In vitro selection of a single-stranded DNA molecular recognition element against clostridium difficile toxin B and sensitive detection in human fecal matter

Journal of Nucleic Acids

Volumn 2015, Issue , 2015, Pages

  Hong, Ka Lok ^a   Maher, Eamonn ^a   Williams, Ryan M ^a,b   Sooter, Letha J ^a  

^a WEST VIRGINIA UNIVERSITY   (United States)

^b MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL TOXIN; BOVINE SERUM ALBUMIN; CHOLERA TOXIN; CLOSTRIDIUM DIFFICILE TOXIN B; PSEUDOMONAS AERUGINOSA EXOTOXIN A; SINGLE STRANDED DNA; STAPHYLOCOCCUS ALPHA TOXIN; UNCLASSIFIED DRUG;

ANTIGEN DETECTION; ARTICLE; BINDING AFFINITY; ENZYME LINKED IMMUNOSORBENT ASSAY; FECES ANALYSIS; IN VITRO STUDY; MOLECULAR RECOGNITION; MOLECULAR RECOGNITION ELEMENT; NONHUMAN; PEPTOCLOSTRIDIUM DIFFICILE; PRIORITY JOURNAL; PSEUDOMONAS AERUGINOSA; STAPHYLOCOCCUS AUREUS; TOXIN ANALYSIS; VIBRIO CHOLERAE;

BACTERIA (MICROORGANISMS); BOVINAE; CLOSTRIDIUM DIFFICILE; PSEUDOMONAS AERUGINOSA; STAPHYLOCOCCUS AUREUS; VIBRIO CHOLERAE;

EID: 84923902473     PISSN: 20900201     EISSN: 2090021X     Source Type: Journal    
DOI: 10.1155/2015/808495     Document Type: Article

References (58)

1. J.G. Bartlett, T.W. Chang, M. Gurwith, S. L. Gorbach, and A.B. Onderdonk, "Antibiotic-associated pseudomembranous colitis due to toxin-producing clostridia,"The New England Journal of Medicine, vol. 298, no. 10, pp. 531-534, 1978.
2. J. Shannon-Lowe, N. J. Matheson, F. J. Cooke, and S. H. Aliyu, "Prevention and medical management of Clostridium difficile infection," BritishMedical Journal, vol. 340, no. 7747, Article ID c1296, p. c1296, 2010.
3. J. Lucado, C. Gould, and A. Elixhauser, "Clostridium difficile infections (CDI) in hospital stays, 2009," HCUP Statistical Brief no. 124, 2011.
4. J. A. O'Brien, B. J. Lahue, J. J. Caro, and D. M. Davidson, "The emerging infectious challenge of Clostridiumdifficile-associated disease in Massachusetts hospitals: clinical and economic consequences," Infection Control andHospital Epidemiology, vol. 28, no. 11, pp. 1219-1227, 2007.
5. E. R. Dubberke, K. A. Reske, M. A. Olsen, L. C. McDonald, and V. J. Fraser, "Short- and long-term attributable costs of Clostridium difficile-associated disease in nonsurgical inpatients," Clinical Infectious Diseases, vol. 46, no. 4, pp. 497-504, 2008.
6. M. D. Redelings, F. Sorvillo, and L. Mascola, "Increase in Clostridiumdifficile-relatedmortality rates,United States, 1999-2004," Emerging Infectious Diseases, vol. 13, no. 9, pp. 1417-1419, 2007.
7. S. A. Kuehne, S.T. Cartman, J.T. Heap,M. L. Kelly, A. Cockayne, and N. P. Minton, "The role of toxin A and toxin B in Clostridium difficile infection," Nature, vol. 467, no. 7316, pp. 711-713, 2010.
8. D. E. Voth and J. D. Ballard, "Clostridium difficile toxins: mechanism of action and role in disease," Clinical Microbiology Reviews, vol. 18, no. 2, pp. 247-263, 2005.
9. K. C. Carroll and J. G. Bartlett, "Biology of clostridium difficile: implications for epidemiology and diagnosis," Annual Review of Microbiology, vol. 65, pp. 501-521, 2011.
10. L. Fenner, A. F. Widmer, G. Goy, S. Rudin, and R. Frei, "Rapid and reliable diagnostic algorithm for detection of Clostridium difficile," Journal of ClinicalMicrobiology, vol. 46, no. 1, pp. 328-330, 2008.
11. V. O. Badger, N. A. Ledeboer, M. B. Graham, and C. E. Edmiston, "Clostridium difficile: epidemiology, pathogenesis, management, and prevention of a recalcitrant healthcare-associated pathogen," Journal of Parenteral & Enteral Nutrition, vol. 36, no. 6, pp. 645-662, 2012.
12. S. H. Cohen, D. N. Gerding, S. Johnson et al., "Clinical practice guidelines for Clostridium difficile infection in adults: 2010 update by the society for healthcare epidemiology of America (SHEA) and the infectious diseases society of America (IDSA)," Infection Control and Hospital Epidemiology, vol. 31, no. 5, pp. 431-455, 2010.
13. H. Vanpoucke, T. de Baere, G. Claeys, M. Vaneechoutte, and G. Verschraegen, "Evaluation of six commercial assays for the rapid detection of Clostridium difficile toxin and/or antigen in stool specimens," Clinical Microbiology and Infection, vol. 7, no. 2, pp. 55-64, 2001.
14. K. C. Carroll, "Tests for the diagnosis of Clostridium difficile infection: the next generation," Anaerobe, vol. 17, no. 4, pp. 170-174, 2011.
15. A. M. Larson, A. M. Fung, and F. C. Fang, "Evaluation of tcdB real-time PCRin a three-step diagnostic algorithmfor detection of toxigenic Clostridium difficile," Journal of Clinical Microbiology, vol. 48, no. 1, pp. 124-130, 2010.
16. J.R. Ticehurst,D.Z. Aird, L.M. Dam, A. P. Borek, J. T. Hargrove, and K. C. Carroll, "Effective detection of toxigenic Clostridium difficile by a two-step algorithm including tests for antigen and cytotoxin," Journal of Clinical Microbiology, vol. 44, no. 3, pp. 1145-1149, 2006.
17. E. M. McConnell, M. R. Holahan, and M. C. DeRosa, "Aptamers as promising molecular recognition elements for diagnostics and therapeutics in the central nervous system," Nucleic Acid Therapeutics, vol. 24, no. 6, pp. 388-404, 2014.
18. M. McKeague and M. C. Derosa, "Challenges and opportunities for small molecule aptamer development," Journal of Nucleic Acids, vol. 2012, Article ID 748913, 20 pages, 2012.
19. H.-M. So, K. Won, Y. H. Kim et al., "Single-walled carbon nanotube biosensors using aptamers as molecular recognition elements," Journal of the American Chemical Society, vol. 127, no. 34, pp. 11906-11907, 2005.
20. T. Fodey, P. Leonard, J. O'Mahony, R. O'Kennedy, and M. Danaher, "Developments in the production of biological and synthetic binders for immunoassay and sensor-based detection of smallmolecules," TrAC-Trends in Analytical Chemistry, vol. 30, no. 2, pp. 254-269, 2011.
21. C. Tuerk and L. Gold, "Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase," Science, vol. 249, no. 4968, pp. 505-510, 1990.
22. R. M. Williams, A. R. Kulick, S. Yedlapalli, L. Battistella, C. J. Hajiran, and L. J. Sooter, "In vitro selection of a single-stranded DNA molecular recognition element specific for bromacil," Journal of Nucleic Acids, vol. 2014, Article ID 102968, 8 pages, 2014.
23. R. M. Williams, E. Maher, and L. J. Sooter, "In vitro selection of a single-stranded DNA molecular recognition element for the pesticide malathion," Combinatorial Chemistry & High Throughput Screening, vol. 17, no. 8, pp. 694-702, 2014.
24. R. Williams, C. Crihfield, S. Gattu, L. Holland, and L. Sooter, "In vitro selection of a single-stranded DNAmolecular recognition element against atrazine," International Journal of Molecular Sciences, vol. 15, no. 8, pp. 14332-14347, 2014.
25. L.-O. Andersson, "Theheterogeneity of bovine serumalbumin," BBA-General Subjects, vol. 117, no. 1, pp. 115-133, 1966.
26. S. Bhakdi and J. Tranum-Jensen, "Alpha-toxin of Staphylococcus aureus,"Microbiological Reviews, vol. 55,no. 4, pp. 733-751, 1991.
27. F.D. Lowy, "Staphylococcus aureus infections,"TheNew England Journal of Medicine, vol. 339, no. 8, pp. 520-532, 1998.
28. M. I. Gómez and A. Prince, "Opportunistic infections in lung disease: pseudomonas infections in cystic fibrosis," Current Opinion in Pharmacology, vol. 7, no. 3, pp. 244-251, 2007.
29. N. K. Ganguly and T. Kaur, "Mechanism of action of cholera toxin and other toxins," Indian Journal of Medical Research, vol. 104, pp. 28-37, 1996.
30. R. Deng, L. Wang, G. Yi, E. Hua, and G. Xie, "Target-induced aptamer release strategy based on electrochemical detection of staphylococcal enterotoxin B using GNPs-ZrO2-Chits film," Colloids and Surfaces B: Biointerfaces, vol. 120, pp. 1-7, 2014.
31. P. Luo, Y. Liu, Y. Xia, H. Xu, and G. Xie, "Aptamer biosensor for sensitive detection of toxin A of Clostridium difficile using gold nanoparticles synthesized by Bacillus stearothermophilus," Biosensors and Bioelectronics, vol. 54, pp. 217-221, 2014.
32. E. Temur, A. Zengin, I. H. Boyacä, F. C. Dudak, H. Torul, and U. Tamer, "Attomole sensitivity of staphylococcal enterotoxin b detection using an aptamer-modified surface-enhanced Raman scattering probe," Analytical Chemistry, vol. 84, no. 24, pp. 10600-10606, 2012.
33. M. Zuker, "Mfold web server for nucleic acid folding and hybridization prediction," Nucleic Acids Research, vol. 31, no. 13, pp. 3406-3415, 2003.
34. J. S. Choi, S. G. Kim, M. Lahousse et al., "Screening and characterization of high-affinity ssDNA aptamers against anthrax protective antigen," Journal of Biomolecular Screening, vol. 16, no. 2, pp. 266-271, 2011.
35. G. J. Connell, M. Illangesekare, and M. Yarus, "Three small ribooligonucleotides with specific arginine sites," Biochemistry, vol. 32, no. 21, pp. 5497-5502, 1993.
36. A. D. Ellington, M. Khrapov, and C. A. Shaw, "The scene of a frozen accident," RNA, vol. 6, no. 4, pp. 485-498, 2000.
37. B. Hall, J. R. Hesselberth, and A. D. Ellington, "Computational selection of nucleic acid biosensors via a slip structure model," Biosensors and Bioelectronics, vol. 22, no. 9-10, pp. 1939-1947, 2007.
38. C. Lozupone, S. Changayil, I. Majerfeld, and M. Yarus, "Selection of the simplest RNA that binds isoleucine," RNA, vol. 9, no. 11, pp. 1315-1322, 2003.
39. I. Majerfeld and M. Yarus, "Isoleucine:RNAsites with associated coding sequences," RNA, vol. 4, no. 4, pp. 471-478, 1998.
40. S. C. B. Gopinath, K. Hayashi, and P. K. R. Kumar, "Aptamer that binds to the gD protein of herpes simplex virus 1 and efficiently inhibits viral entry," Journal of Virology, vol. 86,no. 12, pp. 6732-6744, 2012.
41. Y. Imaizumi, Y. Kasahara, H. Fujita et al., "Efficacy of base-modification on target binding of small molecule DNA aptamers," Journal of the American Chemical Society, vol. 135, no. 25, pp. 9412-9419, 2013.
42. J. Ashley and S. F. Y. Li, "An aptamer based surface plasmon resonance biosensor for the detection of bovine catalase in milk," Biosensors and Bioelectronics, vol. 48, pp. 126-131, 2013.
43. J. L. Su, B. S. Youn, W. P. Ji, J. H. Niazi, S. K. Yeon, and B. G. Man, "ssDNA aptamer-based surface plasmon resonance biosensor for the detection of retinol binding protein 4 for the early diagnosis of type 2 diabetes," Analytical Chemistry, vol. 80, no. 8, pp. 2867-2873, 2008.
44. D. T. Tran, K. Knez, K. P. Janssen, J. Pollet, D. Spasic, and J. Lammertyn, "Selection of aptamers against Ara h 1 protein for FO-SPR biosensing of peanut allergens in food matrices," Biosensors and Bioelectronics, vol. 43, no. 1, pp. 245-251, 2013.
45. L. N. Cella, P. Sanchez, W. Zhong, N. V. Myung, W. Chen, and A. Mulchandani, "Nano aptasensor for protective antigen toxin of anthrax," Analytical Chemistry, vol. 82, no. 5, pp. 2042-2047, 2010.
46. Y. Huang, X. Chen, N. Duan et al., "Selection and characterization of DNA aptamers against Staphylococcus aureus enterotoxin C1," Food Chemistry, vol. 166, pp. 623-629, 2015.
47. J. H. Cummings,M. J. Hill, D. J. A. Jenkins, J. R. Pearson, and H. S. Wiggins, "Changes in fecal composition and colonic function due to cereal fiber,"The American Journal of Clinical Nutrition, vol. 29, no. 12, pp. 1468-1473, 1976.
48. D. J. Patel, A. K. Suri, F. Jiang et al., "Structure, recognition and adaptive binding in RNA aptamer complexes," Journal of Molecular Biology, vol. 272, no. 5, pp. 645-664, 1997.
49. J. G. Bruno and J. L. Kiel, "Use of magnetic beads in selection and detection of biotoxin aptamers by electrochemiluminescence and enzymatic methods," BioTechniques, vol. 32, no. 1, pp. 178-183, 2002.
50. U. A. Ochsner, E. Katilius, and N. Janjic, "Detection of Clostridium difficile toxinsA, B and binary toxinwith slowoff-ratemodified aptamers," Diagnostic Microbiology and Infectious Disease, vol. 76, no. 3, pp. 278-285, 2013.
51. T. Åkerlund, B. Svenungsson, Å. Lagergren, and L. G. Burman, "Correlationofdisease severitywith fecal toxin levels inpatients with Clostridium difficile-associated diarrhea and distribution of PCR ribotypes and toxin yields in vitro of corresponding isolates," Journal of ClinicalMicrobiology, vol. 44, no. 2, pp. 353-358, 2006.
52. K. M. You, S. H. Lee, A. Im, and S. B. Lee, "Aptamers as functional nucleic acids: in vitro selection and biotechnological applications," Biotechnology and Bioprocess Engineering, vol. 8, no. 2, pp. 64-75, 2003.
53. R. E. Wang, H. Wu, Y. Niu, and J. Cai, "Improving the stability of aptamers by chemical modification," Current Medicinal Chemistry, vol. 18, no. 27, pp. 4126-4138, 2011.
54. D. J. Reinert, T. Jank, K. Aktories, and G. E. Schulz, "Structural basis for the function of Clostridium difficile toxin B," Journal of Molecular Biology, vol. 351, no. 5, pp. 973-981, 2005.
55. J. E. Wedekind, C. B. Trame, M. Dorywalska et al., "Refined crystallographic structure of Pseudomonas aeruginosa exotoxin A and its implications for the molecular mechanism of toxicity," Journal of Molecular Biology, vol. 314, no. 4, pp. 823-837, 2001.
56. A. Bujacz, "Structures of bovine, equine and leporine serum albumin," Acta Crystallographica Section D: Biological Crystallography, vol. 68, part 10, pp. 1278-1289, 2012.
57. C. J. O'Neal, M. G. Jobling, R. K. Holmes, and W. G. J. Hol, "Structural basis for the activation of cholera toxin by human ARF6-GTP," Science, vol. 309, no. 5737, pp. 1093-1096, 2005.
58. Y. Tanaka, N. Hirano, J. Kaneko, Y. Kamio, M. Yao, and I. Tanaka, "2-Methyl-2,4-pentanediol induces spontaneous assembly of staphylococcal α-hemolysin into heptameric pore structure," Protein Science, vol. 20, no. 2, pp. 448-456, 2011.