Engineered retrons generate genome-independent protein-binding DNA for cellular control
Open accessPreprint — published as 10.1038/s41557-025-02049-7 · Paper page
Abstract
DNA-protein interactions are core components of myriad natural and synthetic gene networks. Despite the potential new design space, DNA-protein interactions remain underexploited in vivo due to challenges in controlling specific DNA segments, including protein-binding sequences, independently of the genome. Here we engineer retrons, prokaryotic retroelements, to intracellularly generate genome-independent programmable small DNA for sequence-specific protein-binding. Using reprogrammed retron-derived DNA for allosteric transcription factor, we demonstrated dynamic regulation of synthetic gene networks and construction of automated feedback circuits for signal amplification, adaptation, and memory. Furthermore, we developed a new class of stimuli-responsive molecular “bait and prey” that enable modular, rapid, and post-translational control of protein subcellular localization. This work substantially expands possible application area of DNA-protein interactions, laying the foundation for technical advances in synthetic biology. One-Sentence Summary: We demonstrate new ways to control, design, and exploit DNA-protein interactions in living cells using engineered retron-generated small DNA.
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Cites
Natural RNA circles function as efficient microRNA sponges
Hansen, T. B., Jensen, T. I., Clausen, B. H., Bramsen, J. B., Finsen, B., Damgaard, C. K., & Kjems, J. (2013) · Nature · doi:10.1038/nature11993 · Cited by 7,985 · see citing works
The Human Transcription Factors
Lambert, S. A., Jolma, A., Campitelli, L. F., Das, P. K., Yin, Y., Albu, M., Chen, X., Taipale, J., Hughes, T. R., & Weirauch, M. T. (2018) · Cell · doi:10.1016/j.cell.2018.01.029 · Cited by 3,399 · see citing works
Genome editing with engineered zinc finger nucleases
Urnov, F. D., Rebar, E. J., Holmes, M. C., Zhang, H. S., & Gregory, P. D. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2842 · Cited by 2,285 · see citing works
A TALE nuclease architecture for efficient genome editing
Miller, J. C., Tan, S., Qiao, G., Barlow, K. A., Wang, J., Xia, D. F., Meng, X., Paschon, D. E., Leung, E., Hinkley, S. J., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1755 · Cited by 2,098 · see citing works
Endogenous microRNA sponges: evidence and controversy
Thomson, D. W., & Dinger, M. E. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.20 · Cited by 1,833 · see citing works
NUPACK: Analysis and design of nucleic acid systems
Zadeh, J. N., Steenberg, C. D., Bois, J. S., Wolfe, B. R., Pierce, M. B., Khan, A. R., Dirks, R. M., & Pierce, N. A. (2011) · Journal of Computational Chemistry · doi:10.1002/jcc.21596 · Cited by 1,670 · see citing works
MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis
Ducret, A., Quardokus, E. M., & Brun, Y. V. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.77 · Cited by 950 · see citing works
Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds
Zalatan, J. G., Lee, M. E., Almeida, R., Gilbert, L. A., Whitehead, E. H., La Russa, M., Tsai, J. C., Weissman, J. S., Dueber, J. E., Qi, L. S., et al. (2015) · Cell · doi:10.1016/j.cell.2014.11.052 · Cited by 938 · see citing works
Hasty, J., McMillen, D. R., & Collins, J. J. (2002) · Nature · doi:10.1038/nature01257 · Cited by 744 · see citing works
A positive-feedback-based bistable ‘memory module’ that governs a cell fate decision.
Xiong, W., & Ferrell, J. E. (2003) · Nature · doi:10.1038/nature02089 · Cited by 741 · see citing works
Milo, R. (2013) · BioEssays · doi:10.1002/bies.201300066 · Cited by 643 · see citing works
Organization of Intracellular Reactions with Rationally Designed RNA Assemblies
Delebecque, C. J., Lindner, A. B., Silver, P. A., & Aldaye, F. A. (2011) · Science · doi:10.1126/science.1206938 · Cited by 634 · see citing works
Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs
Na, D., Yoo, S. M., Chung, H., Park, H., Park, J. H., & Lee, S. Y. (2013) · Nature Biotechnology · doi:10.1038/nbt.2461 · Cited by 623 · see citing works
Synthetic circuits integrating logic and memory in living cells
Siuti, P., Yazbek, J., & Lu, T. K. (2013) · Nature Biotechnology · doi:10.1038/nbt.2510 · Cited by 531 · see citing works
Bacterial Retrons Function In Anti-Phage Defense
Millman, A., Bernheim, A. G., Stokar-Avihail, A., Fedorenko, T., Voichek, M., Leavitt, A., Oppenheimer‐Shaanan, Y., & Sorek, R. (2020) · Cell · doi:10.1016/j.cell.2020.09.065 · Cited by 406 · see citing works
Cell-free biosensors for rapid detection of water contaminants
Jung, J. K., Alam, K. K., Verosloff, M. S., Capdevila, D. A., Desmau, M., Clauer, P. R., Lee, J. W., Nguyen, P. Q., Pastén, P., Matiasek, S. J., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0571-7 · Cited by 404 · see citing works
Optogenetic regulation of engineered cellular metabolism for microbial chemical production
Zhao, E. M., Zhang, Y., Mehl, J., Park, H., Lalwani, M. A., Toettcher, J. E., & Avalos, J. L. (2018) · Nature · doi:10.1038/nature26141 · Cited by 357 · see citing works
Efficient Intracellular Delivery of Native Proteins
D’Astolfo, D. S., Pagliero, R. J., Pras, A., Karthaus, W. R., Clevers, H. C., Prasad, V., Lebbink, R. J., Rehmann, H., & Geijsen, N. (2015) · Cell · doi:10.1016/j.cell.2015.03.028 · Cited by 343 · see citing works
Complex transcriptional modulation with orthogonal and inducible dCas9 regulators
Gao, Y., Xiong, X., Wong, S. S., Charles, E. J., Lim, W. A., & Qi, L. S. (2016) · Nature Methods · doi:10.1038/nmeth.4042 · Cited by 325 · see citing works
Genomically encoded analog memory with precise in vivo DNA writing in living cell populations
Farzadfard, F., & Lu, T. K. (2014) · Science · doi:10.1126/science.1256272 · Cited by 298 · see citing works
Cascaded amplifying circuits enable ultrasensitive cellular sensors for toxic metals
Wan, X., Volpetti, F., Petrova, E., French, C. E., Maerkl, S. J., & Wang, B. (2019) · Nature Chemical Biology · doi:10.1038/s41589-019-0244-3 · Cited by 283 · see citing works
Next-generation biocontainment systems for engineered organisms
Lee, J. W., Chan, C. T. Y., Slomovic, S., & Collins, J. J. (2018) · Nature Chemical Biology · doi:10.1038/s41589-018-0056-x · Cited by 276 · see citing works
Tunable thermal bioswitches for in vivo control of microbial therapeutics
Piraner, D. I., Abedi, M. H., Moser, B., Lee‐Gosselin, A., & Shapiro, M. G. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2233 · Cited by 266 · see citing works
Rapid and orthogonal logic gating with a gibberellin-induced dimerization system
Miyamoto, T., DeRose, R., Suarez, A., Ueno, T., Chen, M., Sun, T.-P., Wolfgang, M. J., Mukherjee, C., Meyers, D. J., & Inoue, T. (2012) · Nature Chemical Biology · doi:10.1038/nchembio.922 · Cited by 230 · see citing works
Functional Genetic Variants Revealed by Massively Parallel Precise Genome Editing
Sharon, E., Chen, S.-A. A., Khosla, N. M., Smith, J. D., Pritchard, J. K., & Fraser, H. B. (2018) · Cell · doi:10.1016/j.cell.2018.08.057 · Cited by 225 · see citing works
Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes
Praetorius, F., & Dietz, H. (2017) · Science · doi:10.1126/science.aam5488 · Cited by 171 · see citing works
Why Transcription Factor Binding Sites Are Ten Nucleotides Long
Stewart, A. J., Hannenhalli, S. S., & Plotkin, J. B. (2012) · Genetics · doi:10.1534/genetics.112.143370 · Cited by 165 · see citing works
Bacterial retrons encode phage-defending tripartite toxin–antitoxin systems
Bobonis, J., Mitosch, K., Mateus, A., Karcher, N., Kritikos, G., Selkrig, J., Zietek, M., Monzon, V., Pfalz, B., Garcia-Santamarina, S., et al. (2022) · Nature · doi:10.1038/s41586-022-05091-4 · Cited by 165 · see citing works
Programmable synthetic biomolecular condensates for cellular control
Dai, Y., Farag, M., Lee, D., Zeng, X., Kim, K., Son, H.-I., Guo, X., Su, J. C., Peterson, N., Mohammed, J. P., et al. (2023) · Nature Chemical Biology · doi:10.1038/s41589-022-01252-8 · Cited by 161 · see citing works
Lim, D., & Maas, W. K. (1989) · Cell · doi:10.1016/0092-8674(89)90693-4 · Cited by 149 · see citing works
A plasmid system with tunable copy number
Rouches, M. V., Xu, Y., Cortes, L. B. G., & Lambert, G. (2022) · Nature Communications · doi:10.1038/s41467-022-31422-0 · Cited by 134 · see citing works
Sub-1.4 cm3 capsule for detecting labile inflammatory biomarkers in situ
Inda, M. E., Jiménez, M., Liu, Q., Phan, N. V., Ahn, J., Steiger, C., Wentworth, A. J., Riaz, A., Zirtiloglu, T., Wong, K., et al. (2023) · Nature · doi:10.1038/s41586-023-06369-x · Cited by 123 · see citing works
Multicopy single-stranded DNA isolated from a gram-negative bacterium, Myxococcus xanthus
Yee, T., Furuichi, T., Inouye, S., & Inouye, M. (1984) · Cell · doi:10.1016/0092-8674(84)90541-5 · Cited by 123 · see citing works
Wang, B., Barahona, M., & Buck, M. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1388 · Cited by 121 · see citing works
RNA origami design tools enable cotranscriptional folding of kilobase-sized nanoscaffolds
Geary, C. W., Grossi, G., McRae, E. K. S., Rothemund, P. W. K., & Andersen, E. S. (2021) · Nature Chemistry · doi:10.1038/s41557-021-00679-1 · Cited by 119 · see citing works
Transcription factor decoy technology: A therapeutic update
Hecker, M., & Wagner, A. H. (2017) · Biochemical Pharmacology · doi:10.1016/j.bcp.2017.06.122 · Cited by 116 · see citing works
Advanced strategies and tools to facilitate and streamline microbial adaptive laboratory evolution
Wu, Y., Jameel, A., Xing, X., & Zhang, C. (2021) · Trends in biotechnology · doi:10.1016/j.tibtech.2021.04.002 · Cited by 111 · see citing works
Activation of silent biosynthetic gene clusters using transcription factor decoys
Wang, B., Guo, F., Dong, S., & Zhao, H. (2018) · Nature Chemical Biology · doi:10.1038/s41589-018-0187-0 · Cited by 111 · see citing works
Establishing a synthetic orthogonal replication system enables accelerated evolution in E. coli
Tian, R., Rehm, F. B. H., Czernecki, D., Gu, Y., Zürcher, J. F., Liu, K. C., & Chin, J. W. (2024) · Science · doi:10.1126/science.adk1281 · Cited by 99 · see citing works
Conversion of the Vibrio fischeri Transcriptional Activator, LuxR, to a Repressor
Egland, K. A., & Greenberg, E. P. (2000) · Journal of Bacteriology · doi:10.1128/jb.182.3.805-811.2000 · Cited by 98 · see citing works
Precise genome editing across kingdoms of life using retron-derived DNA
Lopez, S. C., Crawford, K. D., Lear, S. K., Bhattarai-Kline, S., & Shipman, S. L. (2021) · Nature Chemical Biology · doi:10.1038/s41589-021-00927-y · Cited by 91 · see citing works
A progesterone biosensor derived from microbial screening
Grazon, C., Baer, R. C., Kuzmanović, U., Nguyen, T., Chen, M., Zamani, M., Chern, M., Aquino, P., Zhang, X., Lecommandoux, S., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14942-5 · Cited by 86 · see citing works
Genetic encoding of DNA nanostructures and their self-assembly in living bacteria
Elbaz, J., Yin, P., & Voigt, C. A. (2016) · Nature Communications · doi:10.1038/ncomms11179 · Cited by 85 · see citing works
Mestre, M. R., González-Delgado, A., Gutierrez-Rus, L. I., Martínez‐Abarca, F., & Toro, N. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1149 · Cited by 84 · see citing works
Computational design of co-assembling protein–DNA nanowires
Mou, K. Y., Yu, J., Wannier, T. M., Guo, C., & Mayo, S. L. (2015) · Nature · doi:10.1038/nature14874 · Cited by 83 · see citing works
Recording gene expression order in DNA by CRISPR addition of retron barcodes
Bhattarai-Kline, S., Lear, S. K., Fishman, C. B., Lopez, S. C., Lockshin, E. R., Schubert, M. G., Nivala, J., Church, G. M., & Shipman, S. L. (2022) · Nature · doi:10.1038/s41586-022-04994-6 · Cited by 78 · see citing works
Engineered bacterial orthogonal DNA replication system for continuous evolution
Tian, R., Zhao, R., Guo, H., Yan, K., Wang, C., Lu, C., Lv, X., Li, J., Liu, L., Du, G., et al. (2023) · Nature Chemical Biology · doi:10.1038/s41589-023-01387-2 · Cited by 72 · see citing works
A modular positive feedback-based gene amplifier
Nistala, G. J., Wu, K., Rao, C. V., & Bhalerao, K. D. (2010) · Journal of Biological Engineering · doi:10.1186/1754-1611-4-4 · Cited by 69 · see citing works
Mechanisms of immunomodulation by mammalian and viral decoy receptors: insights from structures
Félix, J., & Savvides, S. N. (2016) · Nature reviews. Immunology · doi:10.1038/nri.2016.134 · Cited by 68 · see citing works
Wang, Y., Guan, Z., Wang, C., Nie, Y., Chen, Y., Qian, Z., Cui, Y., Xu, H., Wang, Q., Zhao, F., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01197-7 · Cited by 65 · see citing works
Phage-triggered reverse transcription assembles a toxic repetitive gene from a noncoding RNA
Wilkinson, M. E., Li, D., Gao, L., Macrae, R. K., & Zhang, F. (2024) · Science · doi:10.1126/science.adq3977 · Cited by 61 · see citing works
Light-Inducible Recombinases for Bacterial Optogenetics
Sheets, M. B., Wong, W. W., & Dunlop, M. J. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.9b00395 · Cited by 58 · see citing works
De novo gene synthesis by an antiviral reverse transcriptase
Tang, S., Conte, V., Zhang, D. J., Žedaveinytė, R., Lampe, G. D., Wiegand, T., Tang, L. C., Wang, M., Walker, M. W. G., George, J. T., et al. (2024) · Science · doi:10.1126/science.adq0876 · Cited by 58 · see citing works
Computational design of sequence-specific DNA-binding proteins
Glasscock, C. J., Pecoraro, R. J., McHugh, R., Doyle, L. A., Chen, W., Boivin, O., Lonnquist, B., Na, E., Politanska, Y., Haddox, H. K., et al. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01669-4 · Cited by 58 · see citing works
Self-citationInducible plasmid copy number control for synthetic biology in commonly used E. coli strains
Joshi, S. H.-N., Yong, C., & György, A. (2022) · Nature Communications · doi:10.1038/s41467-022-34390-7 · Cited by 56 · see citing works
Vezeau, G. E., Gadila, L. R., & Salis, H. M. (2023) · Nature Communications · doi:10.1038/s41467-023-38098-0 · Cited by 46 · see citing works
Engineering ACE2 decoy receptors to combat viral escapability
Arimori, T., Ikemura, N., Okamoto, T., Takagi, J., Standley, D. M., & Hoshino, A. (2022) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2022.06.011 · Cited by 45 · see citing works
A synthetic system for asymmetric cell division in Escherichia coli
Molinari, S., Shis, D. L., Bhakta, S. P., Chappell, J., Igoshin, O. A., & Bennett, M. R. (2019) · Nature Chemical Biology · doi:10.1038/s41589-019-0339-x · Cited by 44 · see citing works
Wang, T., Tague, N., Whelan, S. A., & Dunlop, M. J. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1234 · Cited by 44 · see citing works
Synthetic protein-binding DNA sponge as a tool to tune gene expression and mitigate protein toxicity
Wan, X., Pinto, F., Yu, L., & Wang, B. (2020) · Nature Communications · doi:10.1038/s41467-020-19552-9 · Cited by 43 · see citing works
Cooperative assembly confers regulatory specificity and long-term genetic circuit stability
Bragdon, M. D. J., Patel, N., Chuang, J., Levien, E., Bashor, C. J., & Khalil, A. S. (2023) · Cell · doi:10.1016/j.cell.2023.07.012 · Cited by 41 · see citing works
Reinventing the Wheel: Synthetic Circular RNAs for Mammalian Cell Engineering
Costello, A., Lao, N. T., Barron, N., & CLYNES, M. M. (2019) · Trends in biotechnology · doi:10.1016/j.tibtech.2019.07.008 · Cited by 37 · see citing works
Localization of the Tat translocon components in Escherichia coli
Berthelmann, F., & Brüser, T. (2004) · FEBS Letters · doi:10.1016/j.febslet.2004.05.054 · Cited by 35 · see citing works
Continuous multiplexed phage genome editing using recombitrons
Fishman, C. B., Crawford, K. D., Bhattarai-Kline, S., Poola, D., Zhang, K. H., González-Delgado, A., Rojas-Montero, M., & Shipman, S. L. (2024) · Nature Biotechnology · doi:10.1038/s41587-024-02370-5 · Cited by 32 · see citing works
Construction of intracellular asymmetry and asymmetric division in Escherichia coli
Lin, D., Liu, Y., Lee, Y.-Q., Yang, P.-J., Ho, C.-T., Hong, J.-C., Hsiao, J., Liao, D.-C., Liang, A., Hung, T.-C., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21135-1 · Cited by 32 · see citing works
Miyata, S., Ohshima, A., Inouye, S., & Inouye, M. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.13.5735 · Cited by 28 · see citing works
Simultaneous multi-site editing of individual genomes using retron arrays
González-Delgado, A., Lopez, S. C., Rojas-Montero, M., Fishman, C. B., & Shipman, S. L. (2024) · Nature Chemical Biology · doi:10.1038/s41589-024-01665-7 · Cited by 27 · see citing works
Wu, T., Cao, Y., Liu, Q. L., Wu, X., Shang, Y., Piao, J., Li, Y., Dong, Y., Liu, D., Wang, H., et al. (2022) · Journal of the American Chemical Society · doi:10.1021/jacs.2c01760 · Cited by 26 · see citing works
Long-term positioning and polar preference of chemoreceptor clusters in E. coli
Koler, M., Peretz, E., Aditya, C., Shimizu, T. S., & Vaknin, A. (2018) · Nature Communications · doi:10.1038/s41467-018-06835-5 · Cited by 26 · see citing works
Tet repressor residues indirectly recognizing anhydrotetracycline
Schubert, P., Pfleiderer, K., & Hillen, W. (2004) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.2004.04130.x · Cited by 22 · see citing works
Gao, R., Helfant, L. J., Wu, T., Li, Z., Brokaw, S. E., & Stock, A. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab935 · Cited by 21 · see citing works
DNA Replication Initiation Is Blocked by a Distant Chromosome–Membrane Attachment
Magnan, D. R., Joshi, M. C., Barker, A. K., Visser, B. J., & Bates, D. B. (2015) · Current Biology · doi:10.1016/j.cub.2015.06.058 · Cited by 21 · see citing works
Mechanisms of Cre recombinase synaptic complex assembly and activation illuminated by Cryo-EM
Stachowski, K., Norris, A. S., Potter, D., Wysocki, V. H., & Foster, M. P. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac032 · Cited by 19 · see citing works
Kalvapalle, P. B., Sridhar, S., Silberg, J. J., & Stadler, L. B. (2024) · Applied and Environmental Microbiology · doi:10.1128/aem.02363-23 · Cited by 11 · see citing works
Localized Proteolysis for the Construction of Intracellular Asymmetry in Escherichia coli
Hong, J.-C., Fan, H.-C., Yang, P.-J., Lin, D., Wu, H., & Huang, H. (2021) · ACS Synthetic Biology · doi:10.1021/acssynbio.1c00200 · Cited by 8 · see citing works
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Buffington, J., Kuo, H., Hu, K., Chang, Y.-C., Javanmardi, K., Voigt, B., Li, Y.-R., Little, M. E., Devanathan, S. K., Xhemalçe, B., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-025-02879-3 · Cited by 11 · see citing works
González-Delgado, A., Bonillo-Lopez, L., Johnson, M. S., Knödlseder, N., Ko, C., Lekbach, Y., Oh, J., Selvakumar, H., Wold, M. C., Yu, Z., et al. (2026) · Nature Biotechnology · doi:10.1038/s41587-026-03076-6 · Cited by 8 · see citing works
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- Authors
- Lee, G., & Kim, J.
- Affiliations
- Pohang University of Science and Technology (KR)
- Corresponding author
- Lee, Geonhu
- Kim, Jongmin
- Venue
- Nature Chemistry
- Publisher
- openRxiv
- Published
- 2023-09-28
- Volume
- 18
- Issue
- 6
- Pages
- 1042-1052
- ISSN
- 1755-4330 (ISSN-L)
- OpenAlex
- W7124464577
- Cited by
- 15
- References
- 75
- Citations by year
- 2026: 5 · 2025: 2 · 2024: 8
- FWCI
- 10.26
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc-nd
- Locations
- Nature Chemistry (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- National Research Foundation (BK21 FOUR)
- Ministry of Environment (NIBR202333202)
- Korea Health Industry Development Institute (RS‐2023‐00304637)
- National Research Foundation of Korea (BK 21 four, 2021R1A6C101A390, 2022R1F1A1066642)
- Ministry of Education, India
- Ministry of Science and ICT, South Korea
- National Institute of Biological Resources (NIBR202333202)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- retron, protein-DNA interactions, synthetic gene regulation, feedback circuits, post-translational regulation, allosteric transcription factors, synthetic biology
- MeSH terms
- DNA, DNA-Binding Proteins, Escherichia coli, Protein Binding
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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