{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T13:20:07Z","timestamp":1762608007662,"version":"build-2065373602"},"reference-count":84,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2020,9,2]],"date-time":"2020-09-02T00:00:00Z","timestamp":1599004800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002803","name":"Fondazione Cariplo","doi-asserted-by":"publisher","award":["2012-0907"],"award-info":[{"award-number":["2012-0907"]}],"id":[{"id":"10.13039\/501100002803","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Sensors"],"abstract":"<jats:p>The urgent need to develop a detection system for Staphylococcus aureus, one of the most common causes of infection, is prompting research towards novel approaches and devices, with a particular focus on point-of-care analysis. Biosensors are promising systems to achieve this aim. We coupled the selectivity and affinity of aptamers, short nucleic acids sequences able to recognize specific epitopes on bacterial surface, immobilized at high density on a nanostructured zirconium dioxide surface, with the rational design of specifically interacting fluorescent peptides to assemble an easy-to-use detection device. We show that the displacement of fluorescent peptides upon the competitive binding of S. aureus to immobilized aptamers can be detected and quantified through fluorescence loss. This approach could be also applied to the detection of other bacterial species once aptamers interacting with specific antigens will be identified, allowing the development of a platform for easy detection of a pathogen without requiring access to a healthcare environment.<\/jats:p>","DOI":"10.3390\/s20174977","type":"journal-article","created":{"date-parts":[[2020,9,2]],"date-time":"2020-09-02T09:29:28Z","timestamp":1599038968000},"page":"4977","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Rational Design of a User-Friendly Aptamer\/Peptide-Based Device for the Detection of Staphylococcus aureus"],"prefix":"10.3390","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5389-2669","authenticated-orcid":false,"given":"Luca","family":"Ronda","sequence":"first","affiliation":[{"name":"Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy"},{"name":"Institute of Biophysics, National Research Council, 56124 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessandro","family":"Tonelli","sequence":"additional","affiliation":[{"name":"DNAPhone s.r.l., 43126 Parma, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2097-4358","authenticated-orcid":false,"given":"Elisa","family":"Sogne","sequence":"additional","affiliation":[{"name":"CIMAINA and Department of Physics, University of Milan, 20133 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8886-8063","authenticated-orcid":false,"given":"Ida","family":"Autiero","sequence":"additional","affiliation":[{"name":"Molecular Horizon s.r.l, 06084 Perugia, Italy"},{"name":"Institute of Biostructures and Bioimaging, National Research Council, 80145 Naples, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4016-227X","authenticated-orcid":false,"given":"Francesca","family":"Spyrakis","sequence":"additional","affiliation":[{"name":"Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2325-3583","authenticated-orcid":false,"given":"Sara","family":"Pellegrino","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, University of Milan, 20133 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2502-4127","authenticated-orcid":false,"given":"Giorgio","family":"Abbiati","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, University of Milan, 20133 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5539-1825","authenticated-orcid":false,"given":"Elisa","family":"Maffioli","sequence":"additional","affiliation":[{"name":"CIMAINA and Department of Veterinary Medicine, University of Milan, 20133 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7554-5342","authenticated-orcid":false,"given":"Carsten","family":"Schulte","sequence":"additional","affiliation":[{"name":"CIMAINA and Department of Physics, University of Milan, 20133 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Riccardo","family":"Piano","sequence":"additional","affiliation":[{"name":"Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pietro","family":"Cozzini","sequence":"additional","affiliation":[{"name":"Department of Food and Drug, University of Parma, 43124 Parma, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3762-0062","authenticated-orcid":false,"given":"Andrea","family":"Mozzarelli","sequence":"additional","affiliation":[{"name":"Institute of Biophysics, National Research Council, 56124 Pisa, Italy"},{"name":"Department of Food and Drug, University of Parma, 43124 Parma, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6787-0594","authenticated-orcid":false,"given":"Stefano","family":"Bettati","sequence":"additional","affiliation":[{"name":"Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy"},{"name":"Institute of Biophysics, National Research Council, 56124 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3483-5914","authenticated-orcid":false,"given":"Francesca","family":"Clerici","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, University of Milan, 20133 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9325-4963","authenticated-orcid":false,"given":"Paolo","family":"Milani","sequence":"additional","affiliation":[{"name":"CIMAINA and Department of Physics, University of Milan, 20133 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5522-6803","authenticated-orcid":false,"given":"Cristina","family":"Lenardi","sequence":"additional","affiliation":[{"name":"CIMAINA and Department of Physics, University of Milan, 20133 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gabriella","family":"Tedeschi","sequence":"additional","affiliation":[{"name":"CIMAINA and Department of Veterinary Medicine, University of Milan, 20133 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0743-5499","authenticated-orcid":false,"given":"Maria Luisa","family":"Gelmi","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, University of Milan, 20133 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2020,9,2]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1016\/j.foodcont.2013.09.062","article-title":"Food handler-associated methicillin-resistant Staphylococcus aureus in public hospitals in Salvador, Brazil","volume":"37","author":"Ferreira","year":"2014","journal-title":"Food Control"},{"key":"ref_2","first-page":"97","article-title":"Staphylococcal and streptococcal infections","volume":"33","author":"Day","year":"2014","journal-title":"Medicine (Baltimore)"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/S0924-2244(02)00030-4","article-title":"Enterotoxigenic staphylococci and their toxins in restaurant foods","volume":"13","author":"Soriano","year":"2002","journal-title":"Trends Food Sci. Technol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1128\/CMR.00081-09","article-title":"Community-associated methicillin-resistant Staphylococcus aureus: Epidemiology and clinical consequences of an emerging epidemic","volume":"23","author":"David","year":"2010","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_5","first-page":"384","article-title":"Staphylococcus, Micrococcus, and other catalase-positive cocci that grow aerobically","volume":"Volume 1","author":"Murray","year":"2003","journal-title":"Manual of Clinical Microbiology"},{"key":"ref_6","unstructured":"Press, A. (2002). Rapid Systems and Instruments for the Identification of Bacteria. Manual of Commercial Methods in Clinical Microbiology, American Society of Microbiology."},{"key":"ref_7","unstructured":"Press, A. (2002). Rapid Systems and Instruments for Antimicrobial Susceptibility Testing of Bacteria. Manual of Commercial Methods in Clinical Microbiology, American Society of Microbiology."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1099\/jmm.0.46225-0","article-title":"Evaluation of six agglutination tests for Staphylococcus aureus identification depending upon local prevalence of meticillin-resistant S. aureus (MRSA)","volume":"55","author":"Weist","year":"2006","journal-title":"J. Med. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"3284","DOI":"10.1128\/JCM.00182-11","article-title":"Phoenix 100 versus Vitek 2 in the identification of gram-positive and gram-negative bacteria: A comprehensive meta-analysis","volume":"49","author":"Chatzigeorgiou","year":"2011","journal-title":"J. Clin. Microbiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1016\/j.bios.2011.10.021","article-title":"Label-free detection of Staphylococcus aureus in skin using real-time potentiometric biosensors based on carbon nanotubes and aptamers","volume":"31","author":"Blondeau","year":"2012","journal-title":"Biosens. Bioelectron."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1016\/j.bios.2014.08.075","article-title":"A smart DNA sensing system for detecting methicillin-resistant Staphylococcus aureus using modified nanoparticle probes","volume":"67","author":"Watanabe","year":"2015","journal-title":"Biosens. Bioelectron."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1911","DOI":"10.1128\/JCM.00389-14","article-title":"Multiplex real-time PCR assay for rapid detection of methicillin-resistant staphylococci directly from positive blood cultures","volume":"52","author":"Wang","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"S361","DOI":"10.1093\/cid\/cir052","article-title":"Molecular laboratory tests for the diagnosis of respiratory tract infection due to Staphylococcus aureus","volume":"52","author":"Peterson","year":"2011","journal-title":"Clin. Infect. Dis."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1128\/JCM.06169-11","article-title":"Clinical impact of a real-time PCR assay for rapid identification of staphylococcal bacteremia","volume":"50","author":"Frye","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/nrmicro2243","article-title":"Mass spectrometry tools for the classification and identification of bacteria","volume":"8","author":"Sauer","year":"2010","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1007\/s10337-014-2839-x","article-title":"Mass spectrometry in clinical microbiology and infectious diseases","volume":"78","author":"Fleurbaaij","year":"2015","journal-title":"Chromatographia"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1099\/jmm.0.016733-0","article-title":"Identification of molecularly defined Staphylococcus aureus strains using matrix-assisted laser desorption\/ionization time of flight mass spectrometry and the Biotyper 2.0 database","volume":"59","author":"Szabados","year":"2010","journal-title":"J. Med. Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/j.jhin.2014.11.025","article-title":"Development of a novel matrix-assisted laser desorption\/ionization time-of-flight mass spectrum (MALDI-TOF-MS)-based typing method to identify meticillin-resistant Staphylococcus aureus clones","volume":"90","author":"Ueda","year":"2015","journal-title":"J. Hosp. Infect."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1002\/1615-9861(200206)2:6<747::AID-PROT747>3.0.CO;2-V","article-title":"Identification and discrimination of Staphylococcus aureus strains using matrix-assisted laser desorption\/ionization-time of flight mass spectrometry","volume":"2","author":"Bernardo","year":"2002","journal-title":"Proteomics"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.fbio.2013.08.002","article-title":"Development of PEI-GA modified antibody based sensor for the detection of S. aureus in food samples","volume":"4","author":"Majumdar","year":"2013","journal-title":"Food Biosci."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1016\/j.bios.2006.04.003","article-title":"Lytic phage as a specific and selective probe for detection of Staphylococcus aureus\u2014A surface plasmon resonance spectroscopic study","volume":"22","author":"Balasubramanian","year":"2007","journal-title":"Biosens. Bioelectron."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1016\/j.bios.2015.03.041","article-title":"Detection of methicillin-resistant staphylococci by biosensor assay consisting of nanoscale films on optical fiber long-period gratings","volume":"70","author":"Bandara","year":"2015","journal-title":"Biosens. Bioelectron."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1763","DOI":"10.3390\/s130201763","article-title":"Recent advances in bacteriophage based biosensors for food-borne pathogen detection","volume":"13","author":"Singh","year":"2013","journal-title":"Sensors"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"12659","DOI":"10.1021\/jf503914f","article-title":"Rapid and sensitive detection of foodborne pathogenic bacteria (Staphylococcus aureus) using an electrochemical DNA genomic biosensor and its application in fresh beef","volume":"62","author":"Abdalhai","year":"2014","journal-title":"J. Agric. Food Chem."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2424","DOI":"10.1016\/j.bios.2004.11.006","article-title":"Analytical applications of aptamers","volume":"20","author":"Tombelli","year":"2005","journal-title":"Biosens. Bioelectron."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"7754","DOI":"10.3390\/s150407754","article-title":"Rationally designing aptamer sequences with reduced affinity for controlled sensor performance","volume":"15","author":"White","year":"2015","journal-title":"Sensors"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"4621","DOI":"10.1093\/nar\/gkp489","article-title":"Combining use of a panel of ssDNA aptamers in the detection of Staphylococcus aureus","volume":"37","author":"Cao","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"8884","DOI":"10.3390\/s150408884","article-title":"Comparison of whole-cell SELEX methods for theidentification of Staphylococcus aureus-specific DNA aptamers","volume":"15","author":"Moon","year":"2015","journal-title":"Sensors"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1016\/j.foodchem.2014.06.039","article-title":"Selection and characterization of DNA aptamers against Staphylococcus aureus enterotoxin C1","volume":"166","author":"Huang","year":"2015","journal-title":"Food Chem."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1016\/j.bios.2014.10.017","article-title":"A new aptamer\/graphene interdigitated gold electrode piezoelectric sensor for rapid and specific detection of Staphylococcus aureus","volume":"65","author":"Lian","year":"2015","journal-title":"Biosens. Bioelectron."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/j.bios.2014.12.040","article-title":"Aptamer-conjugated silver nanoparticles for electrochemical dual-aptamer-based sandwich detection of Staphylococcus aureus","volume":"68","author":"Abbaspour","year":"2015","journal-title":"Biosens. Bioelectron."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/j.ijfoodmicro.2017.11.002","article-title":"Capture and detection of Staphylococcus aureus with dual labeled aptamers to cell surface components","volume":"265","author":"Ramlal","year":"2018","journal-title":"Int. J. Food Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1016\/j.biopha.2017.07.011","article-title":"Aptamer-assisted novel technologies for detecting bacterial pathogens","volume":"93","author":"Alizadeh","year":"2017","journal-title":"Biomed. Pharmacother."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"989","DOI":"10.1007\/s00216-007-1346-4","article-title":"Aptamers: Molecular tools for analytical applications","volume":"390","author":"Mairal","year":"2008","journal-title":"Anal. Bioanal. Chem."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1039\/b926958d","article-title":"Solid-contact potentiometric aptasensor based on aptamer functionalized carbon nanotubes for the direct determination of proteins","volume":"135","author":"Duzgun","year":"2010","journal-title":"Analyst"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1863","DOI":"10.1038\/srep01863","article-title":"Rapid single cell detection of Staphylococcus aureus by aptamer-conjugated gold nanoparticles","volume":"3","author":"Chang","year":"2013","journal-title":"Sci. Rep."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1038\/nature02388","article-title":"Designing materials for biology and medicine","volume":"428","author":"Langer","year":"2004","journal-title":"Nature"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1016\/j.copbio.2006.10.004","article-title":"Functional DNA nanotechnology: Emerging applications of DNAzymes and aptamers","volume":"17","author":"Lu","year":"2006","journal-title":"Curr. Opin. Biotechnol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1038\/nmat2344","article-title":"Physical approaches to biomaterial design","volume":"8","author":"Mitragotri","year":"2009","journal-title":"Nat. Mater."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1038\/nmat1249","article-title":"New approaches to biomaterials design","volume":"3","author":"Kohn","year":"2004","journal-title":"Nat. Mater."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"112018","DOI":"10.1016\/j.bios.2020.112018","article-title":"Aptamers in nanostructure-based electrochemical biosensors for cardiac biomarkers and cancer biomarkers: A review","volume":"152","author":"Negahdary","year":"2020","journal-title":"Biosens. Bioelectron."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.bios.2017.04.030","article-title":"Principles and applications of photoelectrochemical sensing strategies based on biofunctionalized nanostructures","volume":"96","author":"Zang","year":"2017","journal-title":"Biosens. Bioelectron."},{"key":"ref_43","first-page":"205","article-title":"High-throughput tools for the study of protein-nanostructured surface interaction","volume":"14","author":"Scopelliti","year":"2011","journal-title":"Comb. Chem. High Throughput Screen."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Scopelliti, P.E., Borgonovo, A., Indrieri, M., Giorgetti, L., Bongiorno, G., Carbone, R., Podesta, A., and Milani, P. (2010). The effect of surface nanometre-scale morphology on protein adsorption. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0011862"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"e1905611","DOI":"10.1002\/smll.201905611","article-title":"An integrated plasmo-photoelectronic nanostructure biosensor detects an infection biomarker accompanying cell death in neutrophils","volume":"16","author":"Park","year":"2020","journal-title":"Small"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"12185","DOI":"10.1021\/acs.analchem.7b02830","article-title":"High surface area electrodes generated via electrochemical roughening improve the signaling of electrochemical aptamer-based biosensors","volume":"89","author":"Scida","year":"2017","journal-title":"Anal. Chem."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"5191","DOI":"10.1364\/BOE.8.005191","article-title":"Label-free fiber optic optrode for the detection of class C \u03b2-lactamases expressed by drug resistant bacteria","volume":"8","author":"Zuppolini","year":"2017","journal-title":"Biomed. Opt. Express"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1016\/j.snb.2016.02.086","article-title":"Long period fiber grating working in reflection mode as valuable biosensing platform for the detection of drug resistant bacteria","volume":"230","author":"Quero","year":"2016","journal-title":"Sens. Actuator B Chem."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1955","DOI":"10.1002\/jcc.20954","article-title":"Energy-based prediction of amino acid-nucleotide base recognition","volume":"29","author":"Marabotti","year":"2008","journal-title":"J. Comput. Chem."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"2469","DOI":"10.1021\/jm0200299","article-title":"Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 1. Models without explicit constrained water","volume":"45","author":"Cozzini","year":"2002","journal-title":"J. Med. Chem."},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Ahmed, M.H., Spyrakis, F., Cozzini, P., Tripathi, P.K., Mozzarelli, A., Scarsdale, J.N., Safo, M.A., and Kellogg, G.E. (2011). Bound water at protein-protein interfaces: Partners, roles and hydrophobic bubbles as a conserved motif. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0024712"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1016\/j.jmb.2006.01.053","article-title":"Mapping the energetics of water-protein and water-ligand interactions with the \u201cnatural\u201d HINT forcefield: Predictive tools for characterizing the roles of water in biomolecules","volume":"358","author":"Amadasi","year":"2006","journal-title":"J. Mol. Biol."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Spyrakis, F., Cozzini, P., Bertoli, C., Marabotti, A., Kellogg, G.E., and Mozzarelli, A. (2007). Energetics of the protein-DNA-water interaction. BMC Struct. Biol., 7.","DOI":"10.1186\/1472-6807-7-4"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.1016\/j.bbagen.2018.01.014","article-title":"The intrinsic flexibility of the aptamer targeting the ribosomal protein S8 is a key factor for the molecular recognition","volume":"1862","author":"Autiero","year":"2018","journal-title":"Biochim. Biophys. Acta"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1126\/science.287.5454.820","article-title":"Adaptive recognition by nucleic acid aptamers","volume":"287","author":"Hermann","year":"2000","journal-title":"Science"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1995","DOI":"10.1007\/s00726-012-1274-2","article-title":"Expedient chemical synthesis of 75mer DNA binding domain of MafA: An insight on its binding to insulin enhancer","volume":"43","author":"Pellegrino","year":"2012","journal-title":"Amino Acids"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"10653","DOI":"10.1021\/ac5026623","article-title":"Agarose-based microfluidic device for point-of-care concentration and detection of pathogen","volume":"86","author":"Li","year":"2014","journal-title":"Anal. Chem."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/j.bioelechem.2012.05.007","article-title":"Electrochemical DNA biosensor with chitosan-Co3O4 nanorod-graphene composite for the sensitive detection of Staphylococcus aureus nuc gene sequence","volume":"88","author":"Qi","year":"2012","journal-title":"Bioelectrochemistry"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/nature06684","article-title":"The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data","volume":"452","author":"Parisien","year":"2008","journal-title":"Nature"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1006\/jmbi.1998.1848","article-title":"Crystal structure of \u03bb-Cro bound to a consensus operator at 3.0 \u00c5 resolution","volume":"280","author":"Albright","year":"1998","journal-title":"J. Mol. Biol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1021\/ct700301q","article-title":"GRGMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation","volume":"4","author":"Hess","year":"2008","journal-title":"J. Chem. Theory Comput."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"3863","DOI":"10.1021\/jz501780a","article-title":"Building water models: A different approach","volume":"5","author":"Izadi","year":"2014","journal-title":"J. Phys. Chem. Lett."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"6269","DOI":"10.1021\/j100308a038","article-title":"The missing term in effective pair potentials","volume":"91","author":"Berendsen","year":"1987","journal-title":"J. Phys. Chem."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"103165","DOI":"10.1016\/j.bioorg.2019.103165","article-title":"A combined experimental and computational study on peptide nucleic acid (PNA) analogues of tumor suppressive miRNA-34a","volume":"91","author":"Piacenti","year":"2019","journal-title":"Bioorg. Chem."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"12582","DOI":"10.1021\/jp074954o","article-title":"Ligand migration in nonsymbiotic hemoglobin AHb1 from Arabidopsis thaliana","volume":"111","author":"Abbruzzetti","year":"2007","journal-title":"J. Phys. Chem. B"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"3699","DOI":"10.1039\/C7CP07400J","article-title":"Energetics and dynamics of the non-natural fluorescent 4AP:DAP base pair","volume":"20","author":"Chawla","year":"2018","journal-title":"PCCP"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"2118","DOI":"10.1039\/c3mb70086k","article-title":"In silico investigation and targeting of amyloid \u03b2 oligomers of different size","volume":"9","author":"Autiero","year":"2013","journal-title":"Molecular BioSystems"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: Visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph."},{"key":"ref_69","first-page":"5","article-title":"PyMOL","volume":"700","author":"DeLano","year":"2002","journal-title":"DeLano Sci. San Carlos CA"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1002\/(SICI)1521-3773(19990115)38:1\/2<236::AID-ANIE236>3.0.CO;2-M","article-title":"Peptide folding: When simulation meets experiment","volume":"38","author":"Daura","year":"1999","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"20333","DOI":"10.1038\/s41598-019-56708-0","article-title":"Tuning PFKFB3 bisphosphatase activity through allosteric interference","volume":"9","author":"Macut","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1002\/bip.20853","article-title":"Protein secondary structure analyses from circular dichroism spectroscopy: Methods and reference databases","volume":"89","author":"Whitmore","year":"2008","journal-title":"Biopolymers"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"W668","DOI":"10.1093\/nar\/gkh371","article-title":"DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data","volume":"32","author":"Whitmore","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/j.cossms.2004.08.002","article-title":"Manipulation of nanoparticles in supersonic beams for the production of nanostructured materials","volume":"8","author":"Piseri","year":"2004","journal-title":"Curr. Opin. Solid State Mater. Sci."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"055302","DOI":"10.1063\/1.4960441","article-title":"Cluster-assembled cubic zirconia films with tunable and stable nanoscale morphology against thermal annealing","volume":"120","author":"Borghi","year":"2016","journal-title":"J. Appl. Phys."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"18264","DOI":"10.1021\/jp905930r","article-title":"Cluster-Assembled nanostructured titanium oxide films with tailored wettability","volume":"113","author":"Bongiorno","year":"2009","journal-title":"J. Phys. Chem. C"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"11637","DOI":"10.1021\/la801910p","article-title":"Adsorption and stability of streptavidin on cluster-assembled nanostructured TiOx films","volume":"24","author":"Giorgetti","year":"2008","journal-title":"Langmuir"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"5973","DOI":"10.1021\/la500738u","article-title":"Nanoscale roughness affects the activity of enzymes adsorbed on cluster-assembled titania films","volume":"30","author":"Gailite","year":"2014","journal-title":"Langmuir"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1021\/cb200523n","article-title":"A Synthetic Peptide mimic of \u03bb-Cro shows sequence-specific binding in vitro and in vivo","volume":"7","author":"Mazumder","year":"2012","journal-title":"ACS Chem. Biol."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1006\/jmbi.1998.1849","article-title":"Refined structure of Cro repressor protein from bacteriophage \u03bb suggests both flexibility and plasticity11Edited by P. E. Wright","volume":"280","author":"Ohlendorf","year":"1998","journal-title":"J. Mol. Biol."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"6298","DOI":"10.1016\/j.bmcl.2009.09.105","article-title":"Synthetic peptides containing a conserved sequence motif of the Id protein family modulate vascular smooth muscle cell phenotype","volume":"19","author":"Pellegrino","year":"2009","journal-title":"Bioorg. Med. Chem. Lett."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.aca.2005.12.038","article-title":"Optimization of aptamer microarray technology for multiple protein targets","volume":"564","author":"Cho","year":"2006","journal-title":"Anal. Chim. Acta"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"10939","DOI":"10.1021\/acs.joc.5b02066","article-title":"Based polarity-sensitive dyes","volume":"80","author":"Ronda","year":"2015","journal-title":"J. Org. Chem."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"107917","DOI":"10.1016\/j.dyepig.2019.107917","article-title":"Synthesis and photophysical properties of isocoumarin-based D-\u03c0-A systems","volume":"173","author":"Pirovano","year":"2020","journal-title":"Dyes Pigment."}],"container-title":["Sensors"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1424-8220\/20\/17\/4977\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T10:05:57Z","timestamp":1760177157000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1424-8220\/20\/17\/4977"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,9,2]]},"references-count":84,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2020,9]]}},"alternative-id":["s20174977"],"URL":"https:\/\/doi.org\/10.3390\/s20174977","relation":{},"ISSN":["1424-8220"],"issn-type":[{"type":"electronic","value":"1424-8220"}],"subject":[],"published":{"date-parts":[[2020,9,2]]}}}