Systematic selection of modified aptamer pairs for diagnostic sandwich assays

BioTechniques

Volumn 56, Issue 3, 2014, Pages 125-133

  Ochsner, Urs A ^a   Green, Louis S ^a   Gold, Larry ^a   Janjic, Nebojsa ^a  

^a SomaLogic Inc   (United States)

Author keywords

Aptamer; Diagnostics; Epitope selection; Modified nucleotides; Sandwich assay; SELEX

Indexed keywords

ANGIOPOIETIN 2; APTAMER; CHORDIN LIKE 1 PROTEIN; CLOSTRIDIUM DIFFICILE TOXIN A; COMPLEMENT COMPONENT C7; ENDOTHELIAL CELL SELECTIVE ADHESION MOLECULE PROTEIN; GLYCOPROTEIN VI; MATRILIN 2; PEPTIDES AND PROTEINS; PLASMINOGEN; THROMBOSPONDIN 2; UNCLASSIFIED DRUG; AFFINITY LABELING; PROTEIN; PROTEIN BINDING; RECOMBINANT PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; ASSAY; BINDING ASSAY; BINDING KINETICS; CLOSTRIDIUM DIFFICILE; CONTROLLED STUDY; DIAGNOSTIC PROCEDURE; DIAGNOSTIC SANDWICH ASSAY; DNA SEQUENCE; EQUILIBRIUM BINDING ASSAY; HUMAN; MULTIPLEXED SANDWICH SCREENING ASSAY; NONHUMAN; SANDWICH FILTER BINDING ASSAY; SANDWICH SELEX; SEQUENCE ANALYSIS; AFFINITY LABELING; CHEMISTRY; ISOLATION AND PURIFICATION; MOLECULAR DIAGNOSIS; PROCEDURES; SYSTEMATIC EVOLUTION OF LIGANDS BY EXPONENTIAL ENRICHMENT APTAMER TECHNIQUE;

AFFINITY LABELS; APTAMERS, NUCLEOTIDE; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; PROTEIN BINDING; PROTEINS; RECOMBINANT PROTEINS; SELEX APTAMER TECHNIQUE;

EID: 84896459700     PISSN: 07366205     EISSN: 19409818     Source Type: Journal    
DOI: 10.2144/000114134     Document Type: Article

References (22)

1. Marx, V. 2013. Calling the next generation of affinity reagents. Nat. Methods 10: 829-833.
2. Zichi, D., B. Eaton, B. Singer, and L. Gold. 2008. Proteomics and diagnostics: Let's Get Specific, again. Curr. Opin. Chem. Biol. 12: 78-85.
3. Perlee, L., J. Christiansen, R. Dondero, B. Grimwade, S. Lejnine, M. Mullenix, W. Shao, M. Sorette, et al. 2004. Development and standardization of multiplexed antibody microarrays for use in quantitative proteomics. Proteome Sci. 2: 9.
4. Brody, E. N., L. Gold, R. M. Lawn, J. J. Walker, and D. Zichi. 2010. High-content affinity-based proteomics: unlocking protein biomarker discovery. Expert Rev. Mol. Diagn. 10: 1013-1022.
5. Gold, L., D. Ayers, J. Bertino, C. Bock, A. Bock, E. N. Brody, J. Carter, A. B. Dalby, et al. 2010. Aptamer-based multiplexed proteomic technology for biomarker discovery. PLoS ONE 5: e15004. 10. 1371/journal. pone. 0015004.
6. Gupta, S., D. Thirstrup, T. C. Jarvis, D. J. Schneider, S. K. Wilcox, J. Carter, C. Zhang, A. Gelinas, et al. 2011. Rapid histochemistry using slow off-rate modified aptamers with anionic competition. Appl. Immunohistochem. Mol. Morphol. 19: 273-278.
7. Ochsner, U. A., E. Katilius, and N. Janjic. 2013. Detection of Clostridium difficile toxins A, B and binary toxin with slow off-rate modified aptamers. Diagn. Microbiol. Infect. Dis. 76: 278-285.
8. Park, J. W., S. Jin Lee, E. J. Choi, J. Kim, J. Y. Song, and M. Bock Gu. 2014. An ultra-sensitive detection of a whole virus using dual aptamers developed by immobilization-free screening. Biosens. Bioelectron. 51: 324-329.
9. Tasset, D. M., M. F. Kubik, and W. Steiner. 1997. Oligonucleotide inhibitors of human thrombin that bind distinct epitopes. J. Mol. Biol. 272: 688-698.
10. Shi, H., X. Fan, A. Sevilimedu, and J. T. Lis. 2007. RNA aptamers directed to discrete functional sites on a single protein structural domain. Proc. Natl. Acad. Sci. USA 104: 3742-3746.
11. Gong, Q., J. Wang, K. M. Ahmad, A. T. Csordas, J. Zhou, J. Nie, R. Stewart, J. A. Thomson, et al. 2012. Selection strategy to generate aptamer pairs that bind to distinct sites on protein targets. Anal. Chem. 84: 5365-5371.
12. Xiao, S. J., P. P. Hu, X. D. Wu, Y. L. Zou, L. Q. Chen, L. Peng, J. Ling, S. J. Zhen, et al. 2010. Sensitive discrimination and detection of prion disease-associated isoform with a dual-aptamer strategy by developing a sandwich structure of magnetic microparticles and quantum dots. Anal. Chem. 82: 9736-9742.
13. Nonaka, Y., K. Sode, and K. Ikebukuro. 2010. Screening and improvement of an anti-VEGF DNA aptamer. Molecules 15: 215-225.
14. Sosic, A., A. Meneghello, E. Cretaio, and B. Gatto. 2011. Human thrombin detection through a sandwich aptamer microarray: interaction analysis in solution and in solid phase. Sensors (Basel). 11: 9426-9441.
15. Tennico, Y. H., D. Hutanu, M. T. Koesdjojo, C. M. Bartel, and V. T. Remcho. 2010. On-chip aptamer-based sandwich assay for thrombin detection employing magnetic beads and quantum dots. Anal. Chem. 82: 5591-5597.
16. Davies, D. R., A. D. Gelinas, C. Zhang, J. C. Rohloff, J. D. Carter, D. O'Connell, S. M. Waugh, S. K. Wolk, et al. 2012. Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets. Proc. Natl. Acad. Sci. USA 109: 19971-19976.
17. Vaught, J. D., C. Bock, J. Carter, T. Fitzwater, M. Otis, D. Schneider, J. Rolando, S. Waugh, et al. 2010. Expanding the chemistry of DNA for in vitro selection. J. Am. Chem. Soc. 132: 4141-4151.
18. Gill, R. D., S. Williams, A. Stewart, R. Mehler, T. Foreman, and B. Singer. 2012. Cardiovascular risk event prediction and uses thereof, p. PCT/US2012/058060. SomaLogic, Inc., USA.
19. Fredriksson, S., M. Gullberg, J. Jarvius, C. Olsson, K. Pietras, S. M. Gustafsdottir, A. Ostman, and U. Landegren. 2002. Protein detection using proximity-dependent DNA ligation assays. Nat. Biotechnol. 20: 473-477.
20. Hu, J., T. Wang, J. Kim, C. Shannon, and C. J. Easley. 2012. Quantitation of femtomolar protein levels via direct readout with the electrochemical proximity assay. J. Am. Chem. Soc. 134: 7066-7072.
21. Jo, M., J. Y. Ahn, J. Lee, S. Lee, S. W. Hong, J. W. Yoo, J. Kang, P. Dua, et al. 2011. Development of single-stranded DNA aptamers for specific Bisphenol A detection. Oligonucleotides 21: 85-91.
22. Lee, J., M. Jo, T. H. Kim, J. Y. Ahn, D. K. Lee, S. Kim, and S. Hong. 2011. Aptamer sandwich-based carbon nanotube sensors for single-carbon-atomic-resolution detection of non-polar small molecular species. Lab Chip 11: 52-56.