2026

References#

The project report's bibliography, supplemented with sources cited in the wiki, in alphabetical order by first author. Background citations use verified journal versions where available; a cited preprint is identified as such.

  1. W.J. Altenburg, N. Rollins, P.A. Silver & T.W. Giessen, “Exploring targeting peptide-shell interactions in encapsulin nanocompartments”. Scientific Reports 11, 4951 (2021). doi:10.1038/s41598-021-84329-z
  2. B. Álvarez, M. Mencía, V. de Lorenzo, L.Á. Fernández, “In vivo diversification of target genomic sites using processive base deaminase fusions blocked by dCas9”. Nature Communications 11, 6436 (2020). doi:10.1038/s41467-020-20230-z
  3. R.J. Austin, T. Xia, J. Ren, T.T. Takahashi, R.W. Roberts, “Designed arginine-rich RNA-binding peptides with picomolar affinity”. Journal of the American Chemical Society 124, 10966–10967 (2002). doi:10.1021/ja026610b
  4. J. Baron-Benhamou, N.H. Gehring, A.E. Kulozik, M.W. Hentze, “Using the lambdaN peptide to tether proteins to RNAs”. Methods in Molecular Biology 257, 135–154 (2004). doi:10.1385/1-59259-750-5:135
  5. D. Bikard, W. Jiang, P. Samai, A. Hochschild, F. Zhang, L.A. Marraffini, “Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system”. Nucleic Acids Research 41, 7429–7437 (2013). doi:10.1093/nar/gkt520
  6. I. Boyton, S.C. Goodchild, D. Diaz, A. Elbourne, L.E. Collins-Praino, A. Care, “Characterizing the Dynamic Disassembly/Reassembly Mechanisms of Encapsulin Protein Nanocages”. ACS Omega 7, 823–836 (2022). doi:10.1021/acsomega.1c05472
  7. J.C. Carlson, A.H. Badran, D.A. Guggiana-Nilo, D.R. Liu, “Negative selection and stringency modulation in phage-assisted continuous evolution”. Nature Chemical Biology 10, 216–222 (2014). doi:10.1038/nchembio.1453
  8. C. Cassidy-Amstutz, L. Oltrogge, C.C. Going, A. Lee, P. Teng, D. Quintanilla et al., “Identification of a Minimal Peptide Tag for in Vivo and in Vitro Loading of Encapsulin”. Biochemistry 55, 3461–3468 (2016). doi:10.1021/acs.biochem.6b00294
  9. C.A. Charron, A. Kaldis, S. Shamriz et al., “Plant-produced encapsulin displays non-typhoidal Salmonella enterica antigens and assembles into mosaic nanoparticles”. The FEBS Journal 293, 1908–1929 (2026). doi:10.1111/febs.70340
  10. Z. Chen, J. Xue, Z. Wang, J. Sun, Y. Cui, T. Zhu et al., “Small RNA Toxin-Assisted Evolution of GC-Preferred ErCas12a for Enhanced Genome Targeting Range”. Advanced Science 12, e17105 (2025). doi:10.1002/advs.202417105
  11. S. Cho, D. Choe, E. Lee, S.C. Kim, B. Palsson, B.K. Cho, “High-Level dCas9 Expression Induces Abnormal Cell Morphology in Escherichia coli”. ACS Synthetic Biology 7, 1085–1094 (2018). doi:10.1021/acssynbio.7b00462
  12. R.E. Cobb, R. Chao, H. Zhao, “Directed Evolution: Past, Present and Future”. AIChE Journal 59, 1432–1440 (2013). doi:10.1002/aic.13995
  13. J.L. Coelho-Silva, N.S. Parducci, M.F.L. Carvalho, V. Vahedian, K. Lima, B.O. de Almeida et al., “Targeting “undruggable” cancer proteins: Pharmacological challenges and emerging strategies”. Translational Cancer Research 15, 336 (2026). doi:10.21037/tcr-2025-1-2830
  14. C.V. Dang, E.P. Reddy, K.M. Shokat, L. Soucek, “Drugging the “Undruggable” Cancer Targets”. Nature Reviews Cancer 17, 502–508 (2017). doi:10.1038/nrc.2017.36
  15. C.S. Diercks, P. Sondermann, C. Rong, T.G. Gillis, Y. Ban, C. Wang et al., “An orthogonal T7 replisome for continuous hypermutation and accelerated evolution in E. coli”. Science 389, 618–622 (2025). doi:10.1126/science.adp9583
  16. Z. Eftekhari, H. Zohrabi, A. Oghalaie, T. Ebrahimi, F.S. Shariati, M. Behdani et al., “Advancements and challenges in mRNA and ribonucleoprotein-based therapies: From delivery systems to clinical applications”. Molecular Therapy Nucleic Acids 35, 102313 (2024). doi:10.1016/j.omtn.2024.102313
  17. A.A. Eltoukhy, D. Chen, O. Veiseh, J.M. Pelet, H. Yin, Y. Dong et al., “Nucleic acid-mediated intracellular protein delivery by lipid-like nanoparticles”. Biomaterials 35, 6454–6461 (2014). doi:10.1016/j.biomaterials.2014.04.014
  18. K.M. Esvelt, J.C. Carlson, D.R. Liu, “A system for the continuous directed evolution of biomolecules”. Nature 472, 499–503 (2011). doi:10.1038/nature09929
  19. D.A. Fancy, K. Melcher, S.A. Johnston, T. Kodadek, “New chemistry for the study of multiprotein complexes: the six-histidine tag as a receptor for a protein crosslinking reagent”. Chemistry & Biology 3, 551–559 (1996). doi:10.1016/s1074-5521(96)90146-5
  20. T.W. Giessen, B.J. Orlando, A.A. Verdegaal, M.G. Chambers, J. Gardener, D.C. Bell et al., “Large protein organelles form a new iron sequestration system with high storage capacity”. eLife 8, e46070 (2019). doi:10.7554/eLife.46070
  21. I.B. Hilton, A.M. D'Ippolito, C.M. Vockley, P.I. Thakore, G.E. Crawford, T.E. Reddy et al., “Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers”. Nature Biotechnology 33, 510–517 (2015). doi:10.1038/nbt.3199
  22. M. Jinek, K. Chylinski, I. Fonfara, M. Hauer, J.A. Doudna & E. Charpentier, “A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity”. Science 337, 816–821 (2012). doi:10.1126/science.1225829
  23. J.A. Jones, R. Benisch, T.W. Giessen, “Encapsulin cargo loading: Progress and potential”. Journal of Materials Chemistry B 11, 4377–4388 (2023). doi:10.1039/d3tb00288h
  24. J.A. Jones, A.S. Cristie-David, M.P. Andreas & T.W. Giessen, “Triggered reversible disassembly of an engineered protein nanocage”. Angewandte Chemie International Edition 60, 25034–25041 (2021). doi:10.1002/anie.202110318
  25. R.L. Juliano, “The delivery of therapeutic oligonucleotides”. Nucleic Acids Research 44, 6518–6548 (2016). doi:10.1093/nar/gkw236
  26. S. Konermann, M.D. Brigham, A.E. Trevino, J. Joung, O.O. Abudayyeh, C. Barcena et al., “Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex”. Nature 517, 583–588 (2014). doi:10.1038/nature14136
  27. S. Konermann, M.D. Brigham, A.E. Trevino, J. Joung, O.O. Abudayyeh, C. Barcena et al., “Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex”. Nature 517, 583–588 (2015). doi:10.1038/nature14136
  28. J.A. Kulkarni, D. Witzigmann, S.B. Thomson, S. Chen, B.R. Leavitt, P.R. Cullis et al., “The current landscape of nucleic acid therapeutics”. Nature Nanotechnology 16, 630–643 (2021). doi:10.1038/s41565-021-00898-0
  29. S. Kwon, M.P. Andreas, J.A. Jones & T.W. Giessen, “A permeable protein nanocage enables facile cargo loading and cytosolic protein delivery”. Nature Communications (2026), published 14 August 2026. doi:10.1038/s41467-026-76849-x. Earlier bioRxiv version
  30. S. Kwon, M.P. Andreas & T.W. Giessen, “Pore engineering as a general strategy to improve protein-based enzyme nanoreactor performance”. ACS Nano 18, 25740–25753 (2024). doi:10.1021/acsnano.4c08186
  31. S. Kwon & T.W. Giessen, “Engineered protein nanocages for concurrent RNA and protein packaging in vivo”. ACS Synthetic Biology 11, 3504–3515 (2022). doi:10.1021/acssynbio.2c00391
  32. P. Lagoutte et al., “Simultaneous surface display and cargo loading of encapsulin nanocompartments and their use for rational vaccine design”. Vaccine 36, 3622–3628 (2018). doi:10.1016/j.vaccine.2018.05.034
  33. D. Lazinski, E. Grzadzielska, A. Das, “Sequence-specific recognition of RNA hairpins by bacteriophage antiterminators requires a conserved arginine-rich motif”. Cell 59, 207–218 (1989). doi:10.1016/0092-8674(89)90882-9
  34. Y.W. Lee, D.C. Luther, J.A. Kretzmann, A. Burden, T. Jeon, S. Zhai et al., “Protein Delivery into the Cell Cytosol using Non-Viral Nanocarriers”. Theranostics 9, 3280–3292 (2019). doi:10.7150/thno.34412
  35. P. Legault, J. Li, J. Mogridge, L.E. Kay, J. Greenblatt, “NMR structure of the bacteriophage λ N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif”. Cell 93, 289–299 (1998). doi:10.1016/S0092-8674(00)81579-2
  36. M. Li, L. Gong, F. Cheng, H. Yu, D. Zhao, R. Wang et al., “Toxin-antitoxin RNA pairs safeguard CRISPR-Cas systems”. Science 372 (2021). doi:10.1126/science.abe5601
  37. C. Liu, L. Zhang, H. Liu, K. Cheng, “Delivery strategies of the CRISPR-Cas9 gene-editing system for therapeutic applications”. Journal of Controlled Release 266, 17–26 (2017). doi:10.1016/j.jconrel.2017.09.012
  38. S.R. McCutcheon, K.L. Chiu, D.D. Lewis, C. Tan, “CRISPR-Cas Expands Dynamic Range of Gene Expression From T7RNAP Promoters”. Biotechnology Journal 13, e1700167 (2018). doi:10.1002/biot.201700167
  39. A.J. Meyer, T.H. Segall-Shapiro, E. Glassey, J. Zhang, C.A. Voigt, “Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors”. Nature Chemical Biology 15, 196–204 (2018). doi:10.1038/s41589-018-0168-3
  40. S.M. Miller, T. Wang, D.R. Liu, “Phage-assisted continuous and non-continuous evolution”. Nature Protocols 15, 4101–4127 (2020). doi:10.1038/s41596-020-00410-3
  41. C.L. Moore, L.J. Papa, M.D. Shoulders, “A Processive Protein Chimera Introduces Mutations Across Defined DNA Regions In Vivo”. Journal of the American Chemical Society 140, 11560–11564 (2018). doi:10.1021/jacs.8b04001
  42. M.S. Morrison, C.J. Podracky, D.R. Liu, “The developing toolkit of continuous directed evolution”. Nature Chemical Biology 16, 610–619 (2020). doi:10.1038/s41589-020-0532-y
  43. H. Nagaraj, V. Lehot, N. Nasim, Y.A. Cicek, R. Goswami, T. Jeon et al., “Breaking the cellular delivery bottleneck: Recent developments in direct cytosolic delivery of biologics”. RSC Pharmaceutics 2, 850–864 (2025). doi:10.1039/d5pm00129c
  44. A.A.K. Nielsen, C.A. Voigt, “Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks”. Molecular Systems Biology 10, 763 (2014). doi:10.15252/msb.20145735
  45. A. Panek, O. Pietrow, P. Filipkowski, J. Synowiecki, “Effects of the polyhistidine tag on kinetics and other properties of trehalose synthase from Deinococcus geothermalis”. Acta Biochimica Polonica 60, 163–166 (2013).
  46. L.S. Qi, M.H. Larson, L.A. Gilbert, J.A. Doudna, J.S. Weissman, A.P. Arkin et al., “Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression”. Cell 152, 1173–1183 (2013). doi:10.1016/j.cell.2013.02.022
  47. A. Ravikumar, A. Arrieta, C.C. Liu, “An orthogonal DNA replication system in yeast”. Nature Chemical Biology 10, 175–177 (2014). doi:10.1038/nchembio.1439
  48. A. Ravikumar, G.A. Arzumanyan, M.K.A. Obadi, A.A. Javanpour & C.C. Liu, “Scalable, continuous evolution of genes at mutation rates above genomic error thresholds”. Cell 175, 1946–1957.e13 (2018). doi:10.1016/j.cell.2018.10.021
  49. R. Siddiquee, F. Lie, T.N. Szyszka, A. Loustau, M.P. Andreas, T.W. Giessen & Y.H. Lau, “Directed evolution of multimeric proteins is enabled by dual-compensatory gene duplication”. bioRxiv (2026), preprint version consulted. doi:10.64898/2026.01.12.698938
  50. X. Sun, S. Setrerrahmane, C. Li, J. Hu, H. Xu, “Nucleic acid drugs: Recent progress and future perspectives”. Signal Transduction and Targeted Therapy 9, 316 (2024). doi:10.1038/s41392-024-02035-4
  51. M. Sutter, D. Boehringer, S. Gutmann, S. Günther, D. Prangishvili, M.J. Loessner et al., “Structural basis of enzyme encapsulation into a bacterial nanocompartment”. Nature Structural & Molecular Biology 15, 939–947 (2008). doi:10.1038/nsmb.1473
  52. N. Terasaka, Y. Azuma, D. Hilvert, “Laboratory evolution of virus-like nucleocapsids from nonviral protein cages”. Proceedings of the National Academy of Sciences 115, 5432–5437 (2018). doi:10.1073/pnas.1800527115
  53. S. Tetter, N. Terasaka, A. Steinauer, R.J. Bingham, S. Clark, A.J.P. Scott et al., “Evolution of a virus-like architecture and packaging mechanism in a repurposed bacterial protein”. Science 372, 1220–1224 (2021). doi:10.1126/science.abg2822
  54. Y. Tian, M.V. Tirrell, J.L. LaBelle, “Harnessing the Therapeutic Potential of Biomacromolecules through Intracellular Delivery of Nucleic Acids, Peptides, and Proteins”. Advanced Healthcare Materials 11, 2102600 (2022). doi:10.1002/adhm.202102600
  55. A. Vigouroux, E. Oldewurtel, L. Cui, D. Bikard, S. Van Teeffelen, “Tuning dCas9’s ability to block transcription enables robust, noiseless knockdown of bacterial genes”. Molecular Systems Biology 14, e7899 (2018). doi:10.15252/msb.20177899
  56. Q. Wang, J. Zhang, Z. Zhao, Y. Li, J. You, Y. Wang et al., “Dual genetic level modification engineering accelerate genome evolution of Corynebacterium glutamicum”. Nucleic Acids Research 52, 8609–8627 (2024). doi:10.1093/nar/gkae577
  57. M. Wang, J.A. Zuris, F. Meng, H. Rees, S. Sun, P. Deng et al., “Efficient delivery of genome-editing proteins using bioreducible lipid nanoparticles”. Proceedings of the National Academy of Sciences 113, 2868–2873 (2016). doi:10.1073/pnas.1520244113
  58. T. Wei, Q. Cheng, Y.-L. Min, E.N. Olson & D.J. Siegwart, “Systemic nanoparticle delivery of CRISPR-Cas9 ribonucleoproteins for effective tissue specific genome editing”. Nature Communications 11, 3232 (2020). doi:10.1038/s41467-020-17029-3
  59. J. Wu, M. Filutowicz, “Hexahistidine (His6)-tag dependent protein dimerization: a cautionary tale”. Acta Biochimica Polonica 46, 591–599 (1999). doi:10.18388/abp.1999_4131
  60. F. Xu, K. Wang, K. Lu, T. Hou, Y. Chen, X. Wang et al., “Nucleic Acid Therapeutics for “Undruggable” Cancer Targets: Mechanisms, Challenges, and Prospects”. Advanced Science 13, e75837 (2026). doi:10.1002/advs.75837
  61. X. Yu, Z. Weng, Z. Zhao, J. Xu, Z. Qi, J. Liu, “Assembly of Protein Cages for Drug Delivery”. Pharmaceutics 14, 2609 (2022). doi:10.3390/pharmaceutics14122609