{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:58:23Z","timestamp":1792792703410,"version":"4.5.0"},"reference-count":90,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2024,12,1]],"date-time":"2024-12-01T00:00:00Z","timestamp":1733011200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,12,1]],"date-time":"2024-12-01T00:00:00Z","timestamp":1733011200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,8,21]],"date-time":"2024-08-21T00:00:00Z","timestamp":1724198400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100013377","name":"Nederlandse Onderzoekschool Voor Astronomie","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100013377","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003151","name":"Quebec Research Fund Nature and Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003151","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Biosensors and Bioelectronics"],"published-print":{"date-parts":[[2024,12]]},"DOI":"10.1016\/j.bios.2024.116680","type":"journal-article","created":{"date-parts":[[2024,8,22]],"date-time":"2024-08-22T19:00:06Z","timestamp":1724353206000},"page":"116680","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":34,"special_numbering":"C","title":["Truncations and in silico docking to enhance the analytical response of aptamer-based biosensors"],"prefix":"10.1016","volume":"265","author":[{"given":"Minh-Dat","family":"Nguyen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meghan T.","family":"Osborne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guy Terence","family":"Prevot","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zachary R.","family":"Churcher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5573-4891","authenticated-orcid":false,"given":"Philip E.","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lena","family":"Simine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0490-7115","authenticated-orcid":false,"given":"Philippe","family":"Dauphin-Ducharme","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"23","key":"10.1016\/j.bios.2024.116680_bib1","doi-asserted-by":"crossref","first-page":"4229","DOI":"10.3390\/molecules24234229","article-title":"Aptamers: A review of their chemical properties and modifications for therapeutic application","volume":"24","author":"Adachi","year":"2019","journal-title":"Molecules"},{"key":"10.1016\/j.bios.2024.116680_bib2","doi-asserted-by":"crossref","DOI":"10.1016\/j.jmgm.2021.107872","article-title":"In silico approach for post-SELEX DNA aptamers: a mini-review","volume":"105","author":"Ahmad","year":"2021","journal-title":"J. Mol. Graphics Modell."},{"issue":"1","key":"10.1016\/j.bios.2024.116680_bib3","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1038\/ncomms1791","article-title":"Electrochemical tunnelling sensors and their potential applications","volume":"3","author":"Albrecht","year":"2012","journal-title":"Nat. Commun."},{"issue":"13","key":"10.1016\/j.bios.2024.116680_bib4","doi-asserted-by":"crossref","first-page":"1731","DOI":"10.1021\/acs.accounts.3c00113","article-title":"Using exonucleases for aptamer characterization, engineering, and sensing","volume":"56","author":"Alkhamis","year":"2023","journal-title":"Acc. Chem. Res."},{"issue":"4","key":"10.1016\/j.bios.2024.116680_bib5","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1073\/pnas.1613458114","article-title":"Real-time measurement of small molecules directly in awake, ambulatory animals","volume":"114","author":"Arroyo-Curr\u00e1s","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"issue":"10","key":"10.1016\/j.bios.2024.116680_bib6","doi-asserted-by":"crossref","first-page":"1288","DOI":"10.1039\/D0AY00026D","article-title":"From the beaker to the body: translational challenges for electrochemical, aptamer-based sensors","volume":"12","author":"Arroyo-Curr\u00e1s","year":"2020","journal-title":"Anal. Methods"},{"issue":"10","key":"10.1016\/j.bios.2024.116680_bib7","doi-asserted-by":"crossref","first-page":"387","DOI":"10.6026\/97320630006387","article-title":"VSDK: virtual screening of small molecules using AutoDock Vina on windows platform","volume":"6","author":"Baba","year":"2011","journal-title":"Bioinformation"},{"issue":"12","key":"10.1016\/j.bios.2024.116680_bib8","doi-asserted-by":"crossref","first-page":"860","DOI":"10.3390\/antibiotics9120860","article-title":"Investigation of a truncated aptamer for ofloxacin detection using a rapid FRET-based apta-assay","volume":"9","author":"Ben Aissa","year":"2020","journal-title":"Antibiotics"},{"key":"10.1016\/j.bios.2024.116680_bib9","unstructured":"Biovia, D. S. Dassault Syst\u00e8mes. San Diego 2017."},{"key":"10.1016\/j.bios.2024.116680_bib10","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1146\/annurev.pharmtox.010909.105547","article-title":"Discovery and development of therapeutic aptamers","volume":"50","author":"Bouchard","year":"2010","journal-title":"Annu. Rev. Pharmacol. Toxicol."},{"issue":"22","key":"10.1016\/j.bios.2024.116680_bib11","doi-asserted-by":"crossref","first-page":"8420","DOI":"10.3390\/ijms21228420","article-title":"Methods and applications of in silico aptamer design and modeling","volume":"21","author":"Buglak","year":"2020","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.bios.2024.116680_bib12","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1023\/B:JCAM.0000017496.76572.6f","article-title":"Comparative study of several algorithms for flexible ligand docking","volume":"17","author":"Bursulaya","year":"2003","journal-title":"J. Comput. Aided Mol. Des."},{"issue":"31","key":"10.1016\/j.bios.2024.116680_bib13","doi-asserted-by":"crossref","first-page":"9961","DOI":"10.1021\/jacs.8b04975","article-title":"No structure-switching required: a generalizable exonuclease-mediated aptamer-based assay for small-molecule detection","volume":"140","author":"Canoura","year":"2018","journal-title":"J. Am. Chem. Soc."},{"issue":"4","key":"10.1016\/j.bios.2024.116680_bib14","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1021\/ja109295x","article-title":"On the origin of the efficient nanoparticle mediated electron transfer across a self-assembled monolayer","volume":"133","author":"Chazalviel","year":"2011","journal-title":"J. Am. Chem. Soc."},{"key":"10.1016\/j.bios.2024.116680_bib15","doi-asserted-by":"crossref","DOI":"10.1016\/j.jhazmat.2023.130798","article-title":"Docking-aided rational tailoring of a fluorescence-and affinity-enhancing aptamer for a label-free ratiometric malachite green point-of-care aptasensor","volume":"447","author":"Chen","year":"2023","journal-title":"J. Hazard Mater."},{"issue":"7","key":"10.1016\/j.bios.2024.116680_bib16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00604-019-3504-8","article-title":"An aptamer based fluorometric microcystin-LR assay using DNA strand-based competitive displacement","volume":"186","author":"Chinnappan","year":"2019","journal-title":"Microchim. Acta"},{"key":"10.1016\/j.bios.2024.116680_bib17","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bas006","article-title":"Aptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments","volume":"2012","author":"Cruz-Toledo","year":"2012","journal-title":"Database"},{"key":"10.1016\/j.bios.2024.116680_bib18","doi-asserted-by":"crossref","unstructured":"Dauphin Ducharme, P.; Churcher, Z. R.; Shoara, A. A.; Rahbarimehr, E.; Slavkovic, S.; Fontaine, N.; Boisvert, O.; Johnson, P. E. Redox Reporter\u2013Ligand Competition to Support Signaling in the Cocaine\u2010binding Electrochemical Aptamer\u2010based Biosensor. Chem. Eur J. e202300618. https:\/\/doi.org\/10.1002\/chem.202300618.","DOI":"10.1002\/chem.202300618"},{"issue":"10","key":"10.1016\/j.bios.2024.116680_bib19","doi-asserted-by":"crossref","first-page":"2832","DOI":"10.1021\/acssensors.9b01616","article-title":"Electrochemical aptamer-based sensors for improved therapeutic drug monitoring and high-precision, feedback-controlled drug delivery","volume":"4","author":"Dauphin-Ducharme","year":"2019","journal-title":"ACS Sens."},{"issue":"1","key":"10.1016\/j.bios.2024.116680_bib20","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1038\/s43586-023-00238-7","article-title":"In vitro selection of aptamers and their applications","volume":"3","author":"DeRosa","year":"2023","journal-title":"Nat. Rev. Methods Primers"},{"issue":"9","key":"10.1016\/j.bios.2024.116680_bib21","doi-asserted-by":"crossref","first-page":"4819","DOI":"10.1093\/nar\/gky268","article-title":"Crystal structures of thrombin in complex with chemically modified thrombin DNA aptamers reveal the origins of enhanced affinity","volume":"46","author":"Dolot","year":"2018","journal-title":"Nucleic Acids Res."},{"issue":"8","key":"10.1016\/j.bios.2024.116680_bib22","doi-asserted-by":"crossref","first-page":"3891","DOI":"10.1021\/acs.jcim.1c00203","article-title":"AutoDock Vina 1.2.0: new docking methods, expanded force field, and Python bindings","volume":"61","author":"Eberhardt","year":"2021","journal-title":"J. Chem. Inf. Model."},{"issue":"8","key":"10.1016\/j.bios.2024.116680_bib23","doi-asserted-by":"crossref","first-page":"4955","DOI":"10.1021\/acsomega.7b00782","article-title":"DNA aptamer\u2013target binding motif revealed using a fluorescent guanine probe: implications for food toxin detection","volume":"2","author":"Fadock","year":"2017","journal-title":"ACS Omega"},{"issue":"213","key":"10.1016\/j.bios.2024.116680_bib24","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.3007095","article-title":"Real-time, aptamer-based tracking of circulating therapeutic agents in living animals","volume":"5","author":"Ferguson","year":"2013","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.bios.2024.116680_bib25","doi-asserted-by":"crossref","DOI":"10.1016\/j.coelec.2023.101361","article-title":"Confounding effects on the response of electrochemical aptamer-based biosensors","author":"Fontaine","year":"2023","journal-title":"Curr. Opin. Electrochem."},{"issue":"5","key":"10.1016\/j.bios.2024.116680_bib26","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1038\/nprot.2016.051","article-title":"Computational protein\u2013ligand docking and virtual drug screening with the AutoDock suite","volume":"11","author":"Forli","year":"2016","journal-title":"Nat. Protoc."},{"issue":"1","key":"10.1016\/j.bios.2024.116680_bib27","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1146\/annurev.bi.64.070195.003555","article-title":"Diversity of oligonucleotide functions","volume":"64","author":"Gold","year":"1995","journal-title":"Annu. Rev. Biochem."},{"issue":"6","key":"10.1016\/j.bios.2024.116680_bib28","doi-asserted-by":"crossref","first-page":"2436","DOI":"10.1021\/acssensors.1c00749","article-title":"Selection of a structure-switching aptamer for the specific methotrexate detection","volume":"6","author":"He","year":"2021","journal-title":"ACS Sens."},{"issue":"2","key":"10.1016\/j.bios.2024.116680_bib29","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1039\/D2AN01658C","article-title":"Ultrasensitive therapeutic drug monitoring of methotrexate by a structure-switching aptamer with cascade primer exchange reaction","volume":"148","author":"He","year":"2023","journal-title":"Analyst"},{"issue":"6","key":"10.1016\/j.bios.2024.116680_bib30","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1016\/j.neuron.2018.08.011","article-title":"Molecular dynamics simulation for all","volume":"99","author":"Hollingsworth","year":"2018","journal-title":"Neuron"},{"issue":"43","key":"10.1016\/j.bios.2024.116680_bib31","doi-asserted-by":"crossref","first-page":"18996","DOI":"10.1002\/anie.202008284","article-title":"A generalizable and noncovalent strategy for interfacing aptamers with a microelectrode for the selective sensing of neurotransmitters in vivo","volume":"59","author":"Hou","year":"2020","journal-title":"Angew. Chem., Int. Ed."},{"issue":"8","key":"10.1016\/j.bios.2024.116680_bib32","doi-asserted-by":"crossref","first-page":"2121","DOI":"10.1021\/acschembio.2c00179","article-title":"A DNA aptamer for theophylline with ultrahigh selectivity reminiscent of the classic RNA aptamer","volume":"17","author":"Huang","year":"2022","journal-title":"ACS Chem. Biol."},{"key":"10.1016\/j.bios.2024.116680_bib33","doi-asserted-by":"crossref","DOI":"10.1002\/cbic.202300566","article-title":"Cross\u2010binding of adenosine by aptamers selected using theophylline","author":"Huang","year":"2023","journal-title":"Chembiochem"},{"key":"10.1016\/j.bios.2024.116680_bib34","unstructured":"Huey, R.; Morris, G. M.; Forli, S. Using AutoDock 4 and AutoDock Vina with AutoDockTools: A Tutorial. The Scripps Research Institute Molecular Graphics Laboratory."},{"issue":"35","key":"10.1016\/j.bios.2024.116680_bib35","doi-asserted-by":"crossref","first-page":"8164","DOI":"10.1039\/C9SC01495K","article-title":"Seconds-resolved pharmacokinetic measurements of the chemotherapeutic irinotecan in situ in the living body","volume":"10","author":"Idili","year":"2019","journal-title":"Chem. Sci."},{"issue":"9","key":"10.1016\/j.bios.2024.116680_bib36","doi-asserted-by":"crossref","first-page":"1628","DOI":"10.1093\/clinchem\/45.9.1628","article-title":"An emerging class of molecules that rival antibodies in diagnostics","volume":"45","author":"Jayasena","year":"1999","journal-title":"Clin. Chem."},{"issue":"7","key":"10.1016\/j.bios.2024.116680_bib37","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1038\/nrd3141","article-title":"Aptamers as therapeutics","volume":"9","author":"Keefe","year":"2010","journal-title":"Nat. Rev. Drug Discov."},{"issue":"22","key":"10.1016\/j.bios.2024.116680_bib38","doi-asserted-by":"crossref","first-page":"7146","DOI":"10.1093\/nar\/gkn831","article-title":"Exploring TAR\u2013RNA aptamer loop\u2013loop interaction by X-ray crystallography, UV spectroscopy and surface plasmon resonance","volume":"36","author":"Lebars","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.bios.2024.116680_bib39","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.jelechem.2013.04.008","article-title":"Dependence of the capacitance between an electrode and an electrolyte solution on the thickness of aluminum oxide layers deposited using atomic layer deposition","volume":"700","author":"Lee","year":"2013","journal-title":"J. Electroanal. Chem."},{"issue":"2","key":"10.1016\/j.bios.2024.116680_bib40","doi-asserted-by":"crossref","first-page":"356","DOI":"10.3390\/biomedicines11020356","article-title":"Design and prediction of aptamers assisted by in silico methods","volume":"11","author":"Lee","year":"2023","journal-title":"Biomedicines"},{"issue":"5","key":"10.1016\/j.bios.2024.116680_bib41","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1021\/ar900245u","article-title":"Target-responsive structural switching for nucleic acid-based sensors","volume":"43","author":"Li","year":"2010","journal-title":"Acc. Chem. Res."},{"key":"10.1016\/j.bios.2024.116680_bib42","doi-asserted-by":"crossref","DOI":"10.1016\/j.talanta.2023.124942","article-title":"Application and evaluation of molecular docking for aptamer and small molecular interaction-A case study with tetracycline antibiotics","volume":"266","author":"Liang","year":"2024","journal-title":"Talanta"},{"issue":"11","key":"10.1016\/j.bios.2024.116680_bib43","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1016\/S1074-5521(97)90115-0","article-title":"Structural basis of DNA folding and recognition in an AMP-DNA aptamer complex: distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP","volume":"4","author":"Lin","year":"1997","journal-title":"Chem. Biol."},{"issue":"8","key":"10.1016\/j.bios.2024.116680_bib44","doi-asserted-by":"crossref","first-page":"9491","DOI":"10.1021\/acsami.0c20707","article-title":"Immobilization strategies for enhancing sensitivity of electrochemical aptamer-based sensors","volume":"13","author":"Liu","year":"2021","journal-title":"ACS Appl. Mater. Interfaces"},{"issue":"17","key":"10.1016\/j.bios.2024.116680_bib45","doi-asserted-by":"crossref","first-page":"5108","DOI":"10.1093\/nar\/gkg680","article-title":"3DNA: a software package for the analysis, rebuilding and visualization of three\u2010dimensional nucleic acid structures","volume":"31","author":"Lu","year":"2003","journal-title":"Nucleic Acids Res."},{"issue":"12","key":"10.1016\/j.bios.2024.116680_bib46","doi-asserted-by":"crossref","DOI":"10.1002\/cbic.202200127","article-title":"2\u2010Aminopurine fluorescence spectroscopy for probing a glucose binding aptamer","volume":"23","author":"Lu","year":"2022","journal-title":"Chembiochem"},{"issue":"4","key":"10.1016\/j.bios.2024.116680_bib47","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1021\/ar900165x","article-title":"Folding-based electrochemical biosensors: the case for responsive nucleic acid architectures","volume":"43","author":"Lubin","year":"2010","journal-title":"Acc. Chem. Res."},{"issue":"1","key":"10.1016\/j.bios.2024.116680_bib48","doi-asserted-by":"crossref","first-page":"3549","DOI":"10.1038\/s41467-021-23932-0","article-title":"Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine","volume":"12","author":"Mieczkowski","year":"2021","journal-title":"Nat. Commun."},{"issue":"6412","key":"10.1016\/j.bios.2024.116680_bib49","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1126\/science.aao6750","article-title":"Aptamer-field-effect transistors overcome debye length limitations for small-molecule sensing","volume":"362","author":"Nakatsuka","year":"2018","journal-title":"Science"},{"key":"10.1016\/j.bios.2024.116680_bib50","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1016\/j.biochi.2020.10.005","article-title":"In silico molecular docking in DNA aptamer development","volume":"180","author":"Navien","year":"2021","journal-title":"Biochimie"},{"issue":"39","key":"10.1016\/j.bios.2024.116680_bib51","doi-asserted-by":"crossref","first-page":"8478","DOI":"10.1021\/bi100952k","article-title":"Defining a stem length-dependent binding mechanism for the cocaine-binding aptamer. A combined NMR and calorimetry study","volume":"49","author":"Neves","year":"2010","journal-title":"Biochemistry"},{"issue":"1","key":"10.1016\/j.bios.2024.116680_bib52","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.bpc.2010.09.009","article-title":"Defining the secondary structural requirements of a cocaine-binding aptamer by a thermodynamic and mutation study","volume":"153","author":"Neves","year":"2010","journal-title":"Biophys. Chem."},{"issue":"3","key":"10.1016\/j.bios.2024.116680_bib53","first-page":"1041","article-title":"Salt-Mediated two-site ligand binding by the cocaine-binding aptamer","volume":"45","author":"Neves","year":"2017","journal-title":"Nucleic Acids Res."},{"issue":"10","key":"10.1016\/j.bios.2024.116680_bib54","doi-asserted-by":"crossref","first-page":"1539","DOI":"10.1021\/acssensors.7b00619","article-title":"Optimizing stem length to improve ligand selectivity in a structure-switching cocaine-binding aptamer","volume":"2","author":"Neves","year":"2017","journal-title":"ACS Sens."},{"issue":"12","key":"10.1016\/j.bios.2024.116680_bib55","doi-asserted-by":"crossref","first-page":"4625","DOI":"10.1021\/acssensors.3c01624","article-title":"Electrochemical aptamer-based biosensors for measurements in undiluted human saliva","volume":"8","author":"Nguyen","year":"2023","journal-title":"ACS Sens."},{"key":"10.1016\/j.bios.2024.116680_bib56","article-title":"Whole blood theophylline measurements using an electrochemical DNA aptamer-based biosensor","author":"Nguyen","year":"2024","journal-title":"Under Review"},{"issue":"24","key":"10.1016\/j.bios.2024.116680_bib57","doi-asserted-by":"crossref","first-page":"17651","DOI":"10.1016\/S0021-9258(17)46749-4","article-title":"The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer","volume":"268","author":"Padmanabhan","year":"1993","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.bios.2024.116680_bib58","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1007\/s12551-016-0247-1","article-title":"Software for molecular docking: a review","volume":"9","author":"Pagadala","year":"2017","journal-title":"Biophys. Rev."},{"issue":"7","key":"10.1016\/j.bios.2024.116680_bib59","doi-asserted-by":"crossref","first-page":"2409","DOI":"10.1021\/jacs.7b12382","article-title":"Enhanced electron transfer mediated by conjugated polyelectrolyte and its application to washing-free DNA detection","volume":"140","author":"Park","year":"2018","journal-title":"J. Am. Chem. Soc."},{"key":"10.1016\/j.bios.2024.116680_bib60","article-title":"De novo RNA tertiary structure prediction at atomic resolution using geometric potentials from deep learning","volume":"2022","author":"Pearce","year":"2022","journal-title":"bioRxiv"},{"issue":"4","key":"10.1016\/j.bios.2024.116680_bib61","doi-asserted-by":"crossref","first-page":"2229","DOI":"10.1021\/acs.analchem.2c03566","article-title":"Finding the lost dissociation constant of electrochemical aptamer-based biosensors","volume":"95","author":"Rahbarimehr","year":"2023","journal-title":"Anal. Chem."},{"key":"10.1016\/j.bios.2024.116680_bib62","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1007\/s00604-008-0015-4","article-title":"E-DNA sensors for convenient, label-free electrochemical detection of hybridization","volume":"163","author":"Ricci","year":"2008","journal-title":"Microchim. Acta"},{"issue":"19","key":"10.1016\/j.bios.2024.116680_bib63","doi-asserted-by":"crossref","first-page":"4799","DOI":"10.1021\/acs.jcim.2c00734","article-title":"Prediction of aptamer\u2013small-molecule interactions using metastable states from multiple independent molecular dynamics simulations","volume":"62","author":"Rodr\u00edguez Serrano","year":"2022","journal-title":"J. Chem. Inf. Model."},{"issue":"8","key":"10.1016\/j.bios.2024.116680_bib64","doi-asserted-by":"crossref","first-page":"10537","DOI":"10.3390\/ijms130810537","article-title":"Characterization of aptamer-protein complexes by X-ray crystallography and alternative approaches","volume":"13","author":"Ruigrok","year":"2012","journal-title":"Int. J. Mol. Sci."},{"issue":"1","key":"10.1016\/j.bios.2024.116680_bib65","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1146\/annurev-anchem-071015-041446","article-title":"Structure-switching, electrochemical aptamer-based sensors","volume":"9","author":"Schoukroun-Barnes","year":"2016","journal-title":"Annu. Rev. Anal. Chem."},{"key":"10.1016\/j.bios.2024.116680_bib66","series-title":"The PyMOL Molecular Graphics System","author":"Schrodinger","year":"2010"},{"key":"10.1016\/j.bios.2024.116680_bib67","series-title":"Applications of BIOVIA Materials Studio, LAMMPS, and GROMACS in Various Fields of Science and Engineering","author":"Sharma","year":"2019"},{"issue":"12","key":"10.1016\/j.bios.2024.116680_bib68","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1021\/acssensors.2c01910","article-title":"Optimization of vancomycin aptamer sequence length increases the sensitivity of electrochemical, aptamer-based sensors in vivo","volume":"7","author":"Shaver","year":"2022","journal-title":"ACS Sens."},{"issue":"1","key":"10.1016\/j.bios.2024.116680_bib69","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1002\/(SICI)1097-0134(19990101)34:1<4::AID-PROT2>3.0.CO;2-6","article-title":"Ligand solvation in molecular docking","volume":"34","author":"Shoichet","year":"1999","journal-title":"Proteins: Struct., Funct., Bioinf."},{"issue":"21","key":"10.1016\/j.bios.2024.116680_bib70","doi-asserted-by":"crossref","first-page":"11862","DOI":"10.1080\/07391102.2022.2164057","article-title":"Virtual screening of truncated single stranded DNA aptamers for Staphylococcal enterotoxin type A","volume":"41","author":"Singh","year":"2023","journal-title":"J. Biomol. Struct. Dyn."},{"issue":"1","key":"10.1016\/j.bios.2024.116680_bib71","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-020-76002-8","article-title":"Thermodynamic analysis of cooperative ligand binding by the ATP-binding DNA aptamer indicates a population-shift binding mechanism","volume":"10","author":"Slavkovic","year":"2020","journal-title":"Sci. Rep."},{"issue":"5","key":"10.1016\/j.bios.2024.116680_bib72","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0267961","article-title":"Experimental, molecular docking and molecular dynamic studies of natural products targeting overexpressed receptors in breast cancer","volume":"17","author":"Taghizadeh","year":"2022","journal-title":"PLoS One"},{"issue":"13","key":"10.1016\/j.bios.2024.116680_bib73","doi-asserted-by":"crossref","first-page":"2445","DOI":"10.1039\/C7TB00095B","article-title":"Aptamer-functionalized neural recording electrodes for the direct measurement of cocaine in vivo","volume":"5","author":"Taylor","year":"2017","journal-title":"J. Mater. Chem. B"},{"key":"10.1016\/j.bios.2024.116680_bib74","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1007\/978-1-4939-3197-2_12","article-title":"Crystallographic pursuit of a protein-RNA aptamer complex","author":"Tesmer","year":"2016","journal-title":"Methods Mol. Biol."},{"issue":"12","key":"10.1016\/j.bios.2024.116680_bib75","doi-asserted-by":"crossref","first-page":"2749","DOI":"10.3390\/molecules25122749","article-title":"How \u2018protein-Docking\u2019Translates into the new emerging field of docking small molecules to nucleic acids?","volume":"25","author":"Tessaro","year":"2020","journal-title":"Molecules"},{"issue":"2","key":"10.1016\/j.bios.2024.116680_bib76","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","article-title":"AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading","volume":"31","author":"Trott","year":"2010","journal-title":"J. Comput. Chem."},{"issue":"33","key":"10.1016\/j.bios.2024.116680_bib77","doi-asserted-by":"crossref","first-page":"19370","DOI":"10.1074\/jbc.270.33.19370","article-title":"Selection of a suppressor mutation that restores affinity of an oligonucleotide inhibitor for thrombin using in vitro genetics","volume":"270","author":"Tsiang","year":"1995","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.bios.2024.116680_bib78","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.ymeth.2024.03.007","article-title":"Isothermal titration calorimetry and surface plasmon resonance methods to probe protein\u2013protein interactions","volume":"225","author":"Upadhyay","year":"2024","journal-title":"Methods"},{"issue":"18","key":"10.1016\/j.bios.2024.116680_bib79","doi-asserted-by":"crossref","first-page":"1555","DOI":"10.2174\/156802608786786624","article-title":"Medicinal chemistry and the molecular operating environment (MOE): application of QSAR and molecular docking to drug Discovery","volume":"8","author":"Vilar","year":"2008","journal-title":"Curr. Top. Med. Chem."},{"issue":"13","key":"10.1016\/j.bios.2024.116680_bib80","doi-asserted-by":"crossref","first-page":"e81","DOI":"10.1093\/nar\/gky305","article-title":"Introducing structure-switching functionality into small-molecule-binding aptamers via nuclease-directed truncation","volume":"46","author":"Wang","year":"2018","journal-title":"Nucleic Acids Res."},{"issue":"18","key":"10.1016\/j.bios.2024.116680_bib81","doi-asserted-by":"crossref","first-page":"10513","DOI":"10.1021\/la800801v","article-title":"Optimization of electrochemical aptamer-based sensors via optimization of probe packing density and surface chemistry","volume":"24","author":"White","year":"2008","journal-title":"Langmuir"},{"issue":"3","key":"10.1016\/j.bios.2024.116680_bib82","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1039\/b921253a","article-title":"Re-engineering aptamers to support reagentless, self-reporting electrochemical sensors","volume":"135","author":"White","year":"2010","journal-title":"Analyst"},{"issue":"2","key":"10.1016\/j.bios.2024.116680_bib83","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1021\/acssensors.3c02004","article-title":"Rational approach to optimizing conformation-switching aptamers for biosensing applications","volume":"9","author":"Wolfe","year":"2024","journal-title":"ACS Sens."},{"key":"10.1016\/j.bios.2024.116680_bib84","article-title":"Using spectroscopy to guide the adaptation of aptamers into electrochemical aptamer-based sensors","author":"Wu","year":"2022","journal-title":"Bioconjugate Chem."},{"issue":"11","key":"10.1016\/j.bios.2024.116680_bib85","doi-asserted-by":"crossref","first-page":"2875","DOI":"10.1038\/nprot.2007.413","article-title":"Preparation of electrode-immobilized, redox-modified oligonucleotides for electrochemical DNA and aptamer-based sensing","volume":"2","author":"Xiao","year":"2007","journal-title":"Nat. Protoc."},{"issue":"11","key":"10.1016\/j.bios.2024.116680_bib86","doi-asserted-by":"crossref","first-page":"1267","DOI":"10.1002\/elan.200804564","article-title":"On the signaling of electrochemical aptamer\u2010based sensors: collision\u2010and folding\u2010based mechanisms","volume":"21","author":"Xiao","year":"2009","journal-title":"Electroanalysis"},{"key":"10.1016\/j.bios.2024.116680_bib87","doi-asserted-by":"crossref","DOI":"10.1016\/j.aca.2022.339742","article-title":"Rapid nanomolar detection of methamphetamine in biofluids via a reagentless electrochemical aptamer-based biosensor","volume":"1207","author":"Xie","year":"2022","journal-title":"Anal. Chim. Acta"},{"issue":"17","key":"10.1016\/j.bios.2024.116680_bib88","doi-asserted-by":"crossref","first-page":"7731","DOI":"10.1021\/jacs.2c00478","article-title":"Structural insights into the mechanism of high-affinity binding of ochratoxin A by a DNA aptamer","volume":"144","author":"Xu","year":"2022","journal-title":"J. Am. Chem. Soc."},{"key":"10.1016\/j.bios.2024.116680_bib89","article-title":"Magnetic aptamer copper nanoclusters fluorescent biosensor for the visual detection of zearalenone based on docking-aided rational tailoring","author":"Yu","year":"2024","journal-title":"Food Chem."},{"issue":"10","key":"10.1016\/j.bios.2024.116680_bib90","doi-asserted-by":"crossref","first-page":"2142","DOI":"10.3390\/ijms18102142","article-title":"Recent advances in SELEX technology and aptamer applications in biomedicine","volume":"18","author":"Zhuo","year":"2017","journal-title":"Int. J. Mol. Sci."}],"container-title":["Biosensors and Bioelectronics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0956566324006869?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0956566324006869?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2024,9,10]],"date-time":"2024-09-10T18:37:47Z","timestamp":1725993467000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0956566324006869"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12]]},"references-count":90,"alternative-id":["S0956566324006869"],"URL":"https:\/\/doi.org\/10.1016\/j.bios.2024.116680","relation":{"has-preprint":[{"id-type":"doi","id":"10.26434\/chemrxiv-2024-mshjh","asserted-by":"object"}]},"ISSN":["0956-5663"],"issn-type":[{"value":"0956-5663","type":"print"}],"subject":[],"published":{"date-parts":[[2024,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Truncations and in silico docking to enhance the analytical response of aptamer-based biosensors","name":"articletitle","label":"Article Title"},{"value":"Biosensors and Bioelectronics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.bios.2024.116680","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 The Authors. Published by Elsevier B.V.","name":"copyright","label":"Copyright"}],"article-number":"116680"}}