Electrochemical detection of Pseudomonas aeruginosa 16S rRNA using a biosensor based on immobilized stem-loop structured probe

Enzyme and Microbial Technology

Volumn 49, Issue 3, 2011, Pages 266-271

  Liu, Can ^a   Zeng, Guang Ming ^a   Tang, Lin ^a   Zhang, Yi ^a   Li, Yuan Ping ^a   Liu, Yuan Yuan ^a   Li, Zhen ^a   Wu, Meng Shi ^a   Luo, Jie ^a  

^a HUNAN UNIVERSITY   (China)

Author keywords

Biosensor; Composting degradation; Conformational changes; Electrochemical detection; Pseudomonas aeruginosa 16S rRNA; Stem loop structured probe

Indexed keywords

16S RIBOSOMAL RNA; 16S RRNA; ACID CONCENTRATIONS; AMPEROMETRIC; CONFORMATIONAL CHANGE; CORRELATION COEFFICIENT; CURRENT RESPONSE; DETECTION LIMITS; ELECTROCHEMICAL DETECTION; ELECTROCHEMICAL DNA BIOSENSORS; ENZYMATIC DETECTION; EXPERIMENT CONDITION; GOLD ELECTRODES; P.AERUGINOSA; PSEUDOMONAS AERUGINOSA; REFERENCE VALUES; SPECTROMETRIC DATA; STEM-LOOP;

ALGEBRA; BACTERIA; CHEMICAL DETECTION; COENZYMES; DEGRADATION; PROBES; PROTEINS; RNA;

BIOSENSORS;

BIOTIN; GOLD; HORSERADISH PEROXIDASE; RNA 16S; STREPTAVIDIN;

ACCURACY; AMPEROMETRY; ARTICLE; BACTERIUM DETECTION; BIOSENSOR; CATALYSIS; CONTROLLED STUDY; ELECTROCHEMICAL DETECTION; ENZYME SYNTHESIS; NONHUMAN; NUCLEIC ACID IMMOBILIZATION; PROTEIN ASSEMBLY; PSEUDOMONAS AERUGINOSA; RNA BINDING; RNA DEGRADATION; RNA EXTRACTION; RNA PROBE; SENSITIVITY AND SPECIFICITY; ULTRAVIOLET SPECTROPHOTOMETRY;

BIODEGRADATION, ENVIRONMENTAL; BIOSENSING TECHNIQUES; BIOTINYLATION; CALIBRATION; DNA PROBES; ELECTROCHEMICAL TECHNIQUES; ELECTRODES; EQUIPMENT DESIGN; GLYCOLIPIDS; HORSERADISH PEROXIDASE; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HYBRIDIZATION; PHOTOELECTRON SPECTROSCOPY; PSEUDOMONAS AERUGINOSA; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY; SOIL MICROBIOLOGY; STREPTAVIDIN; SURFACE-ACTIVE AGENTS;

ARMORACIA RUSTICANA; PSEUDOMONAS AERUGINOSA;

EID: 79960590484     PISSN: 01410229     EISSN: 18790909     Source Type: Journal    
DOI: 10.1016/j.enzmictec.2011.06.011     Document Type: Article

References (41)

1. Costa S.G., Nitschke M., Haddad R., Wberlin M.N., Contiero J. Production of Pseudomonas aeruginosa LBI rhamnolipids following growth on Brazilian native oils. Process Biochem 2006, 41:483-488.
2. Thanomsub B., Pumeechockchai W., Limtrakul A., Arunrattiyakorn P., Petchleelaha W., Nitoda T. Chemical structures and biological activities of rhamnolipids produced by Pseudomonas aeruginosa B189 isolated from milk factory waste. Bioresour Technol 2006, 98:1149-1153.
3. Thavasi R., Subramanyam Nambaru V.R., Jayalakshmi S., Balasubramanian T., Banat I.M. Biosurfactant production by Azotobacter chroococcum isolated from the marine environment. Mar Biotechnol 2009, 11:551-556.
4. Desai J.D., Banat I.M. Microbial production of surfactants and their commercial potential. Microbiol Mol Biol Rev 1997, 61:47-64.
5. Ilori M.O., Amobi C.J., Odocha A.C. Factors affecting biosurfactant production by oil degrading Aeromonas spp. isolated from a tropical environment. Chemosphere 2005, 61:985-992.
6. Nitschke M., Pastore G.M. Production and properties of a surfactant obtained from Bacillus subtilis grown on cassava wastewater. Bioresour Technol 2006, 97:336-341.
7. Zhang B.Y., Huang G.H., Chen B. Production of biosurfactants in batch reactor for food waste composting. Waste management and the environment 2003, Wessex Institute of Technology, UK, pp. 131-40. D. Almorza, C.A. Brebbia, D. Sales (Eds.).
8. Vishwanathan S.A., Bagley S.T. Isolation and characterization of solvent-utilizing thermophilic bacterial. 101st General Meeting of the American Society for Microbiology 2001, 641.
9. Tang L., Zeng G., Shen G., Li Y., Zhang Y., Huang G., et al. Simultaneous amperometric determination of lignin peroxidase and manganese peroxidase activities in compost bioremediation using artificial neural networks. Anal Chim Acta 2006, 579:109-116.
10. Banat I.M., Makkar R.S., Cameotra S.S. Potential commercial applications of microbial surfactants. Appl Microbiol Biotechnol 2000, 53:495-508.
11. Dean S.M., Jin Y., Cha D.K., Wilson S.V., Radosevich M. Phenanthrene degradation in soils co-inoculated with phenanthrene-degrading and biosurfactant-producing bacteria. J Environ Qual 2001, 30:1126-1133.
12. Rahman K.S.M., Banat I.M., Thahira J., Thayumanavanb T., Lakshmanaperumalsamy P. Bioremediation of gasoline contaminated soil by a bacterial consortium amended with poultry litter, coir pith and rhamnolipid biosurfactant. Bioresour Technol 2002, 81:25-32.
13. Prabhu Y., Phale P.S. Biodegradation of phenanthrene by Pseudomonas sp. strain PP2: novel metabolic pathway, role of biosurfactant and cell surface hydrophobicity in hydrocarbon assimilation. Appl Microbiol Biotechnol 2003, 61:342-351.
14. Shulga A., Karpenko E., Vildanova-Martsishin R. Biosurfactant-enhanced remediation of oil-contaminated environments. Adsorpt Sci Technol 2000, 18:171-176.
15. Sotirova A., Spasova D., Vasileva-Tonkova E., Galabova D. Effects of rhamnolipid-biosurfactant on cell surface of Pseudomonas aeruginosa. Microbiol Res 2009, 164:297-303.
16. Bockisch B., Grunwald T., Spillner E., Bredehorst R. Immobilized stem-loop structured probes as conformational switches for enzymatic detection of microbial 16S rRNA. Nucleic Acids Res 2005, 33:e101. 10.1093/nar/gni101.
17. Summerer D., Marx A. A molecular beacon for quantitative monitoring of the DNA polymerase reaction in real-time. Angew Chem Int Ed 2002, 41:3620-3622.
18. Goel G., Kumar A., Puniya A.K., Chen W., Singh K. Molecular beacon: a multitask probe. J Appl Microbiol 2005, 99:435-442.
19. Tyagi S., Kramer F.R. Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol 1996, 14:303-308.
20. Kostrikis L.G., Tyagi S., Mhlanga M.M., Ho D.D., Kramer F.R. Spectral genotyping of human alleles. Science 1998, 279:1228-1229.
21. Li J.J., Fang X., Schuster S., Tan W. Molecular beacons: a novel approach to detect protein-DNA interactions. Angew Chem Int Ed 2000, 39:1049-1052.
22. Matsuo T. In situ visualization of messenger RNA for basic fibroblast growth factor in living cells. Biochim Biophys Acta 1998, 1379:178-184.
23. Li J., Geyer R., Tan W. Using molecular beacons as a sensitive fluorescence assay for enzymatic cleavage of single-stranded DNA. Nucleic Acids Res 2000, 28(e52):1-5.
24. Mao X., Jiang J., Xu X., Chu X., Luo Y., Shen G., et al. Enzymatic amplification detection of DNA based on Molecular Beacon biosensors. Biosens Bioelectron 2008, 23:1555-1561.
25. Choi B.K., Wyss C., Gobel U.B. Phylogenetic analysis of pathogen-related oral spirochetes. J Clin Microbiol 1996, 34:1922-1925.
26. Schmalenberger A., Schwieger F., Tebbe C.C. Effect of primers hybridizing to different evolutionarily conserved regions of the smallsubunit rRNA gene in PCR-based microbial community analyses and genetic profiling. Appl Environ Microbiol 2001, 67:3557-3563.
27. Clarridge J.E. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev 2004, 17:840-862.
28. Munson M.A., Banerjee A., Watson T.F., Wade W.G. Molecular analysis of the microflora associated with dental caries. J Clin Microbiol 2004, 42:3023-3029.
29. Petti C.A., Polage C.R., Schreckenberger P. The role of 16S rRNA gene sequencing in identification of microorganisms misidentified by conventional methods. J Clin Microbiol 2005, 43:6123-6125.
30. Chakravorty S., Helb D., Burday M., Connell N., Alland D. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Methods 2007, 69:330-339.
31. Kohne D., Hogan J., Jonas V., Dean E., Adams T. Novel approach for rapid and sensitive detection of microorganisms: DNA probes to RNA 1986, American Society for Microbiology, Washington DC, pp.110-112.
32. London C.J., Griffith L.P. Characterisation of Pseudomonads isolated from diseased fleece. Appl Environ Microbial 1984, 47:993-997.
33. Tang L., Zeng G., Shen G., Li Y., Zhang Y., Huang D. Rapid detection of picloram in agricultural field samples using a disposable immunomembrane-based electrochemical sensor. Environ Sci Technol 2008, 42:1207-1212.
34. Small J., Call D.R., Brockman F.J., Straub T.M., Chandler D.P. Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl Environ Microbiol 2001, 67:4708-4716.
35. Peña S.R., Raina S., Goodrich G.P., Fedoroff N.V., Keating C.D. Hybridization and enzymatic extension of Au nanoparticle-bound oligonucleotides. J Am Chem Soc 2002, 124:7314-7323.
36. Du H., Strohsahl C.M., Camera J., Miller B.L., Krauss T.D. Sensitivity and specificity of metal surface-immobilized " Molecular Beacon" biosensors. J Am Chem Soc 2005, 127:7932-7940.
37. Tang L., Zeng G., Shen G., Li Y., Liu C., Li Z., et al. Sensitive detection of lip genes by electrochemical DNA sensor and its application in polymerase chain reaction amplicons from Phanerochaete chrysosporium. Biosens Bioelectron 2009, 24:1474-1479.
38. Xie H., Zhang C., Gao Z. Amperometric detection of nucleic acid at femtomolar levels with a nucleic acid/electrochemical activator bilayer on gold electrode. Anal Chem 2004, 76:1611-1617.
39. Hianik T., Gajdo V., Krivanek R., Oretskaya T., Metelev V., Volkov E., et al. Amperometric detection of DNA hybridization on a gold surface depends on the orientation of oligonucleotide chains. Bioelectrochemistry 2001, 53:199-204.
40. Caruana D.J., Heller A. Enzyme-amplified amperometric detection of hybridization and of a single base pair mutation in an 18-base oligonucleotide on a 7-μm-diameter microelectrode. J Am Chem Soc 1999, 121:769-774.
41. Chen D., Li J. Interfacial design and functionlization on metal electrodes through self-assembled monolayer. Surf Sci Rep 2006, 61:445-463.