1′) distances and ∠(N9C1′C1′) angles, as well as the degree of propeller-twist and buckle distortions, were carefully compared to the values observed in natural DNA strands. Due to structural changes in the adduct monomer upon inclusion of the sugar moiety, the monomer deformation energy significantly affects the relative hydrogen-bond strengths calculated with the nucleobase and nucleoside models. Therefore, we recommend the use of at least a nucleoside model to accurately evaluate hydrogen-bond strengths of base pairs involving flexible, bulky nucleobase adducts. Our results also emphasize the importance of considering both the magnitude of the hydrogen-bond strength and the structure of the base pair when predicting the preferential binding patterns of nucleobases. Using our best models, we conclude that the Watson−Crick face of the orthophenoxyl adduct forms significantly more stable complexes than the Hoogsteen face, which implies that the antiorientation of the damaged base will be favored by hydrogen bonding in DNA helices. Additionally, regardless of the hydrogen-bonding face involved, cytosine forms the most stable base pair with the orthoadduct, which implies that misincorporation due to this type of damage is unlikely. Similarly, cytosine is the preferred binding partner for the Watson−Crick face of the paraadduct. However, Hoogsteen interactions with the paraadduct are stronger than those with natural 2′-deoxyguanosine or the orthoadduct, and this form of damage binds with nearly equal stability to both cytosine and guanine in the Hoogsteen orientation. Therefore, the paraadduct may adopt multiple orientations in DNA helices and potentially cause mutations by forming pairs with different natural bases. Models of oligonucleotide duplexes must be used in future work to further evaluate other factors (stacking, major groove contacts) that may influence the conformation and binding preference of these adducts in DNA helices. [ABSTRACT FROM AUTHOR]

Detailed (gas-phase) MP2/6-31G*(0.25) potential energy surface scans and CCSD(T) energy calculations at the complete basis set (CBS) limit were used to analyze the (face-to-face) stacking and (edge-to-face) T-shaped interactions between histidine (modeled as imidazole) and the DNA nucleobases. For the first time, a variety of relative monomer arrangements between both neutral and protonated histidine and the natural nucleobases were considered to determine the effects of charge on the optimum dimer geometry and binding strength. Our results reveal that protonation of histidine changes the preferred relative orientations of the monomers and propose that these geometric differences may be combined with experimental crystal structures to assess the protonation state of histidine in different environments. It is also found that protonation affects the nucleobase binding preference, as well as the magnitude of the stacking and T-shaped interactions. Indeed, the maximum possible stacking and T-shaped interactions involving the neutral histidine range between approximately 20 and 45 kJ mol−1, while this range increases to 40−105 kJ mol−1upon protonation, which represents an up to 330% enhancement. Although an increase in the interaction energies upon protonation of histidine is expected, the present work provides a measure of the magnitude of this enhancement in the gas phase and reveals that the amplification is almost entirely due to larger electrostatic contributions. The relative strengthening of different classifications of dimers upon protonation leads to stronger T-shaped interactions than stacking energies for protonated histidine, while the stacking and T-shaped interactions involving neutral histidine are of comparable magnitude. Thus, there is a significant difference in the nature of the πcation−π interactions involving protonated histidine and the π−π interactions involving neutral histidine. The calculated strengths of the interactions studied in the present work suggest that both neutral and cationic histidine contacts will provide significant stabilization to DNA−protein complexes. Although solvation effects will decrease the magnitude of the reported interactions, our results are applicable to a variety of low-polarity, biologically−relevant environments such as nonpolar enzyme active sites. Therefore, our calculations suggest that these interactions may also be important for many biological processes. The proposed significance of these interactions is supported by the large number of histidine−nucleobase contacts that appear in experimental crystal structures. The highly accurate (MP2/6-31G*(0.25)) preferred structures and (CCSD(T)/CBS) binding strengths reported in the present work can be used as benchmarks to analyze the performance of existing, or to develop new, molecular mechanics force fields for use in large-scale molecular dynamics (MD) studies of DNA−protein complexes. [ABSTRACT FROM AUTHOR]

Understanding the multi-scale neoclassical and turbulence physics in the edge region (pedestal + scrape-off layer (SOL)) is required in order to reliably predict performance in future fusion devices. We explore turbulent characteristics in the edge region from a multi-scale neoclassical and turbulent XGC1 gyrokinetic simulation in a DIII-D like tokamak geometry, here excluding neutrals and collisions. For an H-mode type plasma with steep pedestal, it is found that the electron density fluctuations increase towards the separatrix, and stay high well into the SOL, reaching a maximum value of . Blobs are observed, born around the magnetic separatrix surface and propagate radially outward with velocities generally less than 1 km s−1. Strong poloidal motion of the blobs is also present, near 20 km s−1, consistent with E × B rotation. The electron density fluctuations show a negative skewness in the closed field-line pedestal region, consistent with the presence of ‘holes’, followed by a transition to strong positive skewness across the separatrix and into the SOL. These simulations indicate that not only neoclassical phenomena, but also turbulence, including the blob-generation mechanism, can remain important in the steep H-mode pedestal and SOL. Qualitative comparisons will be made to experimental observations. [ABSTRACT FROM AUTHOR]

The beam emission spectroscopy (BES) diagnostic is used to measure fluctuations of electron density in the edge and core of fusion plasmas, and is a key in understanding turbulence in a plasma reactor. A synthetic BES diagnostic for the turbulence simulation code XGC1 has been developed using a realistic neutral beam model and an optical system easily adaptable to different kinds of tokamaks. The beam is modeled using multiple beam energy components, each one with a fraction of the total energy and their own mass and energy (mono-energetic components). The optical system consists of a lens focusing a bundle of optical fibers and resulting in a 2D measurement. The synthetic diagnostic gives similar correlation functions and behaviour of the turbulences than the usual methods that do not take into account the full 3D optical effects. The results, based on a simulation of XGC1, contain an analysis of the correlation (in space and time), a comparison of different approximations possible and their importance in accurately modeling the BES diagnostic. [ABSTRACT FROM AUTHOR]

Dedicated experiments in ion cyclotron range heated enhanced D-alpha (EDA) H-mode and I-mode plasmas have been performed on Alcator C-Mod to identify the location of edge fluctuations inside the pedestal and to determine their plasma frame phase velocity. For this purpose, measurements from gas puff imaging (GPI) and gas puff charge exchange recombination spectroscopy (GP-CXRS) have been collected using the same optical views. The data suggest that the EDA H-mode-specific quasi-coherent mode (QCM) is centered near the radial electric field (Er) well minimum and propagates along the ion diamagnetic drift direction in the plasma frame. The weakly coherent mode (WCM) and the geodesic acoustic mode observed in I-mode, on the other hand, are found to be located around the outer shear layer of the Er well. This results in a weak plasma frame phase velocity mostly along the electron diamagnetic drift direction for the WCM. The findings in these EDA H-mode plasmas differ from probe measurements in ohmic EDA H-mode (LaBombard et al 2014 Phys. Plasmas21 056108), where the QCM was identified as an electron drift-wave located several mm outside the Er well minimum in a region of positive Er. To explore if instrumental effects of the optical diagnostics could be the cause of the difference, a synthetic diagnostic for GPI is introduced. This diagnostic reproduces amplitude ratios and relative radial shifts of the mode profiles determined from poloidally and toroidally oriented optics and, if instrumental effects related to GP-CXRS are also included, indicates that the measured location of the QCM and WCM relative to the Er well reported here is only weakly affected by instrumental effects. [ABSTRACT FROM AUTHOR]