{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T11:43:50Z","timestamp":1792496630043,"version":"4.5.0"},"reference-count":41,"publisher":"American Chemical Society (ACS)","issue":"20","license":[{"start":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T00:00:00Z","timestamp":1791417600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T00:00:00Z","timestamp":1791417600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T00:00:00Z","timestamp":1791417600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/501100001843","name":"Science and Engineering Research Board","doi-asserted-by":"publisher","award":["ANRF\/ARG\/2025\/002756\/LS"],"award-info":[{"award-number":["ANRF\/ARG\/2025\/002756\/LS"]}],"id":[{"id":"10.13039\/501100001843","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001409","name":"Department of Science and Technology, Ministry of Science and Technology, India","doi-asserted-by":"publisher","award":["IF200559"],"award-info":[{"award-number":["IF200559"]}],"id":[{"id":"10.13039\/501100001409","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Phosphorothioated (PST) oligonucleotides are extensively used in RNA therapeutics and biosensing applications. PST-modified linkages remain part of 13 approved oligonucleotide drug backbones (out of 23 total approved drugs). Despite the widespread utilization of PST linkages in oligonucleotide therapeutics, the full spectrum of their interactions with nontarget nucleic acids and DNA polymerases remains inadequately characterized. In this study, we report a novel discovery and the modalities (sequence dependence and length) of an unusual 3\u2032-mismatch bypass activity involving 3\u2032-PST primers, circular DNA (CD) template, and strand displacement DNA polymerases. We demonstrate that this activity persists for at least 24 nt of mismatch, is sequence-independent, and occurs when processed by three major commercially available strand displacement DNA polymerases commonly used in molecular diagnostics (phi29, BST large fragment (LF), BSU large fragment (LF)) with operational conditions spanning a large temperature range and buffer conditions. The 3\u2032-terminal mismatch bypass activity of these three polymerases additionally extended to therapeutically relevant modifications such as locked nucleic acid (LNA) and 2\u2032-O-methyl (2\u2032-OMe). We also found that this mismatch bypass activity could be regulated by oligonucleotides complementary to the mismatch region. The significance of this study lies not only in the discovery and analytical investigation of the novel observation but also in its ramifications for biosensing and the nonspecific interactions of PST oligonucleotides in RNA therapeutics.<\/jats:p>","DOI":"10.1021\/acs.biochem.6c00108","type":"journal-article","created":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T19:01:48Z","timestamp":1791486108000},"page":"3151-3166","source":"Crossref","is-referenced-by-count":0,"title":["Discovery and\nModulation of an Unusual Terminal Mismatch\nBypass Activity Involving 3\u2032-Phosphorothioated Primers and\nCommercial Strand Displacement DNA Polymerases"],"prefix":"10.1021","volume":"65","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6572-1728","authenticated-orcid":true,"given":"Shrawan","family":"Kumar","sequence":"first","affiliation":[{"name":"Mahindra University , , ,","place":["Hyderabad, India, 500043"]},{"name":"Mahindra University , , ,","place":["Hyderabad, India, 500043"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hira Singh","family":"Gariya","sequence":"additional","affiliation":[{"name":"Bennett University , ,","place":["Greater Noida, India, 201310"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chandrika","family":"Sharma","sequence":"additional","affiliation":[{"name":"Mahindra University , , ,","place":["Hyderabad, India, 500043"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saba","family":"Parveen","sequence":"additional","affiliation":[{"name":"Mahindra University , , ,","place":["Hyderabad, India, 500043"]},{"name":"Mahindra University , , ,","place":["Hyderabad, India, 500043"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vandana K","family":"Nair","sequence":"additional","affiliation":[{"name":"Mahindra University , , ,","place":["Hyderabad, India, 500043"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mrittika","family":"Sengupta","sequence":"additional","affiliation":[{"name":"Mahindra University , , ,","place":["Hyderabad, India, 500043"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chitra","family":"Gurnani","sequence":"additional","affiliation":[{"name":"Mahindra University , , ,","place":["Hyderabad, India, 500043"]},{"name":"Mahindra University , , ,","place":["Hyderabad, India, 500043"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8510-1171","authenticated-orcid":true,"given":"Souradyuti","family":"Ghosh","sequence":"additional","affiliation":[{"name":"Mahindra University , , ,","place":["Hyderabad, India, 500043"]},{"name":"Mahindra University , , ,","place":["Hyderabad, India, 500043"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,10,8]]},"reference":[{"issue":"1","key":"2026102007164371300_cit1","doi-asserted-by":"publisher","first-page":"14845","DOI":"10.1038\/s41598-020-71896-w","article-title":"An Artificial\nCationic Oligosaccharide Combined with Phosphorothioate Linkages Strongly\nImproves siRNA Stability","volume":"10","author":"Irie","year":"2020","journal-title":"Sci. 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Chem."},{"issue":"22","key":"2026102007164371300_cit24","doi-asserted-by":"publisher","first-page":"5491","DOI":"10.1039\/D4AN00866A","article-title":"Probing the\nRole of Ligation and Exonuclease Digestion towards Non-Specific Amplification\nin Bioanalytical RCA Assays","volume":"149","author":"Nair","year":"2024","journal-title":"Analyst"},{"issue":"16","key":"2026102007164371300_cit25","doi-asserted-by":"publisher","first-page":"4795","DOI":"10.1039\/C9AN00843H","article-title":"Robust and Highly Specific\nFluorescence Sensing of SalmonellaTyphimurium Based\non Dual-Functional Phi29 DNA Polymerase-Mediated Isothermal Circular\nStrand Displacement Polymerization","volume":"144","author":"Li","year":"2019","journal-title":"Analyst"},{"issue":"10","key":"2026102007164371300_cit26","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1093\/abbs\/gmq082","article-title":"Polymerization Behavior\nof Klenow Fragment and Taq DNA Polymerase in Short\nPrimer Extension Reactions","volume":"42","author":"Zhao","year":"2010","journal-title":"ABBS"},{"key":"2026102007164371300_cit27","doi-asserted-by":"publisher","first-page":"123809","DOI":"10.1016\/j.talanta.2022.123809","article-title":"Evaluation of Indirect Sequence-Specific Magneto-Extraction-Aided\nLAMP for Fluorescence and Electrochemical SARS-CoV-2 Nucleic Acid\nDetection","volume":"252","author":"Tripathy","year":"2023","journal-title":"Talanta"},{"key":"2026102007164371300_cit28","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.trac.2017.10.015","article-title":"Recombinase Polymerase\nAmplification: Basics, Applications\nand Recent Advances","volume":"98","author":"Lobato","year":"2018","journal-title":"TrAC, Trends Anal. Chem."},{"key":"2026102007164371300_cit29","doi-asserted-by":"publisher","first-page":"553474","DOI":"10.3389\/fbioe.2020.553474","article-title":"A Single\nAmino Acid Change to Taq\nDNA Polymerase Enables Faster PCR, Reverse Transcription and Strand-Displacement","volume":"8","author":"Barnes","year":"2021","journal-title":"Front. Bioeng. Biotechnol."},{"issue":"6","key":"2026102007164371300_cit30","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0198480","article-title":"Variable Termination\nSites of DNA\nPolymerases Encountering a DNA\u2013Protein Cross-Link","volume":"13","author":"Yudkina","year":"2018","journal-title":"PLoS One"},{"issue":"39","key":"2026102007164371300_cit31","doi-asserted-by":"publisher","first-page":"27481","DOI":"10.1074\/jbc.274.39.27481","article-title":"Replication\nSlippage of Different\nDNA Polymerases Is Inversely Related to Their Strand Displacement\nEfficiency","volume":"274","author":"Canceill","year":"1999","journal-title":"J. Biol. Chem."},{"issue":"2","key":"2026102007164371300_cit32","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1006\/jmbi.2001.4943","article-title":"In Vitro\nReplication Slippage by\nDNA Polymerases from Thermophilic Organisms","volume":"312","author":"Viguera","year":"2001","journal-title":"J. Mol. Biol."},{"issue":"2","key":"2026102007164371300_cit33","doi-asserted-by":"publisher","first-page":"260","DOI":"10.3390\/pharmaceutics14020260","article-title":"Oligonucleotide Therapeutics: From\nDiscovery and Development to Patentability","volume":"14","author":"Moumne\u0301","year":"2022","journal-title":"Pharmaceutics"},{"issue":"30","key":"2026102007164371300_cit34","doi-asserted-by":"publisher","first-page":"8583","DOI":"10.1007\/s00216-016-9479-y","article-title":"A Primerless Molecular Diagnostic:\nPhosphorothioated-Terminal\nHairpin Formation and Self-Priming Extension (PS-THSP)","volume":"408","author":"Jung","year":"2016","journal-title":"Anal. Bioanal. Chem."},{"issue":"1","key":"2026102007164371300_cit35","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1002\/jcc.21596","article-title":"NUPACK: Analysis\nand Design of Nucleic Acid Systems","volume":"32","author":"Zadeh","year":"2011","journal-title":"J. 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Exp. Microbiol. Immunol."},{"key":"2026102007164371300_cit40","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1016\/j.jpba.2016.05.010","article-title":"Effects of DMSO, Glycerol, Betaine\nand Their Combinations in Detecting Single Nucleotide Polymorphisms\nof Epidermal Growth Factor Receptor (EGFR) Gene Promoter Sequence\nin Non-Small-Cell Lung Cancer (NSCLC) Patients","volume":"128","author":"Juris\u030cic\u0301","year":"2016","journal-title":"J. Pharm. Biomed. Anal."},{"issue":"6650","key":"2026102007164371300_cit41","doi-asserted-by":"publisher","first-page":"1150","DOI":"10.1126\/science.add5892","article-title":"An Enzyme\nCascade Enables Production of Therapeutic Oligonucleotides in a Single\nOperation","volume":"380","author":"Moody","year":"2023","journal-title":"Science"}],"container-title":["Biochemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.biochem.6c00108","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/bichaw\/article-pdf\/doi\/10.1021\/acs.biochem.6c00108\/68792591\/acs.biochem.6c00108.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/bichaw\/article-pdf\/doi\/10.1021\/acs.biochem.6c00108\/68792591\/acs.biochem.6c00108.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T11:29:06Z","timestamp":1792495746000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/bichaw\/article\/65\/20\/3151\/5447297\/Discovery-and-Modulation-of-an-Unusual-Terminal"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,8]]},"references-count":41,"journal-issue":{"issue":"20","published-online":{"date-parts":[[2026,10,8]]},"published-print":{"date-parts":[[2026,10,20]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.biochem.6c00108","relation":{},"ISSN":["0006-2960","1520-4995"],"issn-type":[{"value":"0006-2960","type":"print"},{"value":"1520-4995","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,8]]}}}