Aptamers: Analytical tools for viral components

DNA and RNA Nanobiotechnologies in Medicine: Diagnosis and Treatment of Diseases

Volumn , Issue , 2013, Pages 425-442

  Toulmé, Jean Jacques ^a,b   Di Primo, Carmelo ^a,b   Dausse, Eric ^a,b   Desmecht, Daniel ^c   Cornet, François ^c   Azéma, Laurent ^a,b  

^a INSERM U869   (France)

^b UNIVERSITÉ DE BORDEAUX   (France)

^c UNIVERSITY OF LIÈGE   (Belgium)

Author keywords

Aptamer; HCV; HIV 1; Influenza virus; Oligonucleotide; Screening; SELEX; Surface plasmon resonance

Indexed keywords

FLUORESCENCE; LIBRARIES; OLIGONUCLEOTIDES; PROTEINS; RNA; SCREENING; SURFACE PLASMON RESONANCE; VIRUSES;

APTAMERS; COMBINATORIAL METHOD; HEPATITIS C VIRUS; HIV-1; HUMAN IMMUNODEFICIENCY VIRUS; INFLUENZA VIRUS; PRIMARY SEQUENCES; SELEX;

DISEASES;

EID: 84930964269     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-642-36853-0_17     Document Type: Chapter

References (104)

1. Aldaz-Carroll L, Tallet B, Dausse E et al (2002) Apical loop-internal loop interactions: a new RNA-RNA recognition motif identified through in vitro selection against RNA hairpins of the hepatitis C virus mRNA. Biochemistry 41: 5883-5893
2. Andréola ML, Calmels C, Michel J et al (2000) Towards the selection of phosphorothioate aptamers optimizing in vitro selection steps with phosphorothioate nucleotides. Eur J Biochem 267: 5032-5040
3. Andréola ML, Pileur F, Calmels C et al (2001) DNA aptamers selected against the HIV-1 RNase H display in vitro antiviral activity. Biochemistry 40: 10087-10094
4. Arnold S, Pampalakis G, Kantiotou K et al (2012) One round of SELEX for the generation of DNA aptamers directed against KLK6. Biol Chem 393: 343-353
5. Baudin F, Bach C, Cusack S et al (1994) Structure of influenza virus RNP. I. Influenza virus nucleoprotein melts secondary structure in panhandle RNA and exposes the bases to the solvent. EMBO J 13: 3158-3165
6. Beaurain F, Di Primo C, Toulmé JJ et al (2003) Molecular dynamics reveals the stabilizing role of loop closing residues in kissing interactions: comparison between TAR-TAR* and TARaptamer. Nucleic Acids Res 31: 4275-4284
7. Bellecave P, Andréola ML, VenturaMet al (2003) Selection of DNA aptamers that bind the RNAdependent RNA polymerase of hepatitis C virus and inhibit viral RNA synthesis in vitro. Oligonucleotides 13: 455-463
8. Berezhnoy A, Stewart CA, McNamara JO et al (2012) Isolation and optimization of murine IL-10 receptor blocking oligonucleotide aptamers using high-throughput sequencing. Mol Ther 20: 1242-1250
9. Berezovski M, Musheev M, Drabovich A et al (2006) Non-SELEX selection of aptamers. J Am Chem Soc 128: 1410-1411
10. Berkhout B (2000) Multiple biological roles associated with the repeat (R) region of the HIV-1 RNA genome. Adv Pharmacol 48: 29-73
11. Binning JM, Leung DW (2012) Aptamers in virology: recent advances and challenges. Front Microbiol 3: 29
12. Binning JM, Leung DW, Amarasinghe GK (2012) Aptamers in virology: recent advances and challenges. Front Microbiol 3: 29
13. Biroccio A, Hamm J, Incitti I et al (2002) Selection of RNA aptamers that are specific and highaffinity ligands of the hepatitis C virus RNA-dependent RNA polymerase. J Virol 76: 3688-3696
14. Boiziau C, Dausse E, Yurchenko L et al (1999) DNA aptamers selected against the HIV-1 transactivation-responsive RNA element form RNA-DNA kissing complexes. J Biol Chem 274: 12730-12737
15. Boucard D, Toulmé JJ, Di Primo C (2006) Bimodal loop-loop interactions increase the affinity of RNA aptamers for HIV-1 RNA structures. Biochemistry 45: 1518-1524
16. Bunka DH, Stockley PG (2006) Aptamers come of age-at last. Nat Rev Microbiol 4: 588-596
17. Chen Y, Nakamoto K, Niwa O et al (2012) On-chip synthesis of RNA aptamer microarrays for multiplexed protein biosensing with SPR imaging measurements. Langmuir 28: 8281-8285
18. Choi SK, Lee C, Lee KS et al (2011) DNA aptamers against the receptor binding region of hemagglutinin prevent avian influenza viral infection. Mol Cells 32: 527-533
19. Collett JR, Cho EJ, Ellington AD (2005) Production and processing of aptamer microarrays. Methods 37: 4-15
20. Collin D, van Heijenoort C, Boiziau C et al (2000) NMR characterization of a kissing complex formed between the TAR RNA element of HIV-1 and a DNA aptamer. Nucleic Acids Res 28: 3386-3391
21. Comolli LR, Pelton JG, Tinoco I Jr (1998) Mapping of a protein-RNA kissing hairpin interface: Rom and Tar-Tar*. Nucleic Acids Res 26: 4688-4695
22. Cox JC, Ellington AD (2001) Automated selection of anti-protein aptamers. Bioorg Med Chem 9: 2525-2531
23. Cui ZQ, Ren Q, Wei HP et al (2011) Quantum dot-aptamer nanoprobes for recognizing and labeling influenza A virus particles. Nanoscale 3: 2454-2457
24. Cullen DC, Brown RG, Lowe CR (1987) Detection of immuno-complex formation via surface plasmon resonance on gold-coated diffraction gratings. Biosensors 3: 211-225
25. Da Rocha GS, Dausse E, Toulmé JJ (2004) Determinants of apical loop-internal loop RNA-RNA interactions involving the HCV IRES. Biochem Biophys Res Commun 322: 820-826
26. Darfeuille F, Cazenave C, Gryaznov S et al (2001) RNA and N30->P50 kissing aptamers targeted to the trans-activation responsive (TAR) RNA of the human immunodeficiency virus-1. Nucleosides Nucleotides Nucleic Acids 20: 441-449
27. Darfeuille F, Arzumanov A, Gait MJ et al (2002a) 20-O-methyl-RNA hairpins generate loop-loop complexes and selectively inhibit HIV-1 Tat-mediated transcription. Biochemistry 41: 12186-12192
28. Darfeuille F, Sekkai D, Dausse E et al (2002b) Driving in vitro selection of anti-HIV-1 TAR aptamers by magnesium concentration and temperature. Comb Chem High Throughput Screen 5: 313-525
29. Darfeuille F, Hansen JB, Orum H, Di Primo C, Toulmé JJ (2004) LNA/DNA chimeric oligomers mimic RNA aptamers targeted to the TAR RNA element of HIV-1. Nucleic Acids Res 2004 (2): 3101-3107
30. Darfeuille F, Reigadas S, Hansen JB et al (2006) Aptamers targeted to an RNA hairpin show improved specificity compared to that of complementary oligonucleotides. Biochemistry 45: 12076-12082
31. Dausse E, Cazenave C, Rayner B et al (2005) In vitro selection procedures for identifying DNA and RNA aptamers targeted to nucleic acids and proteins. Methods Mol Biol 288: 391-410
32. Dausse E, Da Rocha GS, Toulmé JJ (2009) Aptamers: a new class of oligonucleotides in the drug discovery pipeline? Curr Opin Pharmacol 9: 602-607
33. Dausse E, Taouji S, Evadé L et al (2011) HAPIscreen, a method for high-throughput aptamer identification. J Nanobiotechnology 9: 25
34. Davis DR, Seth PP (2011) Therapeutic targeting of HCV internal ribosomal entry site RNA. Antivir Chem Chemother 21: 117-128
35. Demeulemeester J, Tintori C, Botta M et al (2012) Development of an AlphaScreen-based HIV-1 integrase dimerization assay for discovery of novel allosteric inhibitors. J Biomol Screen 17: 618-628
36. Di Primo C, Rudloff I, Reigadas S et al (2007) Systematic screening of LNA/20-O-methyl chimeric derivatives of a TAR RNA aptamer. FEBS Lett 581: 771-774
37. Diviney S, Tuplin A, Struthers M et al (2008) A hepatitis C virus cis-acting replication element forms a long-range RNA-RNA interaction with upstream RNA sequences in NS5B. J Virol 82: 9008-9022
38. Ducongé F, Toulmé JJ (1999) In vitro selection identifies key determinants for loop-loop interactions: RNA aptamers selective for the TAR RNA element of HIV-1. RNA 5: 1605-1614
39. Ducongé F, Di Primo C, Toulmé JJ (2000) Is a closing "GA pair” a rule for stable loop-loop RNA complexes? J Biol Chem 275: 21287-21294
40. Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346: 818-822
41. Eulberg D, Buchner K, Maasch C et al (2005) Development of an automated in vitro selection protocol to obtain RNA-based aptamers: identification of a biostable substance P antagonist. Nucleic Acids Res 33: e45
42. Fagerstam LG, Frostell A, Karlsson R et al (1990) Detection of antigen-antibody interactions by surface plasmon resonance. Application to epitope mapping. J Mol Recognit 3: 208-214
43. Finlay BB, McFadden G (2006) Anti-immunology: evasion of the host immune system by bacterial and viral pathogens. Cell 124: 767-782
44. Friebe P, Bartenschlager R (2002) Genetic analysis of sequences in the 30 nontranslated region of hepatitis C virus that are important for RNA replication. J Virol 76: 5326-5538
45. Fu W, Gorelick RJ, Rein A (1994) Characterization of human immunodeficiency virus type 1 dimeric RNA from wild-type and protease-defective virions. J Virol 68: 5013-5508
46. Gold L, Ayers D, Bertino J et al (2010) Aptamer-based multiplexed proteomic technology for biomarker discovery. PLoS One 5: e15004
47. Gopinath SC, Kawasaki K, Kumar PK (2005) Selection of RNA-aptamer against human influenza B virus. Nucleic Acids Symp Ser (Oxf) (49): 85-86
48. Gopinath SC, Sakamaki Y, Kawasaki K et al (2006) An efficient RNA aptamer against human influenza B virus hemagglutinin. J Biochem (Tokyo) 139: 837-846
49. Gordon CG, Mackey JL, Jewett JC et al (2012) Reactivity of biarylazacyclooctynones in copperfree click chemistry. J Am Chem Soc 134: 9199-9208
50. Gregorian RS Jr, Crothers DM (1995) Determinants of RNA hairpin loop-loop complex stability. J Mol Biol 248: 968-984
51. Guedon P, Livache T, Martin F et al (2000) Characterization and optimization of a real-time, parallel, label-free, polypyrrole-based DNA sensor by surface plasmon resonance imaging. Anal Chem 72: 6003-6009
52. Heiny AT, Miotto O, Srinivasan KN et al (2007) Evolutionarily conserved protein sequences of influenza a viruses, avian and human, as vaccine targets. PLoS One 2: e1190
53. Henn C, Boettcher S, Steinbach A et al (2012) Catalytic enzyme activity on a biosensor chip: combination of surface plasmon resonance and mass spectrometry. Anal Biochem 428: 28-30
54. James W (2007) Aptamers in the virologists’ toolkit. J Gen Virol 88: 351-364
55. Jayaprakash KN, Peng CG, Butler D et al (2010) Non-nucleoside building blocks for copperassisted and copper-free click chemistry for the efficient synthesis of RNA conjugates. Org Lett 12: 5410-5413
56. Jeon SH, Kayhan B, Ben-Yedidia T et al (2004) A DNA aptamer prevents influenza infection by blocking the receptor binding region of the viral hemagglutinin. J Biol Chem 279: 48410-48419
57. Karn J (1999) Tackling Tat. J Mol Biol 293: 235-254
58. Kikuchi K, Umehara T, Fukuda K et al (2003) RNA aptamers targeted to domain II of hepatitis C virus IRES that bind to its apical loop region. J Biochem (Tokyo) 133: 263-270
59. Kikuchi K, Umehara T, Fukuda K et al (2005) A hepatitis C virus (HCV) internal ribosome entry site (IRES) domain III-IV-targeted aptamer inhibits translation by binding to an apical loop of domain IIId. Nucleic Acids Res 33: 683-692
60. Kikuchi K, Umehara T, Nishikawa F et al (2009) Increased inhibitory ability of conjugated RNA aptamers against the HCV IRES. Biochem Biophys Res Commun 386: 118-123
61. Kolb G, Reigadas S, Castanotto D et al (2006) Endogenous expression of an anti-TAR aptamer reduces HIV-1 replication. RNA Biol 3: 150-156
62. Kota S, Coito C, Mousseau G et al (2009) Peptide inhibitors of hepatitis C virus core oligomerization and virus production. J Gen Virol 90: 1319-1328
63. Krone JR, Nelson RW, Dogruel D et al (1997) BIA/MS: interfacing biomolecular interaction analysis with mass spectrometry. Anal Biochem 244: 124-132
64. Kupakuwana GV, Crill JE 2nd, McPike MP et al (2011) Acyclic identification of aptamers for human alpha-thrombin using over-represented libraries and deep sequencing. PLoS One 6: e19395
65. Lautner G, Balogh Z, Bardoczy V et al (2010) Aptamer-based biochips for label-free detection of plant virus coat proteins by SPR imaging. Analyst 135: 918-926
66. Lebars I, Legrand P, Aimé A et al (2008) Exploring TAR-RNA aptamer loop-loop interaction by X-ray crystallography, UV spectroscopy and surface plasmon resonance. Nucleic Acids Res 36: 7146-7156
67. Lima WF, Crooke ST (1997) Binding affinity and specificity of Escherichia coli RNase H1: impact on the kinetics of catalysis of antisense oligonucleotide-RNA hybrids. Biochemistry 36: 390-398
68. Lopez F, Pichereaux C, Burlet-Schiltz O et al (2003) Improved sensitivity of biomolecular interaction analysis mass spectrometry for the identification of interacting molecules. Proteomics 3: 402-412
69. Mairal T, Cengiz Ozalp V, Lozano Sanchez P et al (2007) Aptamers: molecular tools for analytical applications. Anal Bioanal Chem 390: 989-1007
70. Marton S, Berzal-Herranz B, Garmendia E et al (2012) Anti-HCV RNA aptamers targeting the genomic cis-acting replication element. Pharmaceuticals 5: 49-60
71. Mascini M, Palchetti I, Tombelli S (2012) Nucleic acid and peptide aptamers: fundamentals and bioanalytical aspects. Angew Chem Int Ed Engl 51: 1316-1332
72. Mayer G (2009) The chemical biology of aptamers. Angew Chem Int Ed Engl 48: 2672-2689
73. Misono TS, Kumar PK (2005) Selection of RNA aptamers against human influenza virus hemagglutinin using surface plasmon resonance. Anal Biochem 342: 312-317
74. Muriaux D, De Rocquigny H, Roques BP et al (1996) NCp7 activates HIV-1Lai RNA dimerization by converting a transient loop-loop complex into a stable dimer. J Biol Chem 271: 33686-33692
75. Nair TM, Myszka DG, Davis DR (2000) Surface plasmon resonance kinetic studies of the HIV TAR RNA kissing hairpin complex and its stabilization by 2-thiouridine modification. Nucleic Acids Res 28: 1935-1940
76. Negri P, Kage A, Nitsche A et al (2011) Detection of viral nucleoprotein binding to anti-influenza aptamers via SERS. Chem Commun (Camb) 47: 8635-8637
77. Negri P, Chen G, Kage A et al (2012) Direct optical detection of viral nucleoprotein binding to an anti-influenza aptamer. Anal Chem 84: 5501-5508
78. Nitsche A, Kurth A, Dunkhorst A et al (2007) One-step selection of Vaccinia virus-binding DNA aptamers by MonoLEX. BMC Biotechnol 7: 48
79. Park SY, Kim S, Yoon H et al (2011) Selection of an antiviral RNA aptamer against hemagglutinin of the subtype H5 avian influenza virus. Nucleic Acid Ther 21: 395-402
80. Pileur F, Andreola ML, Dausse E, Michel J, Moreau S, Yamada H, Gaidamakov SA, Crouch RJ, Toulmé JJ, Cazenave C (2003) Selective inhibitory DNA aptamers of the human RNase H1. Nucleic Acids Res 31: 5776-5788
81. Pinheiro VB, Taylor AI, Cozens C et al (2012) Synthetic genetic polymers capable of heredity and evolution. Science 336: 341-344
82. Remy-Martin F, El Osta M, Lucchi G et al (2012) Surface plasmon resonance imaging in arrays coupled with mass spectrometry (SUPRA-MS): proof of concept of on-chip characterization of a potential breast cancer marker in human plasma. Anal Bioanal Chem 404: 423-432
83. Rich RL, Myszka DG (2011) Survey of the 2009 commercial optical biosensor literature. J Mol Recognit 24: 892-914
84. Robertson DL, Joyce GF (1990) Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 344: 467-468
85. Roh S, Chung T, Lee B (2012) Overview of the characteristics of micro- and nano-structured surface plasmon resonance sensors. Sensors 11: 1565-1588
86. Romero-Lopez C, Diaz-Gonzalez R, Barroso-delJesus A et al (2009) Inhibition of hepatitis C virus replication and internal ribosome entry site-dependent translation by an RNA molecule. J Gen Virol 90: 1659-1669
87. Sehr P, Pawlita M, Lewis J (2007) Evaluation of different glutathione S-transferase-tagged protein captures for screening E6/E6AP interaction inhibitors using AlphaScreen. J Biomol Screen 12: 560-567
88. Stoltenburg R, Reinemann C, Strehlitz B (2007) SELEX-a (r)evolutionary method to generate high-affinity nucleic acid ligands. Biomol Eng 24: 381-403
89. Sundaram P, Kurniawan H, Byrne ME et al (2012) Therapeutic RNA aptamers in clinical trials. Eur J Pharm Sci 48: 259-271
90. Taouji S, Dahan S, Bosse R et al (2009) Current screens based on the AlphaScreen technology for deciphering cell signalling pathways. Curr Genomics 10: 93-101
91. Tintori C, Demeulemeester J, Franchi L et al (2012) Discovery of small molecule HIV-1 integrase dimerization inhibitors. Bioorg Med Chem Lett 22: 3109-3114
92. Tombelli S, Minunni M, Luzi E et al (2005) Aptamer-based biosensors for the detection of HIV-1 Tat protein. Bioelectrochemistry 67: 135-141
93. Toulmé J-J, Di Primo C, Moreau S (2001) Modulation of RNA function by oligonucleotides recognizing RNA structure. Prog Nucleic Acid Res Mol Biol 69: 1-46
94. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249: 505-510
95. Tuerk C, Macdougal S, Gold L (1992) RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc Natl Acad Sci USA 89: 6988-6992
96. Ullman EF, Kirakossian H, Singh S et al (1994) Luminescent oxygen channeling immunoassay: measurement of particle binding kinetics by chemiluminescence. Proc Natl Acad Sci USA 91: 5426-5430
97. Upert G, Di Giorgio A, Upadhyay A et al (2012) Inhibition of HIV replication by cyclic and hairpin PNAs targeting the HIV-1 TAR RNA loop. J Nucleic Acids 2012: 591025
98. Van Melckebeke H, Devany M, Di Primo C et al (2008) Liquid-crystal NMR structure of HIV TAR RNA bound to its SELEX RNA aptamer reveals the origins of the high stability of the complex. Proc Natl Acad Sci USA 105: 9210-9215
99. Wang Z, Wilkop T, Xu D et al (2007) Surface plasmon resonance imaging for affinity analysis of aptamer-protein interactions with PDMS microfluidic chips. Anal Bioanal Chem 389: 819-825
100. Wang RE, Wu H, Niu Y et al (2011) Improving the stability of aptamers by chemical modification. Curr Med Chem 18: 4126-4138
101. Watrin M, Von Pelchrzim F, Dausse E et al (2009) In vitro selection of RNA aptamers derived from a genomic human library against the TAR RNA element of HIV-1. Biochemistry 48: 6278-6284
102. Zhou J, Rossi JJ (2011) Cell-specific aptamer-mediated targeted drug delivery. Oligonucleotides 21: 1-10
103. Zhou J, Bobbin ML, Burnett JC et al (2012) Current progress of RNA aptamer-based therapeutics. Front Genet 3: 234
104. Zimmermann B, Gesell T, Chen D et al (2010) Monitoring genomic sequences during SELEX using high-throughput sequencing: neutral SELEX. PLoS One 5: e9169