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1. Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA

   https://doi.org/10.1016/j.bpj.2020.08.031  

   Ray, D ; Andricioaei, I. ( September 2020 , Biophysical journal)

   Genetic information is encoded in the DNA double helix, which, in its physiological milieu, is characterized by the iconical Watson-Crick nucleo-base pairing. Recent NMR relaxation experiments revealed the transient presence of an alternative, Hoogsteen (HG) base pairing pattern in naked DNA duplexes, and estimated its relative stability and lifetime. In contrast with DNA, such structures were not observed in RNA duplexes. Understanding HG base pairing is important because the underlying "breathing" motion between the two conformations can significantly modulate protein binding. However, a detailed mechanistic insight into the transition pathways and kinetics is still missing. We performed enhanced sampling simulation (with combined metadynamics and adaptive force-bias method) and Markov state modeling to obtain accurate free energy, kinetics, and the intermediates in the transition pathway between Watson-Crick and HG base pairs for both naked B-DNA and A-RNA duplexes. The Markov state model constructed from our unbiased MD simulation data revealed previously unknown complex extrahelical intermediates in the seemingly simple process of base flipping in B-DNA. Extending our calculation to A-RNA, for which HG base pairing is not observed experimentally, resulted in relatively unstable, single-hydrogen-bonded, distorted Hoogsteen-like bases. Unlike B-DNA, the transition pathway primarily involved base paired and intrahelical intermediates with transitionmore »timescales much longer than that of B-DNA. The seemingly obvious flip-over reaction coordinate (i.e., the glycosidic torsion angle) is unable to resolve the intermediates. Instead, a multidimensional picture involving backbone dihedral angles and distance between hydrogen bond donor and acceptor atoms is required to gain insight into the molecular mechanism.« less
2. Reaction of Electrons with DNA: Radiation Damage to Radiosensitization

   https://doi.org/10.3390/ijms20163998  

   Kumar, Anil ; Becker, David ; Adhikary, Amitava ; Sevilla, Michael D. ( August 2019 , International Journal of Molecular Sciences)

   This review article provides a concise overview of electron involvement in DNA radiation damage. The review begins with the various states of radiation-produced electrons: Secondary electrons (SE), low energy electrons (LEE), electrons at near zero kinetic energy in water (quasi-free electrons, (e−qf)) electrons in the process of solvation in water (presolvated electrons, e−pre), and fully solvated electrons (e−aq). A current summary of the structure of e−aq, and its reactions with DNA-model systems is presented. Theoretical works on reduction potentials of DNA-bases were found to be in agreement with experiments. This review points out the proposed role of LEE-induced frank DNA-strand breaks in ion-beam irradiated DNA. The final section presents radiation-produced electron-mediated site-specific formation of oxidative neutral aminyl radicals from azidonucleosides and the evidence of radiosensitization provided by these aminyl radicals in azidonucleoside-incorporated breast cancer cells.
3. Ultrafast Processes Occurring in Radiolysis of Highly Concentrated Solutions of Nucleosides/Tides

   https://doi.org/10.3390/ijms20194963  

   MA, Jun ; Denisov, Sergey A. ; Adhikary, Amitava ; Mostafavi, Mehran ( October 2019 , International Journal of Molecular Sciences)

   Among the radicals (hydroxyl radical (•OH), hydrogen atom (H•), and solvated electron (esol−)) that are generated via water radiolysis, •OH has been shown to be the main transient species responsible for radiation damage to DNA via the indirect effect. Reactions of these radicals with DNA-model systems (bases, nucleosides, nucleotides, polynucleotides of defined sequences, single stranded (ss) and double stranded (ds) highly polymeric DNA, nucleohistones) were extensively investigated. The timescale of the reactions of these radicals with DNA-models range from nanoseconds (ns) to microseconds (µs) at ambient temperature and are controlled by diffusion or activation. However, those studies carried out in dilute solutions that model radiation damage to DNA via indirect action do not turn out to be valid in dense biological medium, where solute and water molecules are in close contact (e.g., in cellular environment). In that case, the initial species formed from water radiolysis are two radicals that are ultrashort-lived and charged: the water cation radical (H2O•+) and prethermalized electron. These species are captured by target biomolecules (e.g., DNA, proteins, etc.) in competition with their inherent pathways of proton transfer and relaxation occurring in less than 1 picosecond. In addition, the direct-type effects of radiation, i.e., ionization of macromoleculemore »plus excitations proximate to ionizations, become important. The holes (i.e., unpaired spin or cation radical sites) created by ionization undergo fast spin transfer across DNA subunits. The exploration of the above-mentioned ultrafast processes is crucial to elucidate our understanding of the mechanisms that are involved in causing DNA damage via direct-type effects of radiation. Only recently, investigations of these ultrafast processes have been attempted by studying concentrated solutions of nucleosides/tides under ambient conditions. Recent advancements of laser-driven picosecond electron accelerators have provided an opportunity to address some long-term puzzling questions in the context of direct-type and indirect effects of DNA damage. In this review, we have presented key findings that are important to elucidate mechanisms of complex processes including excess electron-mediated bond breakage and hole transfer, occurring at the single nucleoside/tide level.« less
4. Thermoresponsive polymer assemblies via variable temperature liquid-phase transmission electron microscopy and small angle X-ray scattering

   https://doi.org/10.1038/s41467-021-26773-z  

   Korpanty, Joanna ; Parent, Lucas R. ; Hampu, Nicholas ; Weigand, Steven ; Gianneschi, Nathan C. ( November 2021 , Nature Communications)

   Herein, phase transitions of a class of thermally-responsive polymers, namely a homopolymer, diblock, and triblock copolymer, were studied to gain mechanistic insight into nanoscale assembly dynamics via variable temperature liquid-cell transmission electron microscopy (VT-LCTEM) correlated with variable temperature small angle X-ray scattering (VT-SAXS). We study thermoresponsive poly(diethylene glycol methyl ether methacrylate) (PDEGMA)-based block copolymers and mitigate sample damage by screening electron flux and solvent conditions during LCTEM and by evaluating polymer survival viapost-mortemmatrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS). Our multimodal approach, utilizing VT-LCTEM with MS validation and VT-SAXS, is generalizable across polymeric systems and can be used to directly image solvated nanoscale structures and thermally-induced transitions. Our strategy of correlating VT-SAXS with VT-LCTEM provided direct insight into transient nanoscale intermediates formed during the thermally-triggered morphological transformation of a PDEGMA-based triblock. Notably, we observed the temperature-triggered formation and slow relaxation of core-shell particles with complex microphase separation in the core by both VT-SAXS and VT-LCTEM.
5. Explaining Kinetic Trends of Inner-Sphere Transition-Metal-Ion Redox Reactions on Metal Electrodes

   https://doi.org/10.1021/acscatal.2c05694  

   Agarwal, Harsh ; Florian, Jacob ; Pert, Daniel ; Goldsmith, Bryan R. ; Singh, Nirala ( January 2023 , ACS Catalysis)

   Transition-metal ions regularly undergo charge transfer (CT) by directly interacting with electrodes, and this CT governs the performance of devices for numerous applications like energy storage and catalysis. These CT reactions are deemed inner sphere because they involve direct formation of a chemical bond between the electrode and the metal ion. Predicting inner-sphere CT kinetics on electrodes using simple physicochemical descriptors would aid the design of electrochemical systems with improved kinetics. Herein, we report that the average energy of the d electrons (i.e., d-band center) of a transition-metal electrode rationalizes the kinetic trends of inner-sphere CT of transition-metal ions. We demonstrate that V2+/V3+, an important redox reaction for flow batteries, is an inner-sphere reaction and that the kinetic parameters correlate with the adsorption strength of the vanadium intermediate on Au, Ag, Cu, Bi, and W electrodes, with W being the most active electrode reported to date. We show that the adsorption strength of the vanadium intermediate linearly correlates with the d-band center such that the d-band center serves as a simple descriptor for the V2+/V3+ kinetics. We extract kinetic data from the literature for four other inner-sphere CT reactions of metal ions involving Cr-, Fe-, and Co-based complexes to showmore »that the d-band center also linearly correlates with kinetic trends for these systems. The d-band center of the electrode is a general descriptor for heterogeneous inner-sphere CT because it correlates with the adsorption strength of the metal-ion intermediate. The d-band center descriptor is analogous to the d-electron configuration of metal ions serving as a descriptor for homogeneous inner-sphere CT because the d-electron configuration controls bond strengths of intermediate metal-ion complexes.« less