DNA-encoded libraries connect the phenotypes of synthetic molecules to a DNA barcode; however, most libraries do not tap into the potential of Darwinian evolution. Herein, we report a DNA-templated synthesis (DTS) architecture to make peptides that are stabilized into α-helical conformations via head-to-tail supramolecular cyclization. Using a pilot library targeting MDM2, we show that repeated screening can amplify a binder from the lowest abundance in the library to a ranking that correlates to binding affinity. The study also highlights the need to design libraries such that the chemistry avoids biases from the heterogeneous yield in DTS.
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http://dx.doi.org/10.1021/jacsau.4c00738 | DOI Listing |
Neurosci Biobehav Rev
January 2025
Department of Medicine and Surgery, Unit of Neuroscience, University of Parma, viale delle Scienze 11A, 43124 Parma (Italy). Electronic address:
Ultimate and proximate levels of analysis offer synergistic explanations can improve the search for causes of disease and their cures. Here we review how several principles of evolutionary biology such as historical contingencies, mismatches, trade-offs, sexual selection and genomic conflict are applied to problems in medicine and psychiatry. The application of evolutionary principles to many other domains of medicine, among them mental disorders, have not received the same reception from preclinical and clinical researchers.
View Article and Find Full Text PDFInt J Mol Sci
December 2024
College of Life Science, Shaanxi Normal University, Xi'an 710119, China.
Functional divergences of coding genes can be caused by divergences in their coding sequences and expression. However, whether and how expression divergences and coding sequence divergences coevolve is not clear. Gene expression divergences in differentiated cells and tissues recapitulate developmental models within a species, while gene expression divergences between analogous cells and tissues resemble traditional phylogenies in different species, suggesting that gene expression divergences are molecular traits that can be used for evolutionary studies.
View Article and Find Full Text PDFNat Chem Biol
January 2025
Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
Directed evolution in mammalian cells offers a powerful approach for advancing synthetic biology applications. However, existing mammalian-based directed evolution methods face substantial bottlenecks, including host genome interference, small library size and uncontrolled mutagenesis. Here we engineered an orthogonal alphaviral RNA replication system to evolve RNA-based devices, enabling RNA replicase-assisted continuous evolution (REPLACE) in proliferating mammalian cells.
View Article and Find Full Text PDFMicrolife
December 2024
Department of Molecular Evolution, Centro de Astrobiología (CAB), CSIC-INTA, Torrejón de Ardoz,28864 Madrid, Spain.
Evolutionary processes acting on populations of organized molecules preceded the origin of living organisms. These prebiotic entities were independently and repeatedly produced [i.e.
View Article and Find Full Text PDFBiosystems
January 2025
ProtoBioCybernetics & Protocellular Metabolomics, The Gene Emergence Project, The Origin of Life Science Foundation, Inc, USA. Electronic address:
Any homeostatic protometabolism would have required orchestration of disparate biochemical pathways into integrated circuits. Extraordinarily specific molecular assemblies were also required at the right time and place. Assembly Theory conflated with its cousins-Complexity Theory, Chaos theory, Quantum Mechanics, Irreversible Nonequilibrium Thermodynamics and Molecular Evolution theory- collectively have great naturalistic appeal in hopes of their providing the needed exquisite steering and controls.
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