Enhanced SNP-sensing using DNA-templated reactions through confined hybridization of minimal substrates (CHOMS)
Open accessAbstract
Confined hybridization of a minimal substrate: striking the right balance between specificity and turnover
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
An additional 4-mer hybridizing adjacent to the 4-mer participating in primer extension improved the rate of reaction and fidelity of primer extension.
“This further improved the rate of reaction and fidelity of primer extension (Figure 3D), consistent with prior work.9,40”
From Sequencing of <scp>d</scp>/<scp>l</scp>-DNA and XNA by Templated-Synthesis (2025) · cites this paper as [40]
The Results and discussion section reports that adjacent hybridization made a DNA-templated reaction with a short substrate faster than a reaction with a three-nucleotide gap. It does not test an additional 4-mer beside a primer-extension 4-mer or report improved primer-extension fidelity; its reaction is a ruthenium-photocatalyzed fluorescence assay. (LLM, conf=0.86)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
A global reference for human genetic variation
The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247 · see citing works
Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS)
Newton, C. R., Graham, A., Heptinstall, L., Powell, S. J., Summers, C. W., Kalsheker, N. A., Smith, J. C., & Markham, A. F. (1989) · Nucleic Acids Research · doi:10.1093/nar/17.7.2503 · Cited by 2,476 · see citing works
The Clinical KRAS(G12C) Inhibitor AMG 510 Drives Anti-Tumour Immunity
Canon, J., Rex, K., Saiki, A. Y., Mohr, C., Cooke, K., Bagal, D., Gaida, K., Holt, T., Knutson, C. G., Koppada, N., et al. (2019) · Nature · doi:10.1038/s41586-019-1694-1 · Cited by 2,277 · see citing works
PNA hybridizes to complementary oligonucleotides obeying the Watson–Crick hydrogen-bonding rules
Egholm, M., Buchardt, O., Christensen, L., Behrens, C., Freier, S. M., Driver, D. A., Berg, R. H., Kim, S. K., Norden, B., & Nielsen, P. E. (1993) · Nature · doi:10.1038/365566a0 · Cited by 2,079 · see citing works
Genes mirror geography within Europe
Novembre, J., Johnson, T., Bryc, K., Kutalik, Z., Boyko, A. R., Auton, A., Indap, A., King, K. S., Bergmann, S., Nelson, M. R., et al. (2008) · Nature · doi:10.1038/nature07331 · Cited by 1,479 · see citing works
A Specific Chemical Difference Between the Globins of Normal Human and Sickle-Cell Anæmia Hæmoglobin
INGRAM, V. M. (1956) · Nature · doi:10.1038/178792a0 · Cited by 896 · see citing works
Stephen, A. G., Esposito, D., Bagni, R. K., & McCormick, F. (2014) · Cancer Cell · doi:10.1016/j.ccr.2014.02.017 · Cited by 795 · see citing works
Moving towards individualized medicine with pharmacogenomics
Evans, W. E., & Relling, M. V. (2004) · Nature · doi:10.1038/nature02626 · Cited by 772 · see citing works
SNP Genotyping: Technologies and Biomedical Applications
Kim, S., & Misra, A. (2007) · Annual Review of Biomedical Engineering · doi:10.1146/annurev.bioeng.9.060906.152037 · Cited by 622 · see citing works
Li, X., & Liu, D. R. (2004) · Angewandte Chemie International Edition · doi:10.1002/anie.200400656 · Cited by 538 · see citing works
Xu, S., Zhan, J., Man, B., Jiang, S., Yue, W., Gao, S., Guo, C., Liu, H., Li, Z., Wang, J., et al. (2017) · Nature Communications · doi:10.1038/ncomms14902 · Cited by 437 · see citing works
Single nucleotide polymorphisms and cancer susceptibility
Deng, N., Zhou, H., Fan, H., & Yuan, Y. (2017) · Oncotarget · doi:10.18632/oncotarget.22372 · Cited by 381 · see citing works
K-ras oncogene mutations in sporadic colorectal cancer in The Netherlands Cohort Study
Brink, M. (2003) · Carcinogenesis · doi:10.1093/carcin/bgg009 · Cited by 315 · see citing works
Binary Probes for Nucleic Acid Analysis
Kolpashchikov, D. M. (2010) · Chemical Reviews · doi:10.1021/cr900323b · Cited by 302 · see citing works
A Simple γ-Backbone Modification Preorganizes Peptide Nucleic Acid into a Helical Structure
Dragulescu-Andrasi, A., Rapireddy, S., Frezza, B. M., Gayathri, C., Gil, R. R., & Ly, D. H. (2006) · Journal of the American Chemical Society · doi:10.1021/ja0625576 · Cited by 286 · see citing works
Detecting RNA and DNA with Templated Chemical Reactions
Silverman, A. P., & Kool, E. T. (2006) · Chemical Reviews · doi:10.1021/cr050057+ · Cited by 239 · see citing works
Son, J. H., Cho, B., Hong, S., Lee, S. H., Hoxha, O., Haack, A. J., & Lee, L. P. (2015) · Light Science & Applications · doi:10.1038/lsa.2015.53 · Cited by 235 · see citing works
Recurrent KRAS codon 146 mutations in human colorectal cancer
Edkins, S., & O’Meara, S. (2006) · Cancer Biology & Therapy · doi:10.4161/cbt.5.8.3251 · Cited by 229 · see citing works
Single-Nucleotide Polymorphisms and Other Mismatches Reduce Performance of Quantitative PCR Assays
Lefever, S., Pattyn, F., Hellemans, J., & Vandesompele, J. (2013) · Clinical Chemistry · doi:10.1373/clinchem.2013.203653 · Cited by 201 · see citing works
Ayyadevara, S., Thaden, J. J., & Reis, R. J. S. (2000) · Analytical Biochemistry · doi:10.1006/abio.2000.4635 · Cited by 180 · see citing works
Seeking the causes and solutions to imatinib-resistance in chronic myeloid leukemia
Bixby, D. L., & Talpaz, M. (2010) · Leukemia · doi:10.1038/leu.2010.238 · Cited by 162 · see citing works
Imaging of mRNA in Live Cells Using Nucleic Acid-Templated Reduction of Azidorhodamine Probes
Pianowski, Z., Gorska, K. I., Oswald, L., Merten, C. A., & Winssinger, N. (2009) · Journal of the American Chemical Society · doi:10.1021/ja809656k · Cited by 158 · see citing works
Self-citationSimulation-guided DNA probe design for consistently ultraspecific hybridization
Wang, J. S., & Zhang, D. Y. (2015) · Nature Chemistry · doi:10.1038/nchem.2266 · Cited by 156 · see citing works
Gorska, K., & Winssinger, N. (2013) · Angewandte Chemie International Edition · doi:10.1002/anie.201208460 · Cited by 155 · see citing works
Self-citationEfficient Nucleic Acid Detection by Templated Reductive Quencher Release
Franzini, R. M., & Kool, E. T. (2009) · Journal of the American Chemical Society · doi:10.1021/ja904138v · Cited by 150 · see citing works
Minamoto, T., Mai, M., & Ronai, Z. A. (2000) · PubMed · Cited by 141 · see citing works
Sando, S., Abe, H., & Kool, E. T. (2004) · Journal of the American Chemical Society · doi:10.1021/ja038665z · Cited by 121 · see citing works
Pianowski, Z., & Winssinger, N. (2007) · Chemical Communications · doi:10.1039/b709611a · Cited by 118 · see citing works
Self-citationChen, S. X., & Seelig, G. (2016) · Journal of the American Chemical Society · doi:10.1021/jacs.6b00277 · Cited by 101 · see citing works
Detection of miRNA in Live Cells by Using Templated RuII‐Catalyzed Unmasking of a Fluorophore
Sadhu, K. K., & Winssinger, N. (2013) · Chemistry - A European Journal · doi:10.1002/chem.201300060 · Cited by 94 · see citing works
Self-citationTherapeutic Options Against BCR-ABL1 T315I-Positive Chronic Myelogenous Leukemia
Quintás‐Cardama, A., & Cortes, J. E. (2008) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-08-0117 · Cited by 93 · see citing works
Li, Y., Wang, G. A., Mason, S. D., Yang, X., Yu, Z., Tang, Y., & Li, F. (2018) · Chemical Science · doi:10.1039/c8sc02761g · Cited by 93 · see citing works
Visible Light Photoredox Catalysis Using Ruthenium Complexes in Chemical Biology
Angerani, S., & Winssinger, N. (2019) · Chemistry - A European Journal · doi:10.1002/chem.201806024 · Cited by 88 · see citing works
Self-citationGenome comparison without alignment using shortest unique substrings
Haubold, B., Pierstorff, N., Möller, F., & Wiehe, T. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-123 · Cited by 87 · see citing works
Itonaga, M., Matsuzaki, I., Warigaya, K., Tamura, T., Shimizu, Y., Fujimoto, M., Kojima, F., Ichinose, M., & Murata, S. (2016) · PLoS ONE · doi:10.1371/journal.pone.0151654 · Cited by 84 · see citing works
Ficht, S., Dose, C., & Seitz, O. (2005) · ChemBioChem · doi:10.1002/cbic.200500229 · Cited by 83 · see citing works
PNA as a Biosupramolecular Tag for Programmable Assemblies and Reactions
Barluenga, S., & Winssinger, N. (2015) · Accounts of Chemical Research · doi:10.1021/acs.accounts.5b00109 · Cited by 77 · see citing works
Self-citationTargeted Detection of Single-Nucleotide Variations: Progress and Promise
Abi, A., & Safavi, A. (2019) · ACS Sensors · doi:10.1021/acssensors.8b01604 · Cited by 76 · see citing works
Chang, D., Lindberg, E., & Winssinger, N. (2017) · Journal of the American Chemical Society · doi:10.1021/jacs.6b12764 · Cited by 72 · see citing works
Self-citationNucleic Acid Templated Reactions for Chemical Biology
Pisa, M. D., & Seitz, O. (2017) · ChemMedChem · doi:10.1002/cmdc.201700266 · Cited by 64 · see citing works
Peptide nucleic acid-templated selenocystine–selenoester ligation enables rapid miRNA detection
Sayers, J., Payne, R. J., & Winssinger, N. (2017) · Chemical Science · doi:10.1039/c7sc02736b · Cited by 61 · see citing works
Self-citationPender, A., García-Murillas, I., Rana, S., Cutts, R. J., Kelly, G. P., Fenwick, K., Kozarewa, I., de Castro, D. G., Bhosle, J., O'Brien, M. E. R., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0139074 · Cited by 60 · see citing works
Wu, T., Xiao, X., Zhang, Z., & Zhao, M. (2014) · Chemical Science · doi:10.1039/c4sc03375b · Cited by 55 · see citing works
Single point mutation detection in living cancer cells by far-red emitting PNA–FIT probes
Kolevzon, N., Hashoul, D., Naik, S., Rubinstein, A., & Yavin, E. (2015) · Chemical Communications · doi:10.1039/c5cc07502e · Cited by 55 · see citing works
JAK2 V617F: a single mutation in the myeloproliferative group of disorders.
McLornan, D. P., Percy, M. J., & McMullin, M. F. (2006) · PubMed Central · Cited by 54 · see citing works
Oligonucleotide-templated chemical reactions: pushing the boundaries of a nature-inspired process
Percivalle, C., Bartolo, J.-F., & Ladame, S. (2012) · Organic & Biomolecular Chemistry · doi:10.1039/c2ob26163d · Cited by 53 · see citing works
Selective targeting of KRAS oncogenic alleles by CRISPR/Cas9 inhibits proliferation of cancer cells
Lee, W., Lee, J. H., Jun, S., Lee, J. H., & Bang, D. (2018) · Scientific Reports · doi:10.1038/s41598-018-30205-2 · Cited by 53 · see citing works
Pentacyclic adenine: a versatile and exceptionally bright fluorescent DNA base analogue
Bood, M., Füchtbauer, A. F., Wranne, M. S., Ro, J. J., Sarangamath, S., El-Sagheer, A. H., Rupert, D. L. M., Fisher, R. S., Magennis, S. W., Jones, A. C., et al. (2018) · Chemical Science · doi:10.1039/c7sc05448c · Cited by 52 · see citing works
Kim, K. T., Angerani, S., Chang, D., & Winssinger, N. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.9b05688 · Cited by 52 · see citing works
Self-citationSholokh, M., Improta, R., Mori, M., Sharma, R., Kenfack, C. A., Shin, D., Voltz, K., Stote, R. H., Zaporozhets, O. A., Botta, M., et al. (2016) · Angewandte Chemie International Edition · doi:10.1002/anie.201601688 · Cited by 51 · see citing works
Nonequilibrium Hybridization Enables Discrimination of a Point Mutation within 5–40 °C
Stancescu, M., Fedotova, T. A., Hooyberghs, J., Balaeff, A., & Kolpashchikov, D. M. (2016) · Journal of the American Chemical Society · doi:10.1021/jacs.6b05628 · Cited by 50 · see citing works
Yoshino, Y., Sato, Y., & Nishizawa, S. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b01997 · Cited by 50 · see citing works
Bioorthogonal reactions challenged: DNA templated native chemical ligation during PCR
Roloff, A., & Seitz, O. (2012) · Chemical Science · doi:10.1039/c2sc20961f · Cited by 48 · see citing works
Selective targeting of point-mutated KRAS through artificial microRNAs
Acunzo, M., Romano, G., Nigita, G., Veneziano, D., Fattore, L., Laganà, A., Zanesi, N. A. O., Fadda, P., Fassan, M., Rizzotto, L., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1620562114 · Cited by 48 · see citing works
Fluorogenic Templated Reaction Cascades for RNA Detection
Velema, W. A., & Kool, E. T. (2017) · Journal of the American Chemical Society · doi:10.1021/jacs.7b00466 · Cited by 44 · see citing works
Fang, G., Chamiolo, J., Kankowski, S., Hövelmann, F., Friedrich, D., Loewer, A., Meier, J. C., & Seitz, O. (2018) · Chemical Science · doi:10.1039/c8sc00457a · Cited by 40 · see citing works
Pei, X., Lai, T., Tao, G., Hong, H., Liu, F., & Li, N. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b00685 · Cited by 34 · see citing works
Allocco, D., Song, Q., Gibbons, G., Ramoni, M., & Kohane, I. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-68 · Cited by 33 · see citing works
Hu, S., Tang, W., Zhao, Y., Li, N., & Liu, F. (2016) · Chemical Science · doi:10.1039/c6sc03048c · Cited by 31 · see citing works
Sandwich probes: two simultaneous reactions for templated nucleic acid detection
Kleinbaum, D. J., & Kool, E. T. (2010) · Chemical Communications · doi:10.1039/c0cc01968b · Cited by 26 · see citing works
Obliosca, J. M., Cheng, S. Y., Chen, Y., Llanos, M. F., Liu, Y., Imphean, D. M., Bell, D. R., Petty, J. T., Ren, P. Y., & Yeh, H. (2017) · Journal of the American Chemical Society · doi:10.1021/jacs.7b03395 · Cited by 21 · see citing works
Hu, S., Li, N., & Liu, F. (2018) · Chemical Communications · doi:10.1039/c8cc00838h · Cited by 19 · see citing works
Kinase-templated abiotic reaction
Saarbach, J., Lindberg, E., Folliet, S., Georgeon, S., Hantschel, O. D., & Winssinger, N. (2017) · Chemical Science · doi:10.1039/c7sc01416c · Cited by 14 · see citing works
Self-citationSpecific and Efficient Regression of Cancers Harboring KRAS Mutation by Targeted RNA Replacement
Kim, S. J., Kim, J. H., Yang, B., Jeong, J., & Lee, S. (2017) · Molecular Therapy · doi:10.1016/j.ymthe.2016.11.005 · Cited by 12 · see citing works
A Quencher‐Free Linear Probe from Serinol Nucleic Acid with a Fluorescent Uracil Analogue
Murayama, K., & Asanuma, H. (2019) · ChemBioChem · doi:10.1002/cbic.201900498 · Cited by 12 · see citing works
Polymerase-amplified release of ATP (POLARA) for detecting single nucleotide variants in RNA and DNA
Mohsen, M. G., Ji, D., & Kool, E. T. (2019) · Chemical Science · doi:10.1039/c8sc03901a · Cited by 11 · see citing works
Flagged first, then by citations
Research works printed but not linked: 2
- Minamoto T. Mai M. Ronai Z. Cancer Detect. Prev. 2000 24 1 12 10757118
- McLornan D. Percy M. McMullin M. F. Ulster Med. J. 2006 75 112 119 16755940 PMC1891745
Cited by
Sorted by citations
Chen, Y., Mei, Y., & Jiang, X. (2021) · Chemical Science · doi:10.1039/d0sc05717g · Cited by 142 · see citing works
Wang, Q., Wang, J., Huang, Y. L., Du, Y., Zhang, Y., Cui, Y., & Kong, D. (2021) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2021.113739 · Cited by 92 · see citing works
A minimal hybridization chain reaction (HCR) system using peptide nucleic acids
Kim, K. T., Angerani, S., & Winssinger, N. (2021) · Chemical Science · doi:10.1039/d1sc01269j · Cited by 42 · see citing works
Self-citationZhao, S.-J., Zheng, P., Wu, Z., & Jiang, J. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.1c05509 · Cited by 40 · see citing works
Biosupramolecular Systems: Integrating Cues into Responses
Watson, E. E., Angerani, S., Sabale, P. M., & Winssinger, N. (2021) · Journal of the American Chemical Society · doi:10.1021/jacs.0c12970 · Cited by 32 · see citing works
Self-citationBai, L., Pang, Y., Wang, T., Wang, S., Guo, K., Xuan, T., Zhang, Z., Liu, D., Qian, F., Yan, Z., et al. (2025) · Theranostics · doi:10.7150/thno.107488 · Cited by 31 · see citing works
Soler, L. F., Gonse, A., Kim, K. T., Barluenga, S., & Winssinger, N. (2022) · Biopolymers · doi:10.1002/bip.23485 · Cited by 26 · see citing works
Self-citationBioorthogonal Chemistry in Translational Research: Advances and Opportunities
Chaudhuri, R., Bhattacharya, S., & Dash, J. (2023) · ChemBioChem · doi:10.1002/cbic.202300474 · Cited by 18 · see citing works
Liu, W., Watson, E. E., & Winssinger, N. (2021) · Helvetica Chimica Acta · doi:10.1002/hlca.202100179 · Cited by 16 · see citing works
Self-citationLópez-Tena, M., Chen, S.-K., & Winssinger, N. (2022) · Bioconjugate chemistry · doi:10.1021/acs.bioconjchem.2c00292 · Cited by 12 · see citing works
Self-citationTepper, O., Appella, D. H., Zheng, H., Dzikowski, R., & Yavin, E. (2024) · ACS Sensors · doi:10.1021/acssensors.3c02553 · Cited by 14 · see citing works
Visible Light Photochemical Reactions for Nucleic Acid-Based Technologies
Koo, B., Yoo, H., Choi, H. J., Kim, M., Kim, C., & Kim, K. T. (2021) · Molecules · doi:10.3390/molecules26030556 · Cited by 14 · see citing works
Self-citationSequencing of <scp>d</scp>/<scp>l</scp>-DNA and XNA by Templated-Synthesis
Joshi, S., Romanens, P., & Winssinger, N. (2025) · Journal of the American Chemical Society · doi:10.1021/jacs.5c00708 · Cited by 4 · see citing works
Self-citationZhao, S.-J., Guo, H., Wu, Z., & Jiang, J. (2022) · Chemical Communications · doi:10.1039/d2cc05628c · Cited by 3 · see citing works
Kim, H., Choi, H., Min, K. S., Han, W. J., Park, J. W., & Kim, K. T. (2022) · Chemical Communications · doi:10.1039/d2cc05447g · Cited by 3 · see citing works
Self-citationNucleic acid‐templated chemical reactions for nucleic acid detection
Ryu, J. Y., Park, H. Y., SHIN, H.-C., & Kim, K. T. (2024) · Bulletin of the Korean Chemical Society · doi:10.1002/bkcs.12924 · Cited by 2 · see citing works
Self-citationChemically Modified Thiazole Orange FIT-PNAs: Superior Nucleic Acid Sensing Molecules
Fadila, A., Chanda, P., Maree, S., Tepper, O., Appella, D. H., Zheng, H., & Yavin, E. (2026) · Chemical & Biomedical Imaging · doi:10.1021/cbmi.6c00116
- Authors
- Kim, K. T., & Winssinger, N.
- Affiliations
- University of Geneva (CH)
- Corresponding author
- Winssinger, Nicolas
- Venue
- Chemical Science
- Publisher
- Royal Society of Chemistry (RSC)
- Published
- 2020
- Volume
- 11
- Issue
- 16
- Pages
- 4150-4157
- ISSN
- 2041-6520 (ISSN-L)
- 2041-6539
- PMC
- PMC8152519
- OpenAlex
- W3013247789
- Cited by
- 17
- References
- 66
- Citations by year
- 2026: 1 · 2025: 2 · 2024: 2 · 2023: 1 · 2022: 5 · 2021: 6
- FWCI
- 0.97
- Type
- journal article
- Language
- en
- Open access
- diamond
- doi.org
- Licence
- Locations
- Chemical Science (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Archive ouverte UNIGE (University of Geneva) (publishedVersion, other-oa)
- Archive ouverte UNIGE (University of Geneva) (submittedVersion, other-oa)
- Funders
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (200020_169141, 200020_188406)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Keywords
- single nucleotide polymorphism detection, signal amplification, single-nucleotide discrimination, π-π stacking, oncogenic mutations, nucleic acid sensing
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 ›
Are you an author, or do you see a problem with this page? Request a review