Functional RNA microarrays for high-throughput screening of antiprotein aptamers

Collett, James R.; Cho, Eun Jeong; Lee, Jennifer F.; Levy, Matthew; Hood, Allysia J.; Wan, Christine; Ellington, Andrew D.

doi:10.1016/j.ab.2004.11.027

Cited by 88 publications

(67 citation statements)

References 42 publications

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“…-- (Tran et al, 2010) DNA 3 nM Electrochemical (voltammetry) 0.5 µg/mL (Cheng et al, 2007) (Kirby et al, 2004) RNAFluorescence (microarray) 70 fM (Collett et al, 2005) Section 2.3 will describe these systems briefly, while three biosensor platforms targeting pathogens in food will be discussed in Section 2.4.…”

Section: Aptamers For Pathogenic Food Safety Targetsmentioning

confidence: 99%

“…Another noteworthy example that has been studied over the past few years is egg-white lysozyme, a protein considered to be an allergen-trigger in consumers with egg allergies. A few promising aptasensor platforms developed so far include label-free voltammetric assays (Cheng et al, 2007), Faradaic impendance spectroscopy (Rodriguez et al, 2005) and RNA microarray technology (Collett et al, 2005).…”

Section: Other Macromolecular Targetsmentioning

confidence: 99%

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Advances in Aptamer-Based Biosensors for Food Safety

McKeague¹,

Giamberardino²,

DeRosa³

2011

Environmental Biosensors

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Section: Aptamers For Pathogenic Food Safety Targetsmentioning

confidence: 99%

Section: Other Macromolecular Targetsmentioning

confidence: 99%

Advances in Aptamer-Based Biosensors for Food Safety

McKeague¹,

Giamberardino²,

DeRosa³

2011

Environmental Biosensors

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“…52,56,[62][63][64][65][66][67][68] This is due to the difficulty in tethering RNA molecules to a surface without loss of functionality. Most initial efforts at RNA microarray fabrication have involved modified RNA sequences such as biotinylated RNA 56,64,65 or thiol-modified RNA. 67 For example, Ellington and coworkers 56 created an aptamer microarray by printing four different (two DNA and two RNA) biotin-modified aptamers onto streptavidin-coated glass slides for the quantitative and simultaneous detection of multiple protein targets.…”

Section: Iii1 Nucleic Acid Aptamer Microarraysmentioning

confidence: 99%

Microarray methods for protein biomarker detection

Lee

Wark

Corn

2008

Analyst

137

108

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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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“…For this reason, microarrays have also been used post-selection to screen enriched pools which contain significantly fewer unique sequences and even fewer aptamer candidates, which can be identified through sequencing and chosen based on population metrics such as multiplicity or enrichment. [105][106][107] Aptamers isolated from selections can also be studied and optimized through mutations and assayed on microarrays to identify key features which are critical to the highest affinity aptamer such as the minimal aptamer structure, structure-function relationships, as well as conserved sequence motifs. [107][108][109] The majority of these selection microarrays rely on the imaging and detection of fluorescently labeled molecules (target or library).…”

Section: Imaging and Detection With Chips: Surface-bound Nucleic Acidsmentioning

confidence: 99%