Photoaptamer arrays applied to multiplexed proteomic analysis

Bock, Chris; Coleman, Michael D.; Collins, Brian D.; Davis, Jody; Foulds, Glenn; Gold, Larry; Greef, Chad; Heil, Jim; Heilig, Joseph S.; Hicke, Brian J.; Hurst, Michele Nelson; Husar, Gregory M.; Miller, Darcey; Ostroff, Rachel; Petach, Helen H.; Schneider, Dan; Vant-Hull, Barry; Waugh, Sheela; Weiss, Allison; Wilcox, Sheri K.; Zichi, Dominic A.

doi:10.1002/pmic.200300631

Cited by 140 publications

(102 citation statements)

References 9 publications

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“…Other array formats used for serum protein analysis include selfassembled monolayer array, filtration-based array, multiplexed photoaptamer-based arrays, phage-based array, and RP array [135][136][137][138][139]. The filtration-based protein array can improve the overall reaction kinetic rate by ten-fold and enhance the sensitivity and specificity of the assay.…”

Section: Protein Arraysmentioning

confidence: 99%

Human body fluid proteome analysis

2006

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The focus of this article is to review the recent advances in proteome analysis of human body fluids, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, and amniotic fluid, as well as its applications to human disease biomarker discovery. We aim to summarize the proteomics technologies currently used for global identification and quantification of body fluid proteins, and elaborate the putative biomarkers discovered for a variety of human diseases through human body fluid proteome (HBFP) analysis. Some critical concerns and perspectives in this emerging field are also discussed. With the advances made in proteomics technologies, the impact of HBFP analysis in the search for clinically relevant disease biomarkers would be realized in the future.

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Section: Protein Arraysmentioning

confidence: 99%

Human body fluid proteome analysis

2006

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“…60,61 This is achieved by substituting thymine bases with 5-bromodeoxyuridine in the DNA aptamer sequence with the resulting photoaptamer selected for a specific protein biomarker via the photochemical SELEX process; 61 this technology is under commercial development by Somalogic, Inc. High-density photoaptamer arrays are created by synthesizing selected photoaptamers with an amine on the 5′-terminus to enable immobilization onto a modified glass surface.…”

Section: Iii1 Nucleic Acid Aptamer Microarraysmentioning

confidence: 99%

Microarray methods for protein biomarker detection

Lee

Wark

Corn

2008

Analyst

137

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The application of protein biomarkers as an aid for the detection and treatment of diseases has been subject to intensified interest in recent years. The quantitative assaying of protein biomarkers in easily obtainable biological fluids such as serum and urine offers the opportunity to improve patient care via earlier and more accurate diagnoses in a convenient, non-invasive manner as well as providing a potential route towards more individually targeted treatment. Essential to achieving progress in biomarker technology is the ability to screen large numbers of proteins simultaneously in a single experiment with high sensitivity and selectivity. In this article, we highlight recent progress in the use of microarrays for high-throughput biomarker profiling and discuss some of the challenges associated with these efforts. I IntroductionThe discovery of protein biomarkers whose change in expression level or state correlates with the progression of a disease is becoming increasingly important. Once validated, proposed biomarkers can be involved in achieving an earlier diagnosis, differentiating between disease types with greater accuracy, and assessing response to treatment. Prominent examples of biomarkers include proteins that are associated with a variety of cancers, 1-4 as well as heart, 5,6 renal, 7,8 andAlzheimer's 9,10 diseases.Most biomarker studies reported to date have focused on serum-, plasmaand urine-based samples. A number of other possibilities include saliva, tears, breath condensates, cerebrospinal fluid and tissue lysates extracted from biopsy samples. There are several excellent reviews detailing biomarker discovery and validation. [11][12][13][14][15] The potential benefits of biomarkers have greatly motivated both academic and industry researchers to apply new proteomic technologies for biomarker discovery and to develop quantitative analytical methodologies for rapid and sensitive biomarker detection. Many clinically relevant biomarkers reside in blood at picomolar concentrations and lower, which is five to seven orders of magnitude lower than the most abundant plasma proteins. Therefore, protein detection with high specificity and sensitivity is required; unfortunately, no universal ultrasensitive enzymatic amplification method (such as PCR for the case of nucleic acid detection) exists for proteins. Additionally, it is desirable to screen multiple proteins simultaneously in a single sample. Multiplexed measurements are attractive not only for economic reasons but also for identifying characteristic signal patterns associated with the relative changes in entire sets of proteins as this will provide much more insight and diagnostic accuracy than individual biomarker measurements.hyejinlee@knu.ac.kr. 14,19,[24][25][26][27][28][29][30] Although microarray methods are wellestablished for high-throughput nucleic acid studies, their application for protein detection has been limited by issues such as the surface immobilization of protein capture probes without loss in bioactivity as well a...

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“…The core of the problem is that dependence only on one reagent in the face of 12 logs of abundance differences between proteins in blood [60] asks more of equilibrium binding than is possible [12,66]. Thus, we had to develop a platform that used novel (and better) aptamers, that had low equilibrium binding constants (e.g., dissociation equilibrium constants [K d s] below 1 nM) but that also allowed a nonequilibrium parameter to provide another element of specificity [70,71,75].…”

Section: Slow Off-rate Modified Aptamersmentioning

confidence: 99%

“…Aptamers bind native confirmations in contrast to antibodies, which often bind linear epitopes. Aptamers are an alternative class of reagents to use for highly multiplexed protein measurements [12,64,[66][67][68][69][70][71][72][73]. Approximately 10 years ago, the entire literature for aptamers may have included the identification of (classic) aptamers for 100 proteins.…”

Section: Slow Off-rate Modified Aptamersmentioning

confidence: 99%