Direct Selection Strategy for Isolating Aptamers with pH-Sensitive Binding Activity

Gordon, Chelsea K. L.; Eisenstein, Michael; Soh, H. Tom

doi:10.1021/acssensors.8b00945

Cited by 18 publications

(15 citation statements)

References 27 publications

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“…Devices showed increases in conductance when the pH of solutions decreased, corresponding to a positive gating effect at n -type In 2 O 3 transistors ( Aroonyadet, et al., 2015 ; Rim, et al., 2015 ; Liu, et al., 2016 ). We note that, in addition to unfunctionalized FETs, devices functionalized with aptamers can be pH sensitive ( Idili et al., 2014 ; Porchetta et al., 2015 ; Gordon et al., 2018 ). As pH decreases, negatively charged oligonucleotide backbones become associated with larger numbers of protons changing local charge near semiconductor surfaces.…”

Section: Resultsmentioning

confidence: 99%

Flexible Multiplexed In2O3 Nanoribbon Aptamer-Field-Effect Transistors for Biosensing

et al. 2020

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Summary Flexible sensors are essential for advancing implantable and wearable bioelectronics toward monitoring chemical signals within and on the body. Developing biosensors for monitoring multiple neurotransmitters in real time represents a key in vivo application that will increase understanding of information encoded in brain neurochemical fluxes. Here, arrays of devices having multiple In 2 O 3 nanoribbon field-effect transistors (FETs) were fabricated on 1.4-μm-thick polyethylene terephthalate (PET) substrates using shadow mask patterning techniques. Thin PET-FET devices withstood crumpling and bending such that stable transistor performance with high mobility was maintained over >100 bending cycles. Real-time detection of the small-molecule neurotransmitters serotonin and dopamine was achieved by immobilizing recently identified high-affinity nucleic-acid aptamers on individual In 2 O 3 nanoribbon devices. Limits of detection were 10 fM for serotonin and dopamine with detection ranges spanning eight orders of magnitude. Simultaneous sensing of temperature, pH, serotonin, and dopamine enabled integration of physiological and neurochemical data from individual bioelectronic devices.

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Section: Resultsmentioning

confidence: 99%

Flexible Multiplexed In2O3 Nanoribbon Aptamer-Field-Effect Transistors for Biosensing

et al. 2020

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“…25 Moreover, immobilized azobenzene molecules seem to yield more mixed cis/trans isomers at the photostationary state. 25 Although a few DNA aptamers that show pH-dependent binding to the targets have been developed recently, 26,27 there is no report of the selection of pH-dependent peptide aptamers.…”

Section: Resultsmentioning

confidence: 99%

Selection of Peptides that Associate with Dye-Conjugated Solid Surfaces in a pH-Dependent Manner Using cDNA Display

2019

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Peptides that recognize artificial materials including synthetic polymers and small molecules are drawing attention in the fields of biotechnology and chemical biology. In particular, reversible peptide aptamers that associate with the target molecules only under specific conditions are interesting. In this work, peptide aptamers that recognize a phenolphthalein derivative (PhP: a pH-sensitive organic dye) immobilized on a solid surface in a pH-dependent manner were selected using an in vitro display method (cDNA display). Considering the hydrophobic and aromatic nature of PhP, we prepared a biased DNA library (3A library) that encodes more aromatic amino acids than the standard random codon and performed seven rounds of selection from >10 10 peptide species. The selected peptides including LVFLIWWM (LV59) associated with PhP-modified solid support (sepharose resin and magnetic beads) in neutral buffer but readily dissociated under basic conditions where PhP undergoes large structural change from lactone to quinoid, which is accompanied by increase of hydrophilicity and anionic charge. Control experiments suggested that LV59 recognized both phenol and lactone moieties, and the association under neutral pH is mainly driven by π-stacking and hydrophobic interaction between the peptide and PhP. Notably, however, total hydrophobicity and number of aromatic rings did not completely explain the affinity, and sequence specificity was observed to some extent. After further optimization, this interaction pair would be practically useful for protein purification.

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“…Adapted with permission. [ 56 ] Copyright 2018, American Chemical Society ( https://pubs.acs.org/doi/10.1021/acssensors.8b00945; further permissions related to the material excerpted should be directed to the ACS).…”

Section: Chemically Induced Switchingmentioning

confidence: 99%

“…More recently, we demonstrated the ability to directly select for pH‐induced binding. [ 56 ] The library for in vitro selection was designed so that a known aptamer for streptavidin, SBA29, was fused to a 20‐nt random region (Figure 12C). Using our previously developed particle display method, [ 57 ] we isolated sequences that bound to fluorescently labeled streptavidin at neutral pH and released their target at pH 5.2.…”

Section: Chemically Induced Switchingmentioning

confidence: 99%

Engineering Aptamer Switches for Multifunctional Stimulus‐Responsive Nanosystems

et al. 2020

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specific and strong recognition of molecular targets (i.e., aptamers), catalyze biochemical reactions (i.e., ribozymes), or form sophisticated and dynamic "smart materials" or even 3D constructs (i.e., DNA origami). [2] There is particular interest in the use of nucleic acids for the construction of molecular switches, which undergo a function-altering structural change in response to an external stimulus. [3] Many such examples exist in nature, where switches enable organisms to sense physiological changes and selectively control biological functions in response. For example, riboswitches exist naturally as domains within messenger RNA (mRNA) transcripts that can bind to specific metabolites with high specificity in order to stabilize a secondary structure that prevents subsequent translation. [4] Synthetic, engineered molecular switches based on nucleic acids can achieve even greater diversity of function. Such designs make use of aptamersnucleic acid-based affinity reagents isolated via an in vitro process of systematic evolution by exponential enrichment (SELEX), in which DNA or RNA sequences with specific ligand binding are isolated from a large pool of random sequences. [5] Aptamers have proven to be robust recognition elements due to their thermal stability, ease of synthesis, and capacity to undergo ready modification with a broad array of functional groups. Importantly, traditional selection methods can be expanded upon by innovative engineering techniques to enable the incorporation of additional functions that further extend the utility of aptamers. Aptamers can adopt various 2-and 3-D structures such as duplexes, hairpins, and G-quadruplexes, and the inducible formation and disruption of these configurations can be exploited to enable complex functions besides simple biosensing. Consequently, aptamers have been incorporated into many intricate configurations, such as logic gates and dynamic nanomachines. Various research groups have also described aptamer-based switches that undergo conformational changes in response to triggers such as shifts in pH, stimulation with light, or the presence of a specific ligand. [6] Although still a relatively young area of research, these efforts could prove highly useful for materials research-conferring even greater and more selective control over devices based on functionalized nucleic acids. Aptamers are becoming increasingly integrated with various organic and inorganic molecules in order to control the assembly and operation of novel functional Although RNA and DNA are best known for their capacity to encode biological information, it has become increasingly clear over the past few decades that these biomolecules are also capable of performing other complex functions, such as molecular recognition (e.g., aptamers) and catalysis (e.g., ribozymes). Building on these foundations, researchers have begun to exploit the predictable base-pairing properties of RNA and DNA in order to utilize nucleic acids as functional materials that can undergo a molecular "switching" ...

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Direct Selection Strategy for Isolating Aptamers with pH-Sensitive Binding Activity

Cited by 18 publications

References 27 publications

Flexible Multiplexed In2O3 Nanoribbon Aptamer-Field-Effect Transistors for Biosensing

Flexible Multiplexed In2O3 Nanoribbon Aptamer-Field-Effect Transistors for Biosensing

Selection of Peptides that Associate with Dye-Conjugated Solid Surfaces in a pH-Dependent Manner Using cDNA Display

Engineering Aptamer Switches for Multifunctional Stimulus‐Responsive Nanosystems

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