1. Visualization of liquid-liquid phase transitions using a tiny G-quadruplex binding proteinBikash Ranjan Sahoo, Xiexiong Deng, Ee Lin Wong, Nathan Clark, Harry J. Yang, Alexey Kovalenko, Vivekanandan Subramanian, Bryan B. Guzman, Sarah E. Harris, Janez Plavec, 2025, original scientific article Published in DiRROS: 27.11.2025; Views: 140; Downloads: 57
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2. Silver binding dichotomy for 7-deazaadenine/thymine : preference for Watson–Crick pairing over homobase interactions in DNACarmen López-Chamorro, Antonio Pérez-Romero, Alicia Domínguez-Martín, Uroš Javornik, Oscar Palacios, Janez Plavec, Miguel A. Galindo, 2025, original scientific article Abstract: DNA strands modified with 7-deazaadenine (X) and 7-deazaguanine (Y) have shown promise in forming silver-DNA assemblies while maintaining canonical Watson–Crick base pairing, highlighting the compatibility of silver binding with standard DNA structures. However, critical questions remain regarding the binding preferences of AgI ions to sequences containing 7-deazapurine bases, particularly the prevalence of silver-modified Watson–Crick base pairs versus alternative homobase pair arrangements. To address this, we examined the binding of AgI to complementary X-T sequences, demonstrating a strong preference for canonical X-AgI-T pairing over homoleptic X-AgI-X or T-AgI-T pairs. Additionally, we report the discovery of a novel metallized DNA duplex featuring continuous X-AgI-X homobase pairs, whose structural analysis at the monomeric level, using model base 9-propyl-7-deazaadenine (pX) and AgI salts, reveals a unique silver-binding pattern through the Watson–Crick face. These findings not only advance our understanding of silver-mediated DNA architectures using 7-deazapurines but also provide a foundation for the rational design of sophisticated metal-DNA nanostructures with tailored properties, opening new avenues for the development of functional DNA-based materials.
Keywords: crystal structure, genetics, ions, silver, solution chemistry
Published in DiRROS: 08.09.2025; Views: 365; Downloads: 154
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3. Determination of silver(I)-binding sites in canonical B-DNA by NMR spectroscopyTabea Lenz, Uroš Javornik, Marian Hebenbrock, Janez Plavec, Jens Müller, 2025, original scientific article Abstract: The interaction of metal ions with nucleic acids was studied by determining the initial binding sites of Ag+ ions at unmodified B-DNA by NMR spectroscopy. In particular, NMR spectra were recorded of the Dickerson-Drew dodecamer sequence in the presence of different ratios of Ag+ ions to DNA. The data indicate that the coordination of the first three Ag+ ions per duplex preferentially takes place inside the B-DNA helix rather than at other possible binding sites such as the negatively charged phosphate backbone and/or the endocyclic N7 position of purine residues. Larger DNA aggregates are formed in the presence of excess Ag+ ions, as indicated by the formation of a precipitate and by significant changes in the circular dichroism spectra. As shown by a titration with chloride ions, the Ag+ ions are only loosely bound to the nucleic acids and can be released by precipitation of AgCl.
Keywords: biochemistry, DNA, spectroscopy, NMR
Published in DiRROS: 08.09.2025; Views: 282; Downloads: 105
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5. Thiol-reactive or redox-active : revising a repurposing screen led to a new invalidation pipeline and identified a true noncovalent inhibitor against papain-like protease from SARS-CoV-2Maria Kuzikov, Stefano Morasso, Jeanette Reinshagen, Markus Wolf, Vittoria Monaco, Flora Cozzolino, Simona Golič Grdadolnik, Primož Šket, Janez Plavec, Daniela Iaconis, 2025, original scientific article Abstract: The SARS-CoV-2 papain-like protease PLpro has multiple roles in the viral replication cycle, related to both its polypeptide cleavage function and its ability to antagonize the host immune response. Targeting the PLpro function is recognized as a promising mechanism to modulate viral replication, while supporting host immune responses. However, the development of PLpro-specific inhibitors remains challenging. Comprehensive investigations utilizing enzymatic, binding studies, and cellular assays revealed the previously reported inhibitors to act in an unspecific manner. At present, GRL-0617 and its derivatives remain the best-validated compounds with demonstrated antiviral activity in cells and in mouse models. In this study, we refer to the pitfalls of the redox sensitivity of PLpro. Using a screening-based approach to identify inhibitors of PLpro’s proteolytic activity, we made extensive efforts to validate active compounds over a range of conditions and readouts, emphasizing the need for comprehensive orthogonal data when profiling putative PLpro inhibitors. The remaining active compound, CPI-169, was shown to be a noncovalent inhibitor capable of competing with GRL-0617 in NMR-based experiments, suggesting that it occupied a similar binding site and inhibited viral replication in Vero-E6 cells, opening new design opportunities for further development as antiviral agents.
Keywords: SARS-CoV-2, drug repurposing, papain-like protease, redox, STD-NMR, CPI-169, GRL-0617
Published in DiRROS: 20.08.2025; Views: 337; Downloads: 163
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7. Lipid phase behaviour of the curvature region of thylakoid membranes of Spinacia oleraceaKinga Böde, Andrea Trotta, Ondřej Dlouhý, Uroš Javornik, Virpi Paakkarinen, Hiroaki Fujii, Ildikó Domonkos, Ottó Zsiros, Janez Plavec, Vladimír Špunda, Eva-Mari Aro, Győző Garab, 2025, original scientific article Published in DiRROS: 16.07.2025; Views: 414; Downloads: 266
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8. Structural basis of G-quadruplex recognition by a camelid antibody fragmentMojca Pevec, Tadej Medved, Matic Kovačič, Neža Žerjav, Jernej Imperl, Janez Plavec, Jurij Lah, Remy Loris, San Hadži, 2025, original scientific article Published in DiRROS: 07.07.2025; Views: 409; Downloads: 210
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