Multiplex isothermal solid-phase recombinase polymerase amplification for the specific and fast DNA-based detection of three bacterial pathogens

Microchimica Acta

Volumn 181, Issue 13-14, 2014, Pages 1715-1723

  Kersting, Sebastian ^a,b   Rausch, Valentina ^a   Bier, Frank F ^a,b   von Nickisch Rosenegk, Markus ^a  

^a FRAUNHOFER INSTITUTE FOR BIOMEDICAL ENGINEERING   (Germany)

^b UNIVERSITY OF POTSDAM   (Germany)

Author keywords

DNA sensor; Isothermal amplification; Microchip; Point of care; RPA

Indexed keywords

EID: 84907861258     PISSN: 00263672     EISSN: 14365073     Source Type: Journal    
DOI: 10.1007/s00604-014-1198-5     Document Type: Article

References (33)

1. Mullis K, Faloona F, Scharf S, Saiki R, Horn G, Erlich H (1986) Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb Symp Quant Biol 51(Pt 1):263–273
2. Yang S, Rothman RE (2004) PCR-based diagnostics for infectious diseases: uses, limitations, and future applications in acute-care settings. Lancet Infect Dis 4:337–348. doi:10.1016/S1473-3099(04)01044-8
3. Zhang Y, Ozdemir P (2009) Microfluidic DNA amplification—a review. Anal Chim Acta 638:115–125. doi:10.1016/j.aca.2009.02.038
4. Gill P, Ghaemi A (2008) Nucleic acid isothermal amplification technologies: a review. Nucleosides Nucleotides Nucleic Acids 27:224–243. doi:10.1080/15257770701845204
5. Notomi T (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28:63e. doi:10.1093/nar/28.12.e63
6. Vincent M, Xu Y, Kong H (2004) Helicase-dependent isothermal DNA amplification. EMBO Rep 5:795–800. doi:10.1038/sj.embor.7400200
7. Walker GT, Fraiser MS, Schram JL, Little MC, Nadeau JG, Malinowski DP (1992) Strand displacement amplification—an isothermal, in vitro DNA amplification technique. Nucleic Acids Res 20:1691–1696. doi:10.1093/nar/20.7.1691
8. Lizardi PM, Ward DC, Huang X, Zhu Z, Bray-Ward P, Thomas DC (1998) Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat Genet 19:225–232. doi:10.1038/898
9. Craw P, Balachandran W (2012) Isothermal nucleic acid amplification technologies for point-of-care diagnostics: a critical review. Lab Chip 12:2469–2486. doi:10.1039/c2lc40100b
10. Reiss E, Hölzel R, Bier FF (2011) Preparation of DNA nanostructures with repetitive binding motifs by rolling circle amplification. Methods Mol Biol 749:151–168. doi:10.1007/978-1-61779-142-0_11
11. Piepenburg O, Williams CH, Stemple DL, Armes NA (2006) DNA detection using recombination proteins. PLoS Biol 4:e204. doi:10.1371/journal.pbio.0040204
12. Boyle DS, Lehman DA, Lillis L, Peterson D, Singhal M, Armes N, Parker M, Piepenburg O, Overbaugh J (2013) Rapid detection of HIV-1 proviral DNA for early infant diagnosis using recombinase polymerase amplification. mBio 4:e00135–13. doi:10.1128/mBio.00135-13
13. Euler M, Wang Y, Otto P, Tomaso H, Escudero R, Anda P, Hufert FT, Weidmann M (2012) Recombinase polymerase amplification assay for rapid detection of francisella tularensis. J Clin Microbiol 50:2234–2238. doi:10.1128/JCM.06504-11
14. Amer H, Wahed AAE, Shalaby M, Almajhdi F, Hufert F, Weidmann M (2013) A new approach for diagnosis of bovine coronavirus using a reverse transcription recombinase polymerase amplification assay. J Virol Methods. doi:10.1016/j.jviromet.2013.06.027
15. Euler M, Wang Y, Nentwich O, Piepenburg O, Hufert FT, Weidmann M (2012) Recombinase polymerase amplification assay for rapid detection of Rift Valley fever virus. J Clin Virol 54:308–312. doi:10.1016/j.jcv.2012.05.006
16. Euler M, Wang Y, Heidenreich D, Patel P, Strohmeier O, Hakenberg S, Niedrig M, Hufert FT, Weidmann M (2013) Development of a panel of recombinase polymerase amplification assays for detection of biothreat agents. J Clin Microbiol 51:1110–1117. doi:10.1128/JCM.02704-12
17. Shen F, Davydova EK, Du W, Kreutz JE, Piepenburg O, Ismagilov RF (2011) Digital isothermal quantification of nucleic acids via simultaneous chemical initiation of recombinase polymerase amplification reactions on SlipChip. Anal Chem 83:3533–3540. doi:10.1021/ac200247e
18. Rohrman BA, Richards-Kortum RR (2012) A paper and plastic device for performing recombinase polymerase amplification of HIV DNA. Lab Chip 12:3082. doi:10.1039/c2lc40423k
19. Lutz S, Weber P, Focke M, Faltin B, Hoffmann J, Müller C, Mark D, Roth G, Munday P, Armes N, Piepenburg O, Zengerle R, von Stetten F (2010) Microfluidic lab-on-a-foil for nucleic acid analysis based on isothermal recombinase polymerase amplification (RPA). Lab Chip 10:887–893. doi:10.1039/b921140c
20. Hakenberg S, Hügle M, Weidmann M, Hufert F, Dame G, Urban GA (2012) A phaseguided passive batch microfluidic mixing chamber for isothermal amplification. Lab Chip 12:4576. doi:10.1039/c2lc40765e
21. Shin Y, Perera AP, Kim KW, Park MK (2013) Real-time, label-free isothermal solid-phase amplification/detection (ISAD) device for rapid detection of genetic alteration in cancers. Lab Chip 13:2106. doi:10.1039/c3lc50129a
22. Bier FF, Nickisch-Rosenegk M, Ehrentreich-Förster E, Reiß E, Henkel J, Strehlow R, Andresen D (2008) DNA microarrays. Adv Biochem Eng Biotechnol 109:433–453. doi:10.1007/10_2007_087
23. Andresen H, Grötzinger C, Zarse K, Kreuzer OJ, Ehrentreich-Förster E, Bier FF (2006) Functional peptide microarrays for specific and sensitive antibody diagnostics. Proteomics 6:1376–1384. doi:10.1002/pmic.200500343
24. Bodrossy L, Sessitsch A (2004) Oligonucleotide microarrays in microbial diagnostics. Curr Opin Microbiol 7:245–254. doi:10.1016/j.mib.2004.04.005
25. von Nickisch-Rosenegk M, Marschan X, Andresen D, Abraham A, Heise C, Bier FF (2005) On-chip PCR amplification of very long templates using immobilized primers on glassy surfaces. Biosens Bioelectron 20:1491–1498. doi:10.1016/j.bios.2004.07.007
26. Nickisch-Rosenegk M, Marschan X, Andresen D, Bier FF (2008) Reverse transcription-polymerase chain reaction on a microarray: the integrating concept of “active arrays”. Anal Bioanal Chem 391:1671–1678. doi:10.1007/s00216-008-2154-1
27. Andresen D, von Nickisch-Rosenegk M, Bier FF (2009) Helicase dependent OnChip-amplification and its use in multiplex pathogen detection. Clin Chim Acta 403:244–248. doi:10.1016/j.cca.2009.03.021
28. Shapero MH, Leuther KK, Nguyen A, Scott M, Jones KW (2001) SNP genotyping by multiplexed solid-phase amplification and fluorescent minisequencing. Genome Res 11:1926–1934. doi:10.1101/gr.205001
29. Vallone PM, Butler JM (2004) AutoDimer: a screening tool for primer-dimer and hairpin structures. BioTech 37:226–231
30. TwistDx (2013) Combined instruction manual. http://www.twistdx.co.uk/images/uploads/docs/TA01cmanual_Combined_Manual_RevF.pdf
31. Galán JE, Ginocchio C, Costeas P (1992) Molecular and functional characterization of the Salmonella invasion gene invA: homology of InvA to members of a new protein family. J Bacteriol 174:4338–4349
32. Hopper S, Wilbur JS, Vasquez BL, Larson J, Clary S, Mehr IJ, Seifert HS, So M (2000) Isolation of Neisseria gonorrhoeae mutants that show enhanced trafficking across polarized T84 epithelial monolayers. Infect Immun 68:896–905
33. Al-Soud WA, Rådström P (2001) Purification and characterization of PCR-inhibitory components in blood cells. J Clin Microbiol 39:485–493. doi:10.1128/JCM.39.2.485-493.2001