Aptamer-based biosensor arrays for detection and quantification of biological macromolecules

McCauley, Thomas G.; Hamaguchi, Nobuko; Stanton, Martin

doi:10.1016/s0003-2697(03)00297-5

Cited by 247 publications

(154 citation statements)

References 22 publications

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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.…”

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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Section: Iii1 Nucleic Acid Aptamer Microarraysmentioning

confidence: 99%

Microarray methods for protein biomarker detection

Lee

Wark

Corn

2008

Analyst

137

108

View full text Add to dashboard Cite

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“…Because of their exquisite specificity and the ease with which they can be engineered, aptamers should prove particularly useful for diagnostic applications. For example, aptamers can be used to distinguish between different isoforms of proteins that are differentially expressed in normal versus cancerous cells, 65 or to detect post-translational modifications such as phosphorylation. 85 Aptamers can also be immobilized on arrays and used to detect their cognate ligands.…”

Section: Discussionmentioning

confidence: 99%

Aptamer-based optical switch for biosensors

Lee¹,

Cho²,

Cho³

2014

Analytical Science and Technology

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Abstract:In this review, we will discuss aptamer technologies including in vitro selection, signal transduction mechanisms, and designing aptamers and aptazyme for label-free biosensors and catalysts. Dye-displacement, a typical label-less method, is described here which allows avoiding relatively complex labeling steps and extending this application to any aptamers without specific conformational changes, in a more simple, sensitive and cost effective way. We will also describe most recent and advanced technologies of signaling aptamer and aptazyme for the various analytical and clinical applications. Quantum dot biosensor (QDB) is explained in detail covering designing and adaptations for multiplexed protein detection. Application to aptamer array utilizing self-assembled signaling aptamer DNA tile and the novel methods that can directly select smart aptamer or aptazyme experimentally and computationally will also be finally discussed, respectively.

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“…More recently, nucleic acid aptamers 9,10 have emerged as recognition elements that possess distinct advantages over antibodies in specific applications. With their ability to bind a target varying in size from metal ions 11 to tissues 12 , aptamers have been widely applied as recognition elements in biosensing platforms 13,14 . Compared to antibodies, aptamers are chemically synthesized, and it is therefore simple to introduce reproducible chemical modifications for surface immobilization or reporting.…”

Section: Introductionmentioning

confidence: 99%

A Method for Selecting Structure-switching Aptamers Applied to a Colorimetric Gold Nanoparticle Assay

Martin

Smith

Warren

et al. 2015

JoVE

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Small molecules provide rich targets for biosensing applications due to their physiological implications as biomarkers of various aspects of human health and performance. Nucleic acid aptamers have been increasingly applied as recognition elements on biosensor platforms, but selecting aptamers toward small molecule targets requires special design considerations. This work describes modification and critical steps of a method designed to select structure-switching aptamers to small molecule targets. Binding sequences from a DNA library hybridized to complementary DNA capture probes on magnetic beads are separated from nonbinders via a target-induced change in conformation. This method is advantageous because sequences binding the support matrix (beads) will not be further amplified, and it does not require immobilization of the target molecule. However, the melting temperature of the capture probe and library is kept at or slightly above RT, such that sequences that dehybridize based on thermodynamics will also be present in the supernatant solution. This effectively limits the partitioning efficiency (ability to separate target binding sequences from nonbinders), and therefore many selection rounds will be required to remove background sequences. The reported method differs from previous structure-switching aptamer selections due to implementation of negative selection steps, simplified enrichment monitoring, and extension of the length of the capture probe following selection enrichment to provide enhanced stringency. The selected structure-switching aptamers are advantageous in a gold nanoparticle assay platform that reports the presence of a target molecule by the conformational change of the aptamer. The gold nanoparticle assay was applied because it provides a simple, rapid colorimetric readout that is beneficial in a clinical or deployed environment. Design and optimization considerations are presented for the assay as proof-of-principle work in buffer to provide a foundation for further extension of the work toward small molecule biosensing in physiological fluids.

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Aptamer-based biosensor arrays for detection and quantification of biological macromolecules

Cited by 247 publications

References 22 publications

Microarray methods for protein biomarker detection

Microarray methods for protein biomarker detection

Aptamer-based optical switch for biosensors

A Method for Selecting Structure-switching Aptamers Applied to a Colorimetric Gold Nanoparticle Assay

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