Vertical electronic excitations in model systems representing single- and double-stranded B-DNA are characterized using electronic structure theory, including both time-dependent density functional theory (TD-DFT) and correlated wave function techniques. Previous TD-DFT predictions of charge-transfer (CT) states well below the optically bright (1)pipi* states are shown to be artifacts of the improper long-range behavior of standard density-functional exchange approximations, which we rectify here using a long-range correction (LRC) procedure. For nucleobase dimers (hydrogen-bonded or pi-stacked), TD-LRC-DFT affords vertical excitation energies in reasonable agreement with the wave function methods, not only for the (1)npi* and (1)pipi* states but also for the CT states, and qualitatively reproduces well-known base-stacking effects on the absorption spectrum of DNA. The emergence of (1)pipi* Frenkel exciton states, localized on a single strand, is clearly evident, and these states (rather than low-energy CT states) are primarily responsible for the fact that DNA's absorption spectrum exhibits a red tail that is absent in monomer absorption spectra. For B-DNA in aqueous solution, the low-energy tail of the CT band (representing both intra- and interstrand CT states) appears at energies comparable to those of the optically bright (1)pipi* exciton states. In systems with more than one base pair, we also observe the emergence of delocalized, interstrand CT excitations, whose excitation energies may be significantly lower than the lowest CT excitation in a single base pair. Together, these observations suggest that a single Watson-Crick base pair is an inadequate model of the photophysics of B-DNA.
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Microbiol Spectr
January 2025
Department of Infection Biology, Institute of Medicine, University of Tsukuba, Ibaraki, Japan.
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Empa Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland.
Fast and accurate representation of heat transfer in laser powder-bed fusion of metals (PBF-LB/M) is essential for thermo-mechanical analyses. As an example, it benefits the detection of thermal hotspots at the design stage. While traditional physics-based numerical approaches such as the finite element (FE) method are applicable to a wide variety of problems, they are computationally too expensive for PBF-LB/M due to the space- and time-discretization requirements.
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January 2025
Department of Clinical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.
Head and neck squamous cell carcinoma (HNSCC) is an aggressive cancer that is notably associated with a high risk of lymph node metastasis, a major cause of cancer mortality. Current therapeutic options remain limited to surgery supplemented by radio- or chemotherapy; however, these interventions often result in high-grade toxicities. Distant metastasis significantly contributed to the poor prognosis and decreased survival rates.
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December 2024
National Research Centre "Kurchatov Institute", Moscow, 123182, Russia.
Bacterial and viral RNA polymerases are promising targets for the development of new transcription inhibitors. One of the potential blockers of RNA synthesis is 7,8-dihydro-8-oxo-1,-ethenoadenine (oxo-εA), a synthetic compound that combines two adenine modifications: 8-oxoadenine and 1,-ethenoadenine. In this study, we synthesized oxo-εA triphosphate (oxo-εATP) and showed that it could be incorporated by the RNA-dependent RNA polymerase of SARS-CoV-2 into synthesized RNA opposite template residues A and G in the presence of Mn ions.
View Article and Find Full Text PDFJ Phys Chem B
January 2025
Department of Physics of Complex Systems, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India.
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