Particle display: a quantitative screening method for generating high-affinity aptamers.

@article{Wang2014ParticleDA,
  title={Particle display: a quantitative screening method for generating high-affinity aptamers.},
  author={Jinpeng Wang and Qiang Gong and Nupur Maheshwari and Michael Eisenstein and Mary Luz Arcila and Kenneth S. Kosik and Hyongsok Tom Soh},
  journal={Angewandte Chemie},
  year={2014},
  volume={53 19},
  pages={
          4796-801
        }
}
We report an aptamer discovery technology that reproducibly yields higher affinity aptamers in fewer rounds compared to conventional selection. Our method (termed particle display) transforms libraries of solution-phase aptamers into "aptamer particles", each displaying many copies of a single sequence on its surface. We then use fluorescence-activated cell sorting (FACS) to individually measure the relative affinities of >10(8) aptamer particles and sort them in a high-throughput manner… Expand
Multiparameter Particle Display (MPPD): A Quantitative Screening Method for the Discovery of Highly Specific Aptamers.
TLDR
This work harnesses the capacity of fluorescence activated cell sorting for multicolor sorting to simultaneously screen for affinity and specificity at a throughput of 107 aptamers per hour and generated DNA aptamer that exhibit picomolar to low nanomolar affinity in human serum for three diverse proteins. Expand
Click-Particle Display for Base-Modified Aptamer Discovery.
TLDR
This work accelerated and generalized the process of generating base-modified aptamers by combining a click-chemistry strategy with a fluorescence-activated cell sorting (FACS)-based screening methodology that measures the affinity and specificity of individual aptamer at a throughput of ~10^7 per hour. Expand
Advancements in Aptamer Discovery Technologies.
TLDR
A body of work from the laboratory in developing advanced methods for consistently producing high-performance aptamers with higher efficiency, fewer resources, and, most importantly, a greater probability of success is described. Expand
High-Throughput Discovery of Aptamers for Sandwich Assays.
TLDR
This work describes an experimental strategy for screening "aptamer pairs" at a throughput of 106 aptamer pairs per hour-which is many orders of magnitude higher than the current state of the art. Expand
A direct selection strategy for isolating aptamers with pH-sensitive binding activity
TLDR
The first experimental strategy for generating pH-responsive aptamers through direct selection is reported and it is found that one aptamer’s affinity-switching behavior is driven by a non-canonical G-A base-pair that controls its folding in a highly pH-dependent manner. Expand
Rapid and Label-Free Strategy to Isolate Aptamers for Metal Ions.
TLDR
An aptamer discovery method is reported that enables us to generate high-quality structure-switching aptamers (SSAs) that undergo a conformational change upon binding a metal ion target, without the requirement of labels or chemical modifications. Expand
Oligonucleotide Functionalised Microbeads: Indispensable Tools for High-Throughput Aptamer Selection
TLDR
Examples and applications of oligonucleotide functionalised microbeads in aptamer selection are explored and new opportunities arising for aptamer science are reflected upon. Expand
Click-PD: A Quantitative Method for Base-Modified Aptamer Discovery
TLDR
This work accelerated and generalized the process of generating base-modified aptamers by combining a click-chemistry strategy with a fluorescence-activated cell sorting (FACS)-based screening methodology that measures the affinity and specificity of individual aptamer at a throughput of ∼10^7 per hour, and generates the most potent inhibitor of Con A-mediated hemagglutination reported to date. Expand
SELEX methods on the road to protein targeting with nucleic acid aptamers.
TLDR
This review will discuss the recent advances in SELEX methods and their advantages and limitations and aptamer applications are briefly outlined in this review. Expand
Machine learning guided aptamer refinement and discovery
TLDR
This work proposes an approach that employs particle display (PD) to partition a library of aptamers by affinity, and uses such data to train machine learning models to predict affinity in silico, and demonstrates how combining machine learning and physical approaches can be used to expedite the discovery of better diagnostic and therapeutic agents. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 28 REFERENCES
Probing the Limits of Aptamer Affinity with a Microfluidic SELEX Platform
TLDR
This work has developed a microfluidic selection process (M-SELEX) that can be used to obtain high affinity aptamers against diverse protein targets and discovers novel aptamer sequences that bind to platelet derived growth factor B and thrombin and a new aptamer that binds to apolipoprotein E3. Expand
Fluorescence-activated cell sorting for aptamer SELEX with cell mixtures
TLDR
The protocol provides a state-of-the-art approach for identifying aptamers that selectively target virtually any cell type under investigation, and provides fewer false positives when using this approach in comparison with other cell-selection approaches. Expand
Generation of high-affinity DNA aptamers using an expanded genetic alphabet
TLDR
Results show that incorporation of unnatural bases can yield aptamers with greatly augmented affinities, suggesting the potential of genetic alphabet expansion as a powerful tool for creating highly functional nucleic acids. Expand
Influence of Target Concentration and Background Binding on In Vitro Selection of Affinity Reagents
TLDR
An improved mathematical model is developed that enables experimentalists to determine appropriate target concentrations as a means for protocol optimization, and reports that both target concentration and the degree of non-specific background binding are critical determinants of SELEX efficiency. Expand
Aptamer-based multiplexed proteomic technology for biomarker discovery
TLDR
A versatile and powerful tool that allows large-scale comparison of proteome profiles among discrete populations, which will enable the discovery of novel biomarkers in a manner that is unencumbered by the incomplete knowledge of biology, thereby helping to advance the next generation of evidence-based medicine. Expand
Applications of aptamers as sensors.
TLDR
Aptamers are ligand-binding nucleic acids whose affinities and selectivities can rival those of antibodies, and they are readily adapted to sequence- (and hence signal-) amplification methods. Expand
Where are all the aptamers?
  • G. Baird
  • Biology, Medicine
  • American journal of clinical pathology
  • 2010
TLDR
This work and Ellington and Szostak’s demonstration that RNA ligands could be found for small molecule dyes were the first of countless studies showing that Systematic Evolution of Ligands by EXponential enrichment, or SELEX, can be applied to nearly any molecular target to generate high-affinity, specific oligonucleotide ligands. Expand
RNA Aptamer Evolution: Two Decades of SELEction
TLDR
This review is an historical follow-up of SELEX method over the two decades since its first appearance and shows how it has evolved along with new technologies positioning itself as an alternative in the design of a new class of therapeutic agents in modern molecular medicine. Expand
Aptamers as therapeutics
TLDR
A series of aptamers currently in development may change how nucleic acid therapeutics are perceived and will increasingly find use in concert with other therapeutic molecules and modalities. Expand
SELEXION. Systematic evolution of ligands by exponential enrichment with integrated optimization by non-linear analysis.
TLDR
This study uses mathematical analysis and computer simulation to predict which variations have the greatest impact and to develop strategies and guidelines for enhanced effectiveness in processes for systematic enrichment of DNA, RNA or peptide ligands. Expand
...
1
2
3
...