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Molecular & Cellular Proteomics 2:11-18, 2003.
© 2003 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

Sensitivity and Specificity of Photoaptamer Probes^*

Drew Smith^,, Brian D. Collins, James Heil and Tad H. Koch^¶,||

SomaLogic, Inc., Boulder, Colorado 80301
^¶ Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215

The potential of photoaptamers as proteomic probes was investigated. Photoaptamers are defined as aptamers that bear photocross-linking functionality, in this report, 5-bromo-2'-deoxyuridine. A key question regarding the use of photoaptamer probes is the specificity of the cross-linking reaction. The specificity of three photoaptamers was explored by comparing their reactions with target proteins and non-target proteins. The range of target/non-target specificity varies from 100- to >10⁶-fold with most values >10⁴-fold. The contributions of the initial binding step and the photocross-linking step were evaluated for each reaction. Photocross-linking never degraded specificity and significantly increased aptamer specificity in some cases. The application of photoaptamer technology to proteomics was investigated in microarray format. Immobilized anti-human immunodeficiency virus-gp120 aptamer was able to detect subnanomolar concentrations of target protein in 5% human serum. The levels of sensitivity and specificity displayed by photoaptamers, combined with other advantageous properties of aptamers, should facilitate development of protein chip technology.

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