High-Affinity Aptamers for <i>In Vitro</i> and <i>In Vivo</i> Cocaine Sensing

Alkhamis, Obtin; Canoura, Juan; Wu, Yuyang; Emmons, Nicole A.; Wang, Yuting; Honeywell, Kevin M.; Plaxco, Kevin W.; Kippin, Tod E.; Xiao, Yi

doi:10.1021/jacs.3c11350

Cited by 4 publications

(5 citation statements)

References 46 publications

(107 reference statements)

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“… 78 , 86 Also, aptamers could be linked to the reaction module and activate the circuit by aptamer/ligand complexes. 17 (ii) The study demonstrated the primer-induced entropy-driven cascaded emergence of two CDNs. Accordingly, by applying seesaw gates, 12 , 36 the primer-induced cascaded evolution of intercommunicating scalable, higher-order CDNs of enhanced complexity and programmable hierarchical functionalities may be envisaged.…”

Section: Discussionmentioning

confidence: 88%

“…Particularly, the biocompatibility of the DNA tetrahedral circuit and its versatile applicability are noteworthy. Beyond demonstrating the unprecedented use of programmed entropy-driven circuits stimulating biological responses in cells and contribution of the principles to the development of biosensors, biomedicine, and Systems Chemistry, broader impacts of the concepts may be envisaged: (i) The triggered release of other functional nucleic acids by the entropy-driven circuit, such as ribozymes, antisense oligonucleotides, or splicing DNAzymes as control units of gene/protein expression pathways, may be designed. , Also, aptamers could be linked to the reaction module and activate the circuit by aptamer/ligand complexes . (ii) The study demonstrated the primer-induced entropy-driven cascaded emergence of two CDNs.…”

Section: Discussionmentioning

confidence: 99%

“…The structural and functional information encoded in the base sequence of nucleic acids provides the foundation for the development of the area of dynamic DNA nanotechnology. − Diverse functional systems including switches, machines, dynamically self-assembled nanostructures, − stimuli-responsive DNA materials, − and logic circuits , were assembled based on these properties of the nucleic acids. Different applications of these structures were reported for sensing, − controlled drug delivery, , guided assembly of programmed nanoparticle structures, − and the construction of nanoscale optical and electronic devices. , In addition, the high programmability of nucleic acids dictated toehold-mediated strand displacement reactions, , entropy-driven DNA reactions, , catalytic hairpin assembly reactions, hybridization chain reactions, , and exponential chain reactions using DNAzyme/ribozyme. , Particularly, entropy-driven DNA reactions were broadly applied to develop computing circuits, , molecular engineering, , nanostructure self-assembly, enzyme activity modulation, and biosensing. ,, …”

Section: Introductionmentioning

confidence: 99%

“… 1 − 3 Diverse functional systems including switches, 4 machines, 5 dynamically self-assembled nanostructures, 6 − 8 stimuli-responsive DNA materials, 9 − 11 and logic circuits 12 , 13 were assembled based on these properties of the nucleic acids. Different applications of these structures were reported for sensing, 14 − 17 controlled drug delivery, 18 , 19 guided assembly of programmed nanoparticle structures, 20 − 23 and the construction of nanoscale optical and electronic devices. 24 , 25 In addition, the high programmability of nucleic acids dictated toehold-mediated strand displacement reactions, 26 , 27 entropy-driven DNA reactions, 28 , 29 catalytic hairpin assembly reactions, 30 hybridization chain reactions, 31 , 32 and exponential chain reactions using DNAzyme/ribozyme.…”

Section: Introductionmentioning

confidence: 99%

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Spatially Localized Entropy-Driven Evolution of Nucleic Acid-Based Constitutional Dynamic Networks for Intracellular Imaging and Spatiotemporal Programmable Gene Therapy

Lin,

Ouyang,

Qin

et al. 2024

J. Am. Chem. Soc.

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The primer-guided entropy-driven high-throughput evolution of the DNA-based constitutional dynamic network, CDN, is introduced. The entropy gain associated with the process provides a catalytic principle for the amplified emergence of the CDN. The concept is applied to develop a programmable, spatially localized DNA circuit for effective in vitro and in vivo theranostic, gene-regulated treatment of cancer cells. The localized circuit consists of a DNA tetrahedron core modified at its corners with four tethers that include encoded base sequences exhibiting the capacity to emerge and assemble into a [2 × 2] CDN. Two of the tethers are caged by a pair of siRNA subunits, blocking the circuit into a mute, dynamically inactive configuration. In the presence of miRNA-21 as primer, the siRNA subunits are displaced, resulting in amplified release of the siRNAs silencing the HIF-1α mRNA and fast dynamic reconfiguration of the tethers into a CDN. The resulting CDN is, however, engineered to be dynamically reconfigured by miRNA-155 into an equilibrated mixture enriched with a DNAzyme component, catalyzing the cleavage of EGR-1 mRNA. The DNA tetrahedron nanostructure stimulates enhanced permeation into cancer cells. The miRNA-triggered entropy-driven reconfiguration of the spatially localized circuit leads to the programmable, cooperative bis-gene-silencing of HIF-1α and EGR-1 mRNAs, resulting in the effective and selective apoptosis of breast cancer cells and effective inhibition of tumors in tumor bearing mice.

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Section: Discussionmentioning

confidence: 88%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Spatially Localized Entropy-Driven Evolution of Nucleic Acid-Based Constitutional Dynamic Networks for Intracellular Imaging and Spatiotemporal Programmable Gene Therapy

Lin,

Ouyang,

Qin

et al. 2024

J. Am. Chem. Soc.

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“…Third, both target- and library-immobilized selection methods can only be practically carried out under ambient conditions. Since these aptamers typically exhibit greatly reduced affinity at physiological temperatures (37 °C), they are ineffective for in vivo biomedical applications or experiments in cultured cells.…”

Section: Introductionmentioning

confidence: 99%

Rapid Nuclease-Assisted Selection of High-Affinity Small-Molecule Aptamers

Wang,

Alkhamis,

Canoura

et al. 2024

J. Am. Chem. Soc.

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Aptamers are nucleic acid bioreceptors that have been widely utilized for a variety of biosensing applications, including in vivo detection methods that would not be possible with antibody-based systems. However, it remains challenging to generate high-quality aptamers for small molecule targets, particularly for use under physiological conditions. We present a highly effective aptamer selection technology for small-molecule targets that utilizes the nuclease EcoRI to remove nonspecific or weakly binding sequences in solution phase, rapidly enriching high-affinity target binders within just a few rounds of selection. As proof-of-concept, we used our nuclease-assisted SELEX (NA-SELEX) method to isolate aptamers for a synthetic cannabinoid, AB-FUBINACA. Within five rounds, we identified two highly specific aptamers that exhibit nanomolar affinity at physiological temperature. We also demonstrate the robustness and reproducibility of NA-SELEX by performing the same selection experiment with fresh reagents and libraries, obtaining the same two aptamers as well as two other high-quality aptamer candidates. Finally, we compare NA-SELEX against a conventional libraryimmobilized SELEX screen for AB-FUBINACA using the same screening conditions, identifying aptamers with 25−100-fold weaker affinity after 11 rounds of selection. NA-SELEX therefore could be an effective selection method for the isolation of high-quality aptamers for small-molecule targets.

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