{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T12:30:50Z","timestamp":1782217850554,"version":"3.54.5"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2006,1,1]],"date-time":"2006-01-01T00:00:00Z","timestamp":1136073600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Background: Rapid detection of biological threat agents is critical for timely therapeutic administration. Fluorogenic PCR provides a rapid, sensitive, and specific tool for molecular identification of these agents. We compared the performance of assays for 7 biological threat agents on the Idaho Technology, Inc. R.A.P.I.D.\u00ae, the Roche LightCycler\u00ae, and the Cepheid Smart Cycler\u00ae.<\/jats:p><jats:p>Methods: Real-time PCR primers and dual-labeled fluorogenic probes were designed to detect Bacillus anthracis, Brucella species, Clostridium botulinum, Coxiella burnetii, Francisella tularensis, Staphylococcus aureus, and Yersinia pestis. DNA amplification assays were optimized by use of Idaho Technology buffers and deoxynucleotide triphosphates supplemented with Invitrogen Platinum\u00ae Taq DNA polymerase, and were subsequently tested for sensitivity and specificity on the R.A.P.I.D., the LightCycler, and the Smart Cycler.<\/jats:p><jats:p>Results: Limit of detection experiments indicated that assay performance was comparable among the platforms tested. Exclusivity and inclusivity testing with a general bacterial nucleic acid cross-reactivity panel containing 60 DNAs and agent-specific panels containing nearest neighbors for the organisms of interest indicated that all assays were specific for their intended targets.<\/jats:p><jats:p>Conclusion: With minor supplementation, such as the addition of Smart Cycler Additive Reagent to the Idaho Technology buffers, assays for DNA templates from biological threat agents demonstrated similar performance, sensitivity, and specificity on all 3 platforms.<\/jats:p>","DOI":"10.1373\/clinchem.2005.052522","type":"journal-article","created":{"date-parts":[[2006,1,4]],"date-time":"2006-01-04T02:03:25Z","timestamp":1136340205000},"page":"141-145","source":"Crossref","is-referenced-by-count":84,"title":["Detection of Biological Threat Agents by Real-Time PCR: Comparison of Assay Performance on the R.A.P.I.D., the LightCycler, and the Smart Cycler Platforms"],"prefix":"10.1093","volume":"52","author":[{"given":"Deanna R","family":"Christensen","sequence":"first","affiliation":[{"name":"United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurie J","family":"Hartman","sequence":"first","affiliation":[{"name":"United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bonnie M","family":"Loveless","sequence":"first","affiliation":[{"name":"United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melissa S","family":"Frye","sequence":"first","affiliation":[{"name":"United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle A","family":"Shipley","sequence":"first","affiliation":[{"name":"United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deanna L","family":"Bridge","sequence":"first","affiliation":[{"name":"United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle J","family":"Richards","sequence":"first","affiliation":[{"name":"United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca S","family":"Kaplan","sequence":"first","affiliation":[{"name":"United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey","family":"Garrison","sequence":"first","affiliation":[{"name":"United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carson D","family":"Baldwin","sequence":"first","affiliation":[{"name":"United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David A","family":"Kulesh","sequence":"first","affiliation":[{"name":"United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David A","family":"Norwood","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2006,1,1]]},"reference":[{"key":"2020022801100409100_R1","doi-asserted-by":"crossref","unstructured":"Dixon TC, Meselson M, Guillemin J, Hanna PC. Anthrax. N Engl J Med1999;341:815-826.","DOI":"10.1056\/NEJM199909093411107"},{"key":"2020022801100409100_R2","doi-asserted-by":"crossref","unstructured":"Franz DR, Jahrling PB, Friedlander AM, McClain DJ, Hoover DL, Bryne WR, et al. Clinical recognition and management of patients exposed to biological warfare agents. JAMA1997;278:399-411.","DOI":"10.1001\/jama.278.5.399"},{"key":"2020022801100409100_R3","doi-asserted-by":"crossref","unstructured":"Ivnitski D, O\u2019Neil DJ, Gattuso A, Schlicht R, Calidonna M, Fisher R. Nucleic acid approaches for detection and identification of biological warfare and infectious disease agents. Biotechniques2003;35:862-869.","DOI":"10.2144\/03354ss03"},{"key":"2020022801100409100_R4","doi-asserted-by":"crossref","unstructured":"Perdue ML. Molecular diagnostics in an insecure world. Avian Dis2003;47:1063-1068.","DOI":"10.1637\/0005-2086-47.s3.1063"},{"key":"2020022801100409100_R5","doi-asserted-by":"crossref","unstructured":"Klietmann WF, Ruoff KL. Bioterrorism: implications for the clinical microbiologist. Clin Microbiol Rev2001;14:364-381.","DOI":"10.1128\/CMR.14.2.364-381.2001"},{"key":"2020022801100409100_R6","doi-asserted-by":"crossref","unstructured":"Hearps A, Zhang Z, Alexandersen S. Evaluation of the portable Cepheid SmartCycler real-time PCR machine for the rapid diagnosis of foot-and-mouth disease. Vet Rec2002;150:625-628.","DOI":"10.1136\/vr.150.20.625"},{"key":"2020022801100409100_R7","doi-asserted-by":"crossref","unstructured":"Kreuzer KA, Bohn A, Lass U, Peters UR, Schmidt CA. Influence of DNA polymerases on quantitative PCR results using TaqMan probe format in the LightCycler instrument. Mol Cell Probes2000;14:57-60.","DOI":"10.1006\/mcpr.1999.0284"},{"key":"2020022801100409100_R8","doi-asserted-by":"crossref","unstructured":"Read SJ. Recovery efficiencies on nucleic acid extraction kits as measured by quantitative LightCycler PCR. Mol Pathol2001;54:86-90.","DOI":"10.1136\/mp.54.2.86"},{"key":"2020022801100409100_R9","doi-asserted-by":"crossref","unstructured":"Wilhelm J, Pingoud A, Hahn M. Comparison between Taq DNA polymerase and its Stoffel fragment for quantitative real-time PCR with hybridization probes. Biotechniques2001;30:1052-6, 1058, 1060.","DOI":"10.2144\/01305rr04"},{"key":"2020022801100409100_R10","doi-asserted-by":"crossref","unstructured":"Kovarova M, Draber P. New specificity and yield enhancer of polymerase chain reactions. Nucleic Acids Res2000;28:E70.","DOI":"10.1093\/nar\/28.13.e70"},{"key":"2020022801100409100_R11","doi-asserted-by":"crossref","unstructured":"Villalva C, Touriol C, Seurat P, Trempat P, Delsol G, Brousset P. Increased yield of PCR products by addition of T4 gene 32 protein to the SMART PCR cDNA synthesis system. Biotechniques2001;31:81-3, 86.","DOI":"10.2144\/01311st04"},{"key":"2020022801100409100_R12","doi-asserted-by":"crossref","unstructured":"Exner MM, Lewinski MA. Sensitivity of multiplex real-time PCR reactions, using the LightCycler and the ABI PRISM 7700 Sequence Detection System, is dependent on the concentration of the DNA polymerase. Mol Cell Probes2002;16:351-357.","DOI":"10.1006\/mcpr.2002.0433"},{"key":"2020022801100409100_R13","doi-asserted-by":"crossref","unstructured":"Holland PM, Abramson RD, Watson R, Gelfand DH. Detection of specific polymerase chain reaction product by utilizing the 5\u2032\u20133\u2032 exonuclease activity of Thermus aquaticus DNA polymerase. Proc Natl Acad Sci U S A1991;88:7276-7280.","DOI":"10.1073\/pnas.88.16.7276"},{"key":"2020022801100409100_R14","doi-asserted-by":"crossref","unstructured":"Livak KJ, Flood SJ, Marmaro J, Giusti W, Deetz K. Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. PCR Methods Appl1995;4:357-362.","DOI":"10.1101\/gr.4.6.357"},{"key":"2020022801100409100_R15","doi-asserted-by":"crossref","unstructured":"Marras SA, Kramer FR, Tyagi S. Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res2002;30:e122.","DOI":"10.1093\/nar\/gnf121"},{"key":"2020022801100409100_R16","doi-asserted-by":"crossref","unstructured":"Wang L, Gaigalas AK, Blasic J, Holden MJ, Gallagher DT, Pires R. Fluorescence resonance energy transfer between donor-acceptor pair on two oligonucleotides hybridized adjacently to DNA template. Biopolymers2003;72:401-412.","DOI":"10.1002\/bip.10482"},{"key":"2020022801100409100_R17","doi-asserted-by":"crossref","unstructured":"Abravaya K, Huff J, Marshall R, Merchant B, Mullen C, Schneider G, et al. Molecular beacons as diagnostic tools: technology and applications. Clin Chem Lab Med2003;41:468-474.","DOI":"10.1515\/CCLM.2003.070"},{"key":"2020022801100409100_R18","doi-asserted-by":"crossref","unstructured":"Tyagi S, Kramer FR. Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol1996;14:303-308.","DOI":"10.1038\/nbt0396-303"},{"key":"2020022801100409100_R19","doi-asserted-by":"crossref","unstructured":"Vet JA, Van der Rijt BJ, Blom HJ. Molecular beacons: colorful analysis of nucleic acids. Expert Rev Mol Diagn2002;2:77-86.","DOI":"10.1586\/14737159.2.1.77"},{"key":"2020022801100409100_R20","doi-asserted-by":"crossref","unstructured":"Whitcombe D, Theaker J, Guy SP, Brown T, Little S. Detection of PCR products using self-probing amplicons and fluorescence. Nat Biotechnol1999;17:804-807.","DOI":"10.1038\/11751"},{"key":"2020022801100409100_R21","doi-asserted-by":"crossref","unstructured":"Bedecarrats GY, O\u2019Neill FH, Norwitz ER, Kaiser UB, Teixeira J. Regulation of gonadotropin gene expression by Mullerian inhibiting substance. Proc Natl Acad Sci U S A2003;100:9348-9353.","DOI":"10.1073\/pnas.1633592100"},{"key":"2020022801100409100_R22","doi-asserted-by":"crossref","unstructured":"Lowe B, Avila HA, Bloom FR, Gleeson M, Kusser W. Quantitation of gene expression in neural precursors by reverse-transcription polymerase chain reaction using self-quenched, fluorogenic primers. Anal Biochem2003;315:95-105.","DOI":"10.1016\/S0003-2697(02)00695-4"},{"key":"2020022801100409100_R23","doi-asserted-by":"crossref","unstructured":"Nazarenko I, Lowe B, Darfler M, Ikonomi P, Schuster D, Rashtchian A. Multiplex quantitative PCR using self-quenched primers labeled with a single fluorophore. Nucleic Acids Res2002;30:e37.","DOI":"10.1093\/nar\/30.9.e37"},{"key":"2020022801100409100_R24","doi-asserted-by":"crossref","unstructured":"Nazarenko I, Pires R, Lowe B, Obaidy M, Rashtchian A. Effect of primary and secondary structure of oligodeoxyribonucleotides on the fluorescent properties of conjugated dyes. Nucleic Acids Res2002;30:2089-2195.","DOI":"10.1093\/nar\/30.9.2089"},{"key":"2020022801100409100_R25","doi-asserted-by":"crossref","unstructured":"Collins ML, Irvine B, Tyner D, Fine E, Zayati C, Chang C, et al. A branched DNA signal amplification assay for quantification of nucleic acid targets below 100 molecules\/ml. Nucleic Acids Res1997;25:2979-2984.","DOI":"10.1093\/nar\/25.15.2979"},{"key":"2020022801100409100_R26","doi-asserted-by":"crossref","unstructured":"Moser MJ, Marshall DJ, Grenier JK, Kieffer CD, Killeen AA, Ptacin JL, et al. Exploiting the enzymatic recognition of an unnatural base pair to develop a universal genetic analysis system. Clin Chem2003;49:407-414.","DOI":"10.1373\/49.3.407"},{"key":"2020022801100409100_R27","doi-asserted-by":"crossref","unstructured":"Piccirilli JA, Krauch T, Moroney SE, Benner SA. Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet. Nature1990;343:33-37.","DOI":"10.1038\/343033a0"},{"key":"2020022801100409100_R28","doi-asserted-by":"crossref","unstructured":"Coyne SR, Craw PD, Norwood DA, Ulrich MP. Comparative analysis of the Schleicher and Schuell IsoCode Stix DNA isolation device and the Qiagen QIAamp DNA Mini Kit. J Clin Microbiol2004;42:4859-4862.","DOI":"10.1128\/JCM.42.10.4859-4862.2004"},{"key":"2020022801100409100_R29","doi-asserted-by":"crossref","unstructured":"Bricker BJ, Halling SM. Differentiation of Brucella abortus bv. 1, 2, and 4, Brucella melitensis, Brucella ovis, and Brucella suis bv. 1 by PCR. J Clin Microbiol1994;32:2660-2666.","DOI":"10.1128\/JCM.32.11.2660-2666.1994"},{"key":"2020022801100409100_R30","doi-asserted-by":"crossref","unstructured":"Afonina I, Zivarts M, Kutyavin I, Lukhtanov E, Gamper H, Meyer RB. Efficient priming of PCR with short oligonucleotides conjugated to a minor groove binder. Nucleic Acids Res1997;25:2657-2660.","DOI":"10.1093\/nar\/25.13.2657"},{"key":"2020022801100409100_R31","doi-asserted-by":"crossref","unstructured":"Kutyavin IV, Lukhtanov EA, Gamper HB, Meyer RB. Oligonucleotides with conjugated dihydropyrroloindole tripeptides: base composition and backbone effects on hybridization. Nucleic Acids Res1997;25:3718-3723.","DOI":"10.1093\/nar\/25.18.3718"},{"key":"2020022801100409100_R32","doi-asserted-by":"crossref","unstructured":"Hartman LJ, Coyne SR, Norwood DA. Development of a novel internal positive control for TaqMan based assays. Mol Cell Probes2005;19:51-59.","DOI":"10.1016\/j.mcp.2004.07.006"}],"container-title":["Clinical Chemistry"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/clinchem\/article-pdf\/52\/1\/141\/32685231\/clinchem0141.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/clinchem\/article-pdf\/52\/1\/141\/32685231\/clinchem0141.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,6]],"date-time":"2023-05-06T02:25:51Z","timestamp":1683339951000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/clinchem\/article\/52\/1\/141\/5626613"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,1,1]]},"references-count":32,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2006,1,1]]},"published-print":{"date-parts":[[2006,1,1]]}},"URL":"https:\/\/doi.org\/10.1373\/clinchem.2005.052522","relation":{},"ISSN":["0009-9147","1530-8561"],"issn-type":[{"value":"0009-9147","type":"print"},{"value":"1530-8561","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2006,1,1]]},"published":{"date-parts":[[2006,1,1]]}}}