{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T13:57:45Z","timestamp":1791295065434,"version":"4.1.0"},"reference-count":61,"publisher":"American Chemical Society (ACS)","issue":"39","license":[{"start":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:00:00Z","timestamp":1790208000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:00:00Z","timestamp":1790208000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:00:00Z","timestamp":1790208000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/501100012190","name":"Ministry of Science and Higher Education of the Russian Federation","doi-asserted-by":"publisher","award":["926010"],"award-info":[{"award-number":["926010"]}],"id":[{"id":"10.13039\/501100012190","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012190","name":"Ministry of Science and Higher Education of the Russian Federation","doi-asserted-by":"publisher","award":["FSER-2025-0019"],"award-info":[{"award-number":["FSER-2025-0019"]}],"id":[{"id":"10.13039\/501100012190","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Priority 2030 Federal Academic Leadership  Program","award":["926010"],"award-info":[{"award-number":["926010"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Sequence-specific detection of double-stranded DNA (dsDNA) under physiological conditions remains challenging because the complementary strand is inaccessible to conventional oligonucleotide probes, often requiring thermal denaturation or protein-assisted strand separation. Here, we developed a binary DNAzyme (BiDz) sensor for sequence-specific dsDNA detection at 37 \u00b0C. While the all-DNA BiDz failed to recognize dsDNA efficiently, incorporating alternating locked nucleic acid (LNA)\/DNA residues into the analyte-binding arms enabled efficient strand invasion and markedly improved signal generation. Integration of the optimized BiDz into a multivalent DNAzyme nanomachine (DNM) further enhanced target binding and reduced the detection limit for dsDNA amplicons to 25 pM, a 3.5-fold improvement over BiDz alone. The DNM also detected long plasmid dsDNA at nanomolar concentrations while maintaining excellent discrimination of centrally located single-base mismatches. Both BiDz and DNM demonstrated excellent discrimination of both A\u2013C and the most challenging G\u2013T mismatches. These findings demonstrate that combining alternating LNA\/DNA-modified binding arms with a multivalent DNM architecture enables sensitive and highly specific dsDNA detection under physiological conditions, providing a promising platform for isothermal nucleic acid analysis.<\/jats:p>","DOI":"10.1021\/acs.analchem.6c02297","type":"journal-article","created":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T04:28:37Z","timestamp":1790310517000},"page":"28757-28766","source":"Crossref","is-referenced-by-count":0,"title":["LNA-Modified\nDNAzyme Nanomachines Enable Physiological-Temperature\nRecognition of Double-Stranded DNA"],"prefix":"10.1021","volume":"98","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2308-9605","authenticated-orcid":true,"given":"Muhannad","family":"Ateiah","sequence":"first","affiliation":[{"name":"ITMO University , , Lomonosov 9 , ,","place":["St. Petersburg, Russia, 191002"]},{"name":"St. Petersburg State University , , Universitetskaya Enb. 7-9 , ,","place":["St. Petersburg, Russia, 199034"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vladislav A.","family":"Reushev","sequence":"additional","affiliation":[{"name":"ITMO University , , Lomonosov 9 , ,","place":["St. Petersburg, Russia, 191002"]},{"name":"Group of Biocondensates and Cell Membrane-Less Organelles of the Institute of Cytology, Russian Academy of Science , Tikhoretsky Ave. 4 , ,","place":["St. Petersburg, Russia, 194064"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nairouz","family":"Deeb","sequence":"additional","affiliation":[{"name":"ITMO University , , Lomonosov 9 , ,","place":["St. Petersburg, Russia, 191002"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria S.","family":"Rubel","sequence":"additional","affiliation":[{"name":"ITMO University , , Lomonosov 9 , ,","place":["St. Petersburg, Russia, 191002"]},{"name":"St. Petersburg State University , , Universitetskaya Enb. 7-9 , ,","place":["St. Petersburg, Russia, 199034"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8682-6553","authenticated-orcid":true,"given":"Dmitry M.","family":"Kolpashchikov","sequence":"additional","affiliation":[{"name":"University of Central Florida , , 4111 Libra Drive , , ,","place":["Orlando, Florida, United States, 32816"]},{"name":"University of Central Florida , , 6900 Lake Nona Blvd , , ,","place":["Orlando, Florida, United States, 32827"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,24]]},"reference":[{"issue":"4","key":"2026100608074174800_cit1","doi-asserted-by":"publisher","DOI":"10.1016\/j.omtn.2024.102348","article-title":"Anti-Gene Oligonucleotide\nClamps Invade dsDNA and Downregulate Huntingtin Expression","volume":"35","author":"Umek","year":"2024","journal-title":"Mol. Ther. Nucleic Acids"},{"issue":"1","key":"2026100608074174800_cit2","doi-asserted-by":"publisher","DOI":"10.1016\/j.xcrm.2023.101354","article-title":"Antitumor Efficacy\nof a Sequence-Specific DNA-Targeted \u03b3PNA-Based c-Myc Inhibitor","volume":"5","author":"Malik","year":"2024","journal-title":"Cell Rep. Med."},{"issue":"84","key":"2026100608074174800_cit3","doi-asserted-by":"publisher","first-page":"9851","DOI":"10.1039\/c3cc45705b","article-title":"Sandwich Assay for\nMixed-Sequence Recognition of Double-Stranded DNA: Invader-Based Detection\nof Targets Specific to Foodborne Pathogens","volume":"49","author":"Denn","year":"2013","journal-title":"Chem. Commun."},{"issue":"4","key":"2026100608074174800_cit4","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1038\/s41557-021-00645-x","article-title":"A Biologically Stable\nDNAzyme That Efficiently Silences Gene Expression in Cells","volume":"13","author":"Wang","year":"2021","journal-title":"Nat. Chem."},{"issue":"6213","key":"2026100608074174800_cit5","doi-asserted-by":"publisher","DOI":"10.1126\/science.1258096","article-title":"Genome editing. The new frontier\nof genome engineering\nwith CRISPR-Cas9","volume":"346","author":"Doudna","year":"2014","journal-title":"Science"},{"issue":"12","key":"2026100608074174800_cit6","doi-asserted-by":"publisher","first-page":"12133","DOI":"10.1007\/s11033-022-07880-6","article-title":"CRISPR\/Cas9\nsystem:\na reliable and facile genome editing tool in modern biology","volume":"49","author":"Javaid","year":"2022","journal-title":"Mol. Biol. Rep."},{"issue":"2","key":"2026100608074174800_cit7","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1007\/s40484-014-0030-x","article-title":"Target\nspecificity of the CRISPR-Cas9\nsystem","volume":"2","author":"Wu","year":"2014","journal-title":"Quant. Biol."},{"issue":"3","key":"2026100608074174800_cit8","doi-asserted-by":"publisher","first-page":"937","DOI":"10.1016\/j.ymthe.2020.11.009","article-title":"Single-Base Resolution:\nIncreasing the Specificity of the CRISPR-Cas\nSystem in Gene Editing","volume":"29","author":"Rabinowitz","year":"2021","journal-title":"Mol. Ther."},{"issue":"16","key":"2026100608074174800_cit9","doi-asserted-by":"publisher","first-page":"7132","DOI":"10.7150\/thno.77830","article-title":"Specificity of oligonucleotide gene\ntherapy (OGT) agents","volume":"12","author":"Nedorezova","year":"2022","journal-title":"Theranostics"},{"issue":"23","key":"2026100608074174800_cit10","doi-asserted-by":"publisher","first-page":"6375","DOI":"10.1039\/D2SC07067G","article-title":"Minimizing\nthe off-target frequency of the CRISPR\/Cas9 system via zwitterionic\npolymer conjugation and peptide fusion","volume":"14","author":"Han","year":"2023","journal-title":"Chem.\nSci."},{"key":"2026100608074174800_cit11","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1016\/j.jconrel.2017.09.012","article-title":"Delivery strategies\nof the CRISPR-Cas9 gene-editing system for therapeutic applications","volume":"266","author":"Liu","year":"2017","journal-title":"J. Controlled Release"},{"key":"2026100608074174800_cit12","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1007\/978-1-60761-947-5_5","article-title":"LATE-PCR and\nAllied Technologies: Real-Time Detection Strategies for Rapid, Reliable\nDiagnosis from Single Cells","volume-title":"PCR Mutation\nDetection Protocols","author":"Pierce","year":"2011"},{"key":"2026100608074174800_cit13","doi-asserted-by":"publisher","first-page":"898","DOI":"10.1016\/j.bios.2010.07.011","article-title":"Lambda exonuclease\npre-treatment for improved DNA-chip performance depends on the relative\nprobe-target position","volume":"26","author":"Brinker","year":"2010","journal-title":"Biosens. 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Chem."},{"issue":"1","key":"2026100608074174800_cit25","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-09147-8","article-title":"LNA Effects on DNA Binding and Conformation:\nFrom Single Strand to Duplex and Triplex Structures","volume":"7","author":"Pabon-Martinez","year":"2017","journal-title":"Sci. Rep."},{"issue":"3","key":"2026100608074174800_cit26","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1039\/D5CB00286A","article-title":"DNA-Targeting Invader Probes: Discovery, Principles,\nand Applications","volume":"7","author":"Hrdlicka","year":"2026","journal-title":"RSC Chem. Biol."},{"issue":"17","key":"2026100608074174800_cit27","doi-asserted-by":"publisher","first-page":"2039","DOI":"10.1002\/cbic.200700384","article-title":"A Binary\nDeoxyribozyme for Nucleic Acid Analysis","volume":"8","author":"Kolpashchikov","year":"2007","journal-title":"ChemBioChem"},{"issue":"6","key":"2026100608074174800_cit28","doi-asserted-by":"publisher","first-page":"811","DOI":"10.1002\/cbic.201000006","article-title":"RNA-cleaving deoxyribozyme sensor\nfor nucleic acid analysis: the limit of detection","volume":"11","author":"Gerasimova","year":"2010","journal-title":"ChemBioChem"},{"issue":"3","key":"2026100608074174800_cit29","doi-asserted-by":"publisher","first-page":"1051","DOI":"10.1021\/ja9076777","article-title":"MNAzymes:\nA Versatile New Class of Nucleic Acid Enzymes That Can Function as\nBiosensors and Molecular Switches","volume":"132","author":"Mokany","year":"2010","journal-title":"J. Am. Chem.\nSoc."},{"issue":"18","key":"2026100608074174800_cit30","doi-asserted-by":"publisher","first-page":"9106","DOI":"10.1021\/ac501811r","article-title":"DNA-Only Cascade: A Universal Tool for Signal Amplification,\nEnhancing the Detection of Target Analytes","volume":"86","author":"Bone","year":"2014","journal-title":"Anal. Chem."},{"issue":"40","key":"2026100608074174800_cit31","doi-asserted-by":"publisher","first-page":"10586","DOI":"10.1002\/anie.201303919","article-title":"Folding of 16S rRNA in a signal-producing structure\nfor the detection of bacteria","volume":"52","author":"Gerasimova","year":"2013","journal-title":"Angew. Chem.,\nInt. Ed."},{"key":"2026100608074174800_cit32","doi-asserted-by":"publisher","DOI":"10.6064\/2012\/928783","article-title":"An Elegant\nBiosensor Molecular Beacon Probe: Challenges and Recent Solutions","volume":"2012","author":"Kolpashchikov","year":"2012","journal-title":"Scientifica"},{"issue":"10","key":"2026100608074174800_cit33","doi-asserted-by":"publisher","first-page":"4988","DOI":"10.1002\/anie.201914919","article-title":"Binary (Split) Light-Up\nAptameric Sensors","volume":"60","author":"Kolpashchikov","year":"2021","journal-title":"Angew. Chem., Int. Ed."},{"issue":"99","key":"2026100608074174800_cit34","doi-asserted-by":"publisher","first-page":"14318","DOI":"10.1039\/C6CC06889H","article-title":"DNA Nanotechnology\nfor Nucleic Acid Analysis: Multifunctional Molecular DNA Machine for\nRNA Detection","volume":"52","author":"Cox","year":"2016","journal-title":"Chem. Commun."},{"issue":"2","key":"2026100608074174800_cit35","doi-asserted-by":"publisher","first-page":"416","DOI":"10.1039\/C8AN02274G","article-title":"A DNA Minimachine\nfor Selective and Sensitive Detection\nof DNA","volume":"144","author":"Lyalina","year":"2019","journal-title":"Analyst."},{"issue":"51","key":"2026100608074174800_cit36","doi-asserted-by":"publisher","first-page":"18667","DOI":"10.1021\/acs.analchem.3c04420","article-title":"DNAzyme Nanomachine\nwith Fluorogenic\nSubstrate Delivery Function: Advancing Sensitivity in Nucleic Acid\nDetection","volume":"95","author":"Hussein","year":"2023","journal-title":"Anal. Chem."},{"issue":"8","key":"2026100608074174800_cit37","doi-asserted-by":"publisher","DOI":"10.3390\/ijms26083652","article-title":"Multicomponent\nDNA Nanomachines for Amplification-Free Viral RNA Detection","volume":"26","author":"Solyanikova","year":"2025","journal-title":"Int. J. Mol. Sci."},{"issue":"23","key":"2026100608074174800_cit38","doi-asserted-by":"publisher","DOI":"10.1002\/cbic.202400572","article-title":"Enhancing Sensitivity in Nucleic\nAcid Detection via Collaborative Multiple Catalytic Cores in DNAzyme\nNanomachines","volume":"25","author":"Hussein","year":"2024","journal-title":"ChemBioChem"},{"issue":"20","key":"2026100608074174800_cit39","doi-asserted-by":"publisher","DOI":"10.1002\/cmdc.202200382","article-title":"Toward\na Home Test for COVID-19 Diagnosis: DNA Machine for Amplification-Free\nSARS-CoV-2 Detection in Clinical Samples","volume":"17","author":"El-Deeb","year":"2022","journal-title":"ChemMedChem"},{"key":"2026100608074174800_cit40","doi-asserted-by":"publisher","DOI":"10.1016\/j.snr.2022.100132","article-title":"Barley\nHaplotyping Using Biplex Deoxyribozyme Nanomachine","volume":"4","author":"Akhmetova","year":"2022","journal-title":"Sens. Actuators Rep."},{"issue":"5","key":"2026100608074174800_cit41","doi-asserted-by":"publisher","DOI":"10.3390\/ijms24054473","article-title":"DNA Nanomachine\n(DNM) Biplex Assay for Differentiating Bacillus cereus Species","volume":"24","author":"Ateiah","year":"2023","journal-title":"Int. J. Mol. Sci."},{"issue":"11","key":"2026100608074174800_cit42","doi-asserted-by":"publisher","first-page":"3260","DOI":"10.1039\/D6AN00265J","article-title":"DNA nanotechnology\nfor nucleic acid analysis: detection of RNA and dsDNA amplicons using\na multifunctional DNAzyme nanomachine (DNM)","volume":"151","author":"Ateiah","year":"2026","journal-title":"Analyst"},{"issue":"4","key":"2026100608074174800_cit43","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1016\/S0968-0896(00)00325-4","article-title":"2\u2032-O,4\u2032-C-Methylene-Bridged Nucleic Acid\n(2\u2032,4\u2032-BNA): Synthesis and Triplex-Forming Properties","volume":"9","author":"Obika","year":"2001","journal-title":"Bioorg. 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Chem."},{"key":"2026100608074174800_cit44","doi-asserted-by":"publisher","first-page":"8735","DOI":"10.1016\/S0040-4039(97)10322-7","article-title":"Synthesis\nof 2\u2032-O,4\u2032-C-Methyleneuridine\nand -Cytidine: Novel Bicyclic Nucleosides Having a Fixed C3\u2032-Endo\nSugar Puckering","volume":"38","author":"Obika","year":"1997","journal-title":"Tetrahedron Lett."},{"issue":"4839","key":"2026100608074174800_cit45","doi-asserted-by":"publisher","first-page":"487","DOI":"10.1126\/science.2448875","article-title":"Primer-Directed\nEnzymatic Amplification of DNA with a Thermostable DNA Polymerase","volume":"239","author":"Saiki","year":"1988","journal-title":"Science"},{"issue":"14","key":"2026100608074174800_cit46","doi-asserted-by":"publisher","first-page":"4160","DOI":"10.1021\/bi036064e","article-title":"Sequence and pH Effects of LNA-Containing\nTriple Helix-Forming Oligonucleotides: Physical Chemistry, Biochemistry,\nand Modeling Studies","volume":"43","author":"Sun","year":"2004","journal-title":"Biochemistry"},{"issue":"11","key":"2026100608074174800_cit47","doi-asserted-by":"publisher","first-page":"8550","DOI":"10.1021\/acs.analchem.5c08162","article-title":"Ultrasensitive Electrochemiluminescence\nNanoprobe for Early Screening\nand Early Diagnosis of Cervical Cancer","volume":"98","author":"Tang","year":"2026","journal-title":"Anal.\nChem."},{"issue":"19","key":"2026100608074174800_cit48","doi-asserted-by":"publisher","first-page":"5427","DOI":"10.1002\/slct.201701179","article-title":"Divide and Control: Comparison of\nSplit and Switch\nHybridization Sensors","volume":"2","author":"Smith","year":"2017","journal-title":"ChemistrySelect"},{"issue":"26","key":"2026100608074174800_cit49","doi-asserted-by":"publisher","first-page":"9435","DOI":"10.1021\/bi9803729","article-title":"Nearest-Neighbor Thermodynamics of\nInternal A\u00b7C Mismatches in DNA: Sequence Dependence and pH Effects","volume":"37","author":"Allawi","year":"1998","journal-title":"Biochemistry"},{"issue":"21","key":"2026100608074174800_cit50","doi-asserted-by":"publisher","first-page":"4925","DOI":"10.1093\/nar\/26.21.4925","article-title":"NMR Solution Structure of a DNA Dodecamer\nContaining Single G\u00b7T Mismatches","volume":"26","author":"Allawi","year":"1998","journal-title":"Nucleic\nAcids Res."},{"issue":"19","key":"2026100608074174800_cit51","doi-asserted-by":"publisher","DOI":"10.1002\/slct.73492","article-title":"Dual-Stage\nMismatch Interrogation (DMI) for High-Fidelity G\u2013T Discrimination\nby a DNA Nanodevice","volume":"11","author":"Patra","year":"2026","journal-title":"ChemistrySelelect"},{"issue":"5","key":"2026100608074174800_cit52","doi-asserted-by":"publisher","first-page":"2848","DOI":"10.1128\/AEM.69.5.2848-2856.2003","article-title":"Optimization of\nsingle-base-pair mismatch discrimination in oligonucleotide microarrays","volume":"69","author":"Urakawa","year":"2003","journal-title":"Appl. Environ. Microbiol."},{"issue":"2","key":"2026100608074174800_cit53","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1016\/j.tibs.2003.12.007","article-title":"Two Sides\nof the Coin: Affinity and Specificity of\nNucleic Acid Interactions","volume":"29","author":"Demidov","year":"2004","journal-title":"Trends Biochem. Sci."},{"issue":"41","key":"2026100608074174800_cit54","doi-asserted-by":"publisher","first-page":"13465","DOI":"10.1021\/jacs.6b05628","article-title":"Nonequilibrium\nHybridization Enables Discrimination of a Point Mutation within 5\u201340\n\u00b0C","volume":"138","author":"Stancescu","year":"2016","journal-title":"J. Am. Chem. Soc."},{"issue":"46","key":"2026100608074174800_cit55","doi-asserted-by":"publisher","first-page":"13052","DOI":"10.1002\/chem.201101987","article-title":"Molecular-beacon-based\ntricomponent probe for SNP analysis in folded nucleic acids","volume":"17","author":"Nguyen","year":"2011","journal-title":"Chem. - Eur. 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