The nickel(II)‐mediated self‐assembly of a multimeric DNA binder is described. The binder is composed of two metal‐chelating peptides derived from a bZIP transcription factor (brHis2) and one short AT‐hook domain equipped with two bipyridine ligands (HkBpy2). These peptides reversibly assemble in the presence of NiII ions at selected DNA sequences of 13 base pairs ; Financial support from the Spanish grants SAF2016‐76689‐R, RTI2018‐099877‐B‐I00, Orfeo‐cinqa network CTQ2016‐81797‐REDC, the Xunta de Galicia (2015‐CP082, ED431C‐2017/19 and Centro Singular de Investigación de Galicia accreditation 019–2022, ED431G 2019/03), the European Union (European Regional Development Fund—ERDF), and the European Research Council (Advanced Grant No. 340055) are gratefully acknowledged. S.L.‐A. thanks the Spanish MINECO for her FPI fellowship (BES‐2017‐080555); J.R. thanks the Xunta de Galicia for her PhD fellowship ; SI
This is the peer reviewed version of the following article: Martínez-Calvo, M.; Guerrini, L.; Rodríguez, J.; Álvarez Puebla, R. A.; Mascareñas, J. L. (2020), Surface-enhanced Raman Scattering Detection of Nucleic Acids exhibiting Sterically Accessible Guanines using Ruthenium-polypyridyl Reagents. J. Phys. Chem. Lett., 11: 7218–7223, which has been published in final form at https://doi.org/10.1021/acs.jpclett.0c02148. This article may be used for non-commercial purposes in accordance with ACS Terms and Conditions for Use of Self-Archived Versions ; Here, we report the application of surface-enhanced Raman scattering (SERS) spectroscopy as a rapid and practical tool for assessing the formation of coordinative adducts between nucleic acid guanines and ruthenium polypyridyl reagents. The technology provides a practical approach for the wash-free and quick identification of nucleic acid structures exhibiting sterically accessible guanines. This is demonstrated for the detection of a quadruplex-forming sequence present in the promoter region of the c-myc oncogene, which exhibits a nonpaired, reactive guanine at a flanking position of the G-quartets ; We are thankful for the financial support from the Xunta de Galicia (Centro singular de investigación de Galicia accreditation 2019-2022, ED431G 2019/03) and the European Union (European Regional Development Fund – ERDF). We also acknowledge the support given by the Spanish Grant SAF2013-41943-R and SAF2016-76689-R, the Xunta de Galicia (Grants 2015-CP082, ED431C 2017/19,), the Spanish Ministry de Economia y Competitividad (CTQ2017-88648R and RYC-2016-20331), the Generalitat de Cataluña (2017SGR883), the Universitat Rovira i Virgili (2019PFR-URV-B2-02), the Universitat Rovira i Virgili and Banco Santander (2017EXIT-08), and the European Research Council (Advanced Grant No. 340055). M.M.-C. thanks the Ministerio de Economı́a y Competitividad for the Postdoctoral fellowship (IJCI-2014-19326) and the Ministerio de Ciencia e Innovación and Ministerio de Universidades for ...
Herein, we describe an approach for the on-demand disassembly of dimeric peptides using a palladium-mediated cleavage of a designed self-immolative linker. The utility of the strategy is demonstrated for the case of dimeric basic regions of bZIP transcription factors. While the dimer binds designed DNA sequences with good affinities, the peptide–DNA complex can be readily dismounted by addition of palladium reagents that trigger the cleavage of the spacer, and the release of unfunctional monomeric peptides ; We are thankful for the financial support from the Xunta de Galicia (Centro singular de investigación de Galicia acreditación 2019–2022, ED431G 2019/03) and the European Union (European Regional Development Fund – ERDF). We also thank support given by the Spanish grants PID2019-108624RB-I00, the Xunta de Galicia (grants 2015-CP082, ED431C 2017/19 and 2021-CP054, ED431C-2021/25) and the European Research Council (Advanced Grant No. 340055). MMC and JR thank the MCIN/AEI for their Postdoctoral fellowships (IJCI-2014-19326 and IJC2019-040358-I) ; SI
A fragment of the DNA basic region (br) of the GCN4 bZIP transcription factor has been modified to include two His residues at designed i and i+4 positions of its N-terminus. The resulting monomeric peptide (brHis2) does not bind to its consensus target DNA site (5′-GTCAT-3′). However, addition of Pd(en)Cl2 (en, ethylenediamine) promotes a high-affinity interaction with exquisite selectivity for this sequence. The peptide–DNA complex is disassembled by addition of a slight excess of a palladium chelator, and the interaction can be reversibly switched multiple times by playing with controlled amounts of either the metal complex or the chelator. Importantly, while the peptide brHis2 fails to translocate across cell membranes on its own, addition of the palladium reagent induces an efficient cell internalization of this peptide. In short, we report (1) a designed, short peptide that displays highly selective, major groove DNA binding, (2) a reversible, metal-dependent DNA interaction, and (3) a metal-promoted cell internalization of this basic peptide ; This work has received financial support from the MINECO (SAF2013-41943-R, SAF2016-76689-R, and CTQ2015-70698-R), the Xunta de Galicia (2015-CP082, ED431C 2017/19, and Centro Singular de Investigación de Galicia Accreditation 2016–2019, ED431G/09), the European Union (European Regional Development Fund, ERDF), and the European Research Council (Advanced Grant No. 340055). Support of COST CM1306 and the orfeo-cinqa network are also acknowledged. J.R. thanks the Xunta de Galicia for a Ph.D. fellowship. We also wish to acknowledge the generous support by the Fundación AECC (IDEAS197VAZQ grant) ; SI
Discrete palladium(II) complexes featuring purposely designed phosphine ligands can promote depropargylation and deallylation reactions in cell lysates. These complexes perform better than other palladium sources, which apparently are rapidly deactivated in such hostile complex media. This good balance between reactivity and stability allows the use of these discrete phosphine palladium complexes in living mammalian cells, whereby they can mediate similar transformations. The presence of a phosphine ligand in the coordination sphere of palladium also provides for the introduction of targeting groups, such as hydrophobic phosphonium moieties, which facilitate the accumulation of the complexes in mitochondria ; We are thankful for the financial support from the Xunta de Galicia (Centro Singular de Investigación de Galicia Acreditación 2016–2019, ED431G/09) and the European Union (European Regional Development Fund–ERDF). We also thank support given by the Spanish Grant No. SAF2016-76689-R, the Xunta de Galicia (Grant Nos. 2015-CP082, ED431C 2017/19), and the European Research Council (Advanced Grant No. 340055). M.M.C. thanks the Ministerio de Economía y Competitividad for the Postdoctoral fellowship (No. IJCI-2014-19326). J.R. and J.M. thank Xunta de Galicia and Ministerio of Educacion, respectively, for predoctoral fellowships. The authors thank R. Menaya-Vargas for technical assistance ; SI
Obtaining artificial proteins that mimic the DNA binding properties of natural transcription factors could open new ways of manipulating gene expression at will. In this context it is particularly interesting to develop simple synthetic systems. Inspired by the modularity of natural transcription factors, we have designed synthetic miniproteins that combine the zinc finger module of the transcription factor GAGA and AT-hook peptide domains. These constructs are capable of binding to composite DNA sequences of up to 14 base pairs with high affinity and good selectivity. In particular, we have synthesized three different chimeras and characterized their DNA binding properties by electrophoresis and fluorescence anisotropy. We have also used, for the first time in the study of peptide-based DNA binders, nanopore force spectroscopy to obtain further data on the DNA interaction. ; This work received support from the MINECO (SAF2013-41943- R, BFU2016-81754-ERC, CTQ2015-70698-R, SAF2014-58398-R, and SAF2016-76689-R), the Xunta de Galicia (2015-CP082, ED431C 2017/19 and Centro singular de investigación de Galicia accreditation 2016–2019, ED431G/09), the Fundación AECC (IDEAS197VAZQ), the European Union (European Regional Development Fund – ERDF), and the European Research Council (Advanced Grant No. 340055). Support of the orfeocinqa network is also acknowledged. J. R. thanks the Xunta de Galicia for a PhD fellowship; D. R.-L. is a recipient of a Ramón y Cajal Fellowship (RYC-2013-12799) ; SI
