Selection and characterization of DNA aptamers against PrPSc

Experimental Biology and Medicine

Volumn 236, Issue 4, 2011, Pages 466-476

  Wang, Ping ^a   Hatcher, Kristen L ^b   Bartz, Jason C ^c   Chen, Shu G ^b   Skinner, Pamela ^a   Richt, Juergen ^d   Liu, Hong ^a   Sreevatsan, Srinand ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

^b CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c CREIGHTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d KANSAS STATE UNIVERSITY   (United States)

Author keywords

CJD; CWD; DNA aptamers; Prion; Scrapie; TSE

Indexed keywords

APTAMER; DNA; DNA APTAMER; ISOPROTEIN; MEMBRANE PROTEIN; PRION PROTEIN; UNCLASSIFIED DRUG; LIGAND; PRIMER DNA;

ANIMAL CELL; ANIMAL TISSUE; ANTIBODY DETECTION; ARTICLE; BINDING AFFINITY; BLOOD CELL; CELL DIFFERENTIATION; COMBINATORIAL CHEMISTRY; CONTROLLED STUDY; HAMSTER; HUMAN; HUMAN TISSUE; MOLECULAR EVOLUTION; NONHUMAN; PRECIPITATION; PRION; SCRAPIE; SENSITIVITY ANALYSIS; SENSITIVITY AND SPECIFICITY; VIRUS DETECTION; VIRUS STRAIN; ANIMAL; ENZYME LINKED IMMUNOSORBENT ASSAY; GEL MOBILITY SHIFT ASSAY; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; WESTERN BLOTTING;

ANIMALIA;

ANIMALS; APTAMERS, NUCLEOTIDE; BASE SEQUENCE; BLOTTING, WESTERN; DNA PRIMERS; ELECTROPHORETIC MOBILITY SHIFT ASSAY; ENZYME-LINKED IMMUNOSORBENT ASSAY; LIGANDS; PRPSC PROTEINS;

EID: 79958865003     PISSN: 15353702     EISSN: 15353699     Source Type: Journal    
DOI: 10.1258/ebm.2011.010323     Document Type: Article

References (69)

1. Prusiner SB. Novel proteinaceous infectious particles cause scrapie. Science 1982;216:136-144
2. Come JH, Fraser PE, Lansbury PT Jr. A kinetic model for amyloid formation in the prion diseases: importance of seeding. Proc Natl Acad Sci USA 1993;90:5959-5963
3. Bessen RA, Marsh RF. Distinct PrP properties suggest the molecular basis of strain variation in transmissible mink encephalopathy. J Virol 1994;68:7859-7868
4. Prusiner SB. Prions. Proc Nat Acad Sci USA 1998;95:13363-13383
5. Aguzzi A, Polymenidou M. Mammalian prion biology: one century of evolving concepts. Cell 2004;116:313-327
6. DeArmond SJ, Qiu Y, Sanchez H, Spilman PR, Ninchak-Casey A, Alonso D, Daggett V. PrPc glycoform heterogeneity as a function of brain region: implications for selective targeting of neurons by prion strains. J Neuropathol Exp Neurol 1999;58:1000-1009
7. Ellington AD, Szostak JW. In vitro selection of RNA molecules that bind specific ligands. Nature 1990;346:818-822
8. Tuerk C, Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990;249:505-510
9. Rhie A, Kirby L, Sayer N, Wellesley R, Disterer P, Sylvester I, Gill A, Hope J, James W, Tahiri-Alaoui A. Characterization of 20-fluoro-RNA aptamers that bind preferentially to disease-associated conformations of prion protein and inhibit conversion. J Biol Chem 2003;278:39697-39705
10. Sayer NM, Cubin M, Rhie A, Bullock M, Tahiri-Alaoui A, James W. Structural determinants of conformationally selective, prion-binding aptamers. J Biol Chem 2004;279:13102-13109
11. Sekiya S, Noda K, Nishikawa F, Yokoyama T, Kumar PK, Nishikawa S. Characterization and application of a novel RNA aptamer against the mouse prion protein. J Biochem 2006;139:383-390
12. Takemura K, Wang P, Vorberg I, Surewicz W, Priola SA, Kanthasamy A, Pottathil R, Chen SG, Sreevatsan S. DNA aptamers that bind to PrP(C) and not PrP(Sc) show sequence and structure specificity [erratum appears in Exp Biol Med (Maywood) 2006 Apr;231(4):485]. Exp Biol Med 2006;231:204-214
13. Mercey R, Lantier I, Maurel MC, Grosclaude J, Lantier F, Marc D. Fast, reversible interaction of prion protein with RNA aptamers containing specific sequence patterns. Arch Virol 2006;151:2197-2214
14. King DJ, Safar JG, Legname G, Prusiner SB. Thioaptamer interactions with prion proteins: sequence-specific and non-specific binding sites. J Mol Biol 2007;369:1001-1014
15. Kouassi GK, Wang P, Sreevatan S, Irudayaraj J. Aptamer-mediated magnetic and gold-coated magnetic nanoparticles as detection assay for prion protein assessment. Biotechnol Prog 2007;23:1239-1244
16. Ogasawara D, Hasegawa H, Kaneko K, Sode K, Ikebukuro K. Screening of DNA aptamer against mouse prion protein by competitive selection. Prion 2007;1:248-254
17. Matsugami A, Mashima T, Nishikawa F, Murakami K, Nishikawa S, Noda K, Yokoyama T, Katahira M. Structural analysis of r(GGA)4 found in RNA aptamer for bovine prion protein. Nucleic Acids Symp Ser (Oxf) 2008;52:179-180
18. Murakami K, Nishikawa F, Noda K, Yokoyama T, Nishikawa S. Anti-bovine prion protein RNA aptamer containing tandem GGA repeat interacts both with recombinant bovine prion protein and its beta isoform with high affinity. Prion 2008;2:73-80
19. Bibby DF, Gill AC, Kirby L, Farquhar CF, Bruce ME, Garson JA. Application of a novel in vitro selection technique to isolate and characterise high affinity DNA aptamers binding mammalian prion proteins. J Virol Methods 2008;151:107-115
20. Ogasawara D, Hachiya NS, Kaneko K, Sode K, Ikebukuro K. Detection system based on the conformational change in an aptamer and its application to simple bound/free separation. Biosens Bioelectron 2009;24:1372-1376
21. Gilch S, Schatzl HM. Aptamers against prion proteins and prions. Cell Mol Life Sci 2009;66:2445-2455
22. Mashima T, Matsugami A, Nishikawa F, Nishikawa S, Katahira M. Unique quadruplex structure and interaction of an RNA aptamer against bovine prion protein. Nucleic Acids Res 2009;37:6249-6258
23. Xiao SJ, Hu PP, Li YF, Huang CZ, Huang T, Xiao GF. Aptamer-mediated turn-on fluorescence assay for prion protein based on guanine quenched fluophor. Talanta 2009;79:1283-1286
24. Hossain MT, Shibata T, Kabashima T, Kai M. Aptamer-mediated chemiluminescence detection of prion protein on a membrane using trimethoxyphenylglyoxal. Anal Sci 2010;26:645-647
25. Marc D. Aptamers to explore prion protein interactions with nucleic acids. Front Biosci 2010;15:550-563
26. Angers RC, Browning SR, Seward TS, Sigurdson CJ, Miller MW, Hoover EA, Telling GC. Prions in skeletal muscles of deer with chronic wasting disease. Science 2006;311:1117
27. Seidel B, Thomzig A, Buschmann A, Groschup MH, Peters R, Beekes M, Terytze K. Scrapie agent (Strain 263K) can transmit disease via the oral route after persistence in soil over years. PLoS ONE 2007;2: e435
28. Mathiason CK, Powers JG, Dahmes SJ, Osborn DA, Miller KV, Warren RJ, Mason GL, Hays SA, Hayes-Klug J, Seelig DM, Wild MA, Wolfe LL, Spraker TR, Miller MW, Sigurdson CJ, Telling GC, Hoover EA. Infectious prions in the saliva and blood of deer with chronic wasting disease. Science 2006;314:133-136
29. Kong Q, Huang S, Zou W, Vanegas D, Wang M, Wu D, Yuan J, Zheng M, Bai H, Deng H, Chen K, Jenny AL, O'Rourke K, Belay ED, Schonberger LB, Petersen RB, Sy MS, Chen SG, Gambetti P. Chronic wasting disease of elk: transmissibility to humans examined by transgenic mouse models. J Neurosci 2005;25:7944-7949
30. Safar J, Wille H, Itri V, Groth D, Serban H, Torchia M, Cohen FE, Prusiner SB. Eight prion strains have PrP(Sc) molecules with different conformations. Nat Med 1998;4:1157-1165
31. Glatzel M, Ott PM, Linder T, Gebbers JO, Gmur A, Wust W, Huber G, Moch H, Podvinec M, Stamm B, Aguzzi A. Human prion diseases: epidemiology and integrated risk assessment. Lancet Neurol 2003;2:757-763
32. Raymond GJ, Chabry J. Purification of the pathological isoform of prion protein (PrPSc or PrPres) from transmissible spongiform encephalopathy-affected brain tissue. In: Lehmann S, Grassi J, eds. Techniques in Prion Research. Switzerland: Birkhauser Verlag Basel, 2004: 16-26
33. Kerstin Elfrink DR. Purification of PrPC. In: Lehmann S, Grassi J, eds. Techniques in Prion Research. Switzerland: Birkhauser Verlag Basel, 2004: 4-15
34. Slomianny MC, Dupont A, Bouanou F, Beseme O, Guihot AL, Amouyel P, Michalski JC, Pinet F. Profiling of membrane proteins from human macrophages: comparison of two approaches. Proteomics 2006;6:2365-2375
35. Kuo TH, Kim HR, Zhu L, Yu Y, Lin HM, Tsang W. Modulation of endoplasmic reticulum calcium pump by Bcl-2. Oncogene 1998;17:1903-1910
36. Schaller O, Fatzer R, Stack M, Clark J, Cooley W, Biffiger K, Egli S, Doherr M, Vandevelde M, Heim D, Oesch B, Moser M. Validation of a western immunoblotting procedure for bovine PrP(Sc) detection and its use as a rapid surveillance method for the diagnosis of bovine spongiform encephalopathy (BSE). Acta Neuropathol (Berl) 1999;98:437-443
37. Glatzel M, Abela E, Maissen M, Aguzzi A. Extraneural pathologic prion protein in sporadic Creutzfeldt-Jakob disease. N Engl J Med 2003;349:1812-1820
38. Merighi M, Majerczak DR, Zianni M, Tessanne K, Coplin DL. Molecular characterization of Pantoea stewartii subsp. stewartii HrpY, a conserved response regulator of the Hrp type III secretion system, and its interaction with the hrpS promoter. J Bacteriol 2006;188:5089-5100
39. Zianni M, Tessanne K, Merighi M, Laguna R, Tabita FR. Identification of the DNA bases of a DNase I footprint by the use of dye primer sequencing on an automated capillary DNA analysis instrument. J Biomol Tech 2006;17:103-113
40. Richt JA, Kasinathan P, Hamir AN, Castilla J, Sathiyaseelan T, Vargas F, Sathiyaseelan J, Wu H, Matsushita H, Koster J, Kato S, Ishida I, Soto C, Robl JM, Kuroiwa Y. Production of cattle lacking prion protein. Nat Biotechnol 2007;25:132-138
41. Parchi P, Giese A, Capellari S, Brown P, Schulz-Schaeffer W, Windl O, Zerr I, Budka H, Kopp N, Piccardo P, Poser S, Rojiani A, Streichemberger N, Julien J, Vital C, Ghetti B, Gambetti P, Kretzschmar H. Classification of sporadic Creutzfeldt-Jakob disease based on molecular and phenotypic analysis of 300 subjects. Ann Neurol 1999;46:224-233
42. Hill AF, Desbruslais M, Joiner S, Sidle KC, Gowland I, Collinge J, Doey LJ, Lantos P. The same prion strain causes vCJD and BSE. Nature 1997;389:448-450, 526
43. Parchi P, Zou W, Wang W, Brown P, Capellari S, Ghetti B, Kopp N, Schulz-Schaeffer WJ, Kretzschmar HA, Head MW, Ironside JW, Gambetti P, Chen SG. Genetic influence on the structural variations of the abnormal prion protein. Proc Natl Acad Sci USA 2000;97:10168-10172
44. Gavier-Widen D, Stack MJ, Baron T, Balachandran A, Simmons M. Diagnosis of transmissible spongiform encephalopathies in animals: a review. J Vet Diagn Invest 2005;17:509-527
45. Takemura K, Kahdre M, Joseph D, Yousef A, Sreevatsan S. An overview of transmissible spongiform encephalopathies. Anim Health Res Rev 2004;5:103-124
46. Korth C, Stierli B, Streit P, Moser M, Schaller O, Fischer R, Schulz-Schaeffer W, Kretzschmar H, Raeber A, Braun U, Ehrensperger F, Hornemann S, Glockshuber R, Riek R, Billeter M, Wuthrich K, Oesch B. Prion (PrPSc)-specific epitope defined by a monoclonal antibody. Nature 1997;390:74-77
47. Safar JG, Scott M, Monaghan J, Deering C, Didorenko S, Vergara J, Ball H, Legname G, Leclerc E, Solforosi L, Serban H, Groth D, Burton DR, Prusiner SB, Williamson RA. Measuring prions causing bovine spongiform encephalopathy or chronic wasting disease by immunoassays and transgenic mice. Nat Biotechnol 2002;20:1147-1150
48. Paramithiotis E, Pinard M, Lawton T, LaBoissiere S, Leathers VL, Zou WQ, Estey LA, Lamontagne J, Lehto MT, Kondejewski LH, Francoeur GP, Papadopoulos M, Haghighat A, Spatz SJ, Head M, Will R, Ironside J, O'Rourke K, Tonelli Q, Ledebur HC, Chakrabartty A, Cashman NR. A prion protein epitope selective for the pathologically misfolded conformation. Nat Med 2003;9:893-899
49. Curin Serbec V, Bresjanac M, Popovic M, Pretnar Hartman K, Galvani V, Rupreht R, Cernilec M, Vranac T, Hafner I, Jerala R. Monoclonal antibody against a peptide of human prion protein discriminates between Creutzfeldt-Jacob's disease-affected and normal brain tissue. J Biol Chem 2004;279:3694-3698
50. Zou WQ, Zheng J, Gray DM, Gambetti P, Chen SG. Antibody to DNA detects scrapie but not normal prion protein. Proc Natl Acad Sci USA 2004;101:1380-1385
51. Chang B, Cheng X, Yin S, Pan T, Zhang H, Wong P, Kang SC, Xiao F, Yan H, Li C, Wolfe LL, Miller MW, Wisniewski T, Greene MI, Sy MS. Test for detection of disease-associated prion aggregate in the blood of infected but asymptomatic animals. Clin Vaccine Immunol 2007;14:36-43
52. Zhang H, Cheng X, Richter M, Greene MI. A sensitive and high-throughput assay to detect low-abundance proteins in serum. Nat Med 2006;12:473-477
53. Barletta JM, Edelman DC, Highsmith WE, Constantine NT. Detection of ultra-low levels of pathologic prion protein in scrapie infected hamster brain homogenates using real-time immuno-PCR. J Virol Methods 2005;127:154-164
54. Castilla J, Hetz C, Soto C. Molecular mechanisms of neurotoxicity of pathological prion protein. Curr Mol Med 2004;4:397-403
55. Saa P, Castilla J, Soto C. Presymptomatic detection of prions in blood. Science 2006;313:92-94
56. Saa P, Castilla J, Soto C. Ultra-efficient replication of infectious prions by automated protein misfolding cyclic amplification. J Biol Chem 2006;281:35245-35252
57. Saa P, Castilla J, Soto C. Cyclic amplification of protein misfolding and aggregation. Methods Mol Biol 2005;299:53-65
58. Castilla J, Saa P, Hetz C, Soto C. In vitro generation of infectious scrapie prions. Cell 2005;121:195-206
59. Castilla J, Saa P, Morales R, Abid K, Maundrell K, Soto C. Protein misfolding cyclic amplification for diagnosis and prion propagation studies. Methods Enzymol 2006;412:3-21
60. Deleault NR, Harris BT, Rees JR, Supattapone S. Formation of native prions from minimal components in vitro. Proc Natl Acad Sci 2007;104:9741-9746
61. Sigurdson CJ, Manco G, Schwarz P, Liberski P, Hoover EA, Hornemann S, Polymenidou M, Miller MW, Glatzel M, Aguzzi A. Strain fidelity of chronic wasting disease upon murine adaptation. J Virol 2006;80:12303-12311
62. Race RE, Raines A, Baron TGM, Miller MW, Jenny A, Williams ES. Comparison of abnormal prion protein glycoform patterns from transmissible spongiform encephalopathy agent-infected deer, elk, sheep, and cattle. J Virol 2002;76:12365-12368
63. Raymond GJ, Raymond LD, Meade-White KD, Hughson AG, Favara C, Gardner D, Williams ES, Miller MW, Race RE, Caughey B. Transmission and adaptation of chronic wasting disease to hamsters and transgenic mice: evidence for strains. J Virol 2007;81:4305-4314
64. Proske D, Blank M, Buhmann R, Resch A. Aptamers - basic research, drug development, and clinical applications. Appl Microbiol Biotechnol 2005;69:367-374
65. Proske D, Gilch S, Wopfner F, Schatzl HM, Winnacker EL, Famulok M. Prion-protein-specific aptamer reduces PrPSc formation. Chembiochem 2002;3:717-725
66. Weiss S, Proske D, Neumann M, Groschup MH, Kretzschmar HA, Famulok M, Winnacker EL. RNA aptamers specifically interact with the prion protein PrP. J Virol 1997;71:8790-8797
67. Hunter N, Foster J, Chong A, McCutcheon S, Parnham D, Eaton S, MacKenzie C, Houston F. Transmission of prion diseases by blood transfusion. J Gen Virol 2002;83:2897-2905
68. Grassi J. Pre-clinical diagnosis of transmissible spongiform encephalopathies using rapid tests. Transfus Clin Biol 2003;10: 19-22
69. Pan T, Chang B, Wong P, Li C, Li R, Kang SC, Robinson JD Thompsett AR, Tein P, Yin S, Barnard G, McConnell I, Brown DR, Wisniewski T, Sy MS. An aggregation-specific enzyme-linked immunosorbent assay: detection of conformational differences between recombinant PrP protein dimers and PrP(Sc) aggregates. J Virol 2005;79:12355-12364