A DNA Aptamer for Theophylline with Ultrahigh Selectivity Reminiscent of the Classic RNA Aptamer

Huang, Po‐Jung Jimmy; Liu, Juewen

doi:10.1021/acschembio.2c00179

Cited by 26 publications

(46 citation statements)

References 54 publications

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“…This is reasonable since the aptamer and PMNT are two polyelectrolytes with strong collective charge attraction. In this case, a correction factor is needed to obtain the true K d of the aptamer/K + binding, which was similar to that in aptamer strand displacement assays. − A further implication is that the system is under kinetic control, where a binding state reached first would have a kinetic advantage, although the system may not be under the thermodynamic equilibrium. Therefore, we chose to add PMNT after the formation of the K + /aptamer complex to better reflect aptamer/target binding.…”

Section: Resultsmentioning

confidence: 99%

General Label-Free Fluorescent Aptamer Binding Assay Using Cationic Conjugated Polymers

Qin

Lopez

et al. 2022

Anal. Chem.

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With more and more new aptamers being reported, a general, cost-effective yet reliable aptamer binding assay is still needed. Herein, we studied cationic conjugated polymer (CCP)-based binding assays taking advantage of the conformational change of aptamer after binding with a target, which is reflected by the fluorescence change of the CCP. Poly(3-(3′-N,N,N-triethylamino-1′-propyloxy)-4-methyl-2,5-thiophene hydrochloride) (PMNT) was used as a model CCP in this study, and the optimal buffer was close to physiological conditions with 100 mM NaCl and 10 mM MgCl2. We characterized four aptamers for K+, adenosine, cortisol, and caffeine. For cortisol and caffeine, the drop in the 580 nm peak intensity was used for quantification, whereas for K+ and adenosine, the fluorescence ratio at 580 over 530 nm was used. The longer stem of the stem-loop structured aptamer facilitated binding of the target and enlarged the detection signal. High specificity was achieved in differentiating targets with analogues. Compared with the SYBR Green I dye-based staining method, our method achieved equal or even higher sensitivity. Therefore, this assay is practicable as a general aptamer binding assay. The simple, label-free, quick response, and cost-effective features will make it a useful method to evaluate aptamer binding. At the same time, this system can also serve as label-free biosensors for target detection.

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Section: Resultsmentioning

confidence: 99%

General Label-Free Fluorescent Aptamer Binding Assay Using Cationic Conjugated Polymers

Qin

Lopez

et al. 2022

Anal. Chem.

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“…Using this algorithm, we analyzed two of our previous aptamer selection results. 30,31 Figure 4 lists the score distributions of the top 1000 highest scoring aptamers for each sequenced round for each target molecule. For the caffeine selection, the majority of the sequences have a score close to zero for the round 12 and 15 libraries, yet the score shifts to above 20 for the round 20 library.…”

Section: An Examplementioning

confidence: 99%

“…To further test the algorithm, we also analyzed the theophylline selection. 30 When we did the theophylline selection, we initially stopped at round 15. However, the round 15 library was still very diverse, and we had to perform additional seven rounds of selections with gradually decreased theophylline concentrations.…”

Section: Prediction Of Theophylline Aptamersmentioning

confidence: 99%

Machine Learning Directed Aptamer Search from Conserved Primary Sequence and Secondary Structure

Tobia

Huang

Narayan

et al. 2022

Preprint

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Computer-aided prediction of aptamer sequences has been focused on primary sequence alignment and motif comparison. We observed that many aptamers have a conserved hairpin, yet the sequence of the hairpin can be highly variable. Taking such a secondary structure information into consideration, a new algorithm combining conserved primary sequences and secondary structures is developed, that combines three scores based on sequence abundance, stability, and structure, respectively. This algorithm was used in the prediction of aptamers from caffeine and theophylline selections. In the late rounds of the selection, when the library was converged, the predicted sequences matched well with the most abundant sequences. When the library was far from convergence and the sequences were deemed impossible for traditional analysis methods, the algorithm still predicted aptamer sequences that were experimentally verified by isothermal titration calorimetry. This algorithm paves a new way to look for patterns in aptamer selection libraries and mimics the sequence evolution process. It will help shorten the aptamer selection time and promote the biosensor application of aptamers.

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“…Our lab recently reported a series of DNA aptamers that can bind caffeine [5] and theophylline, [10] respectively. These aptamers can be used to develop biosensors for selective detection of these molecules.…”

Section: Introductionmentioning

confidence: 99%

“…[7] A lot of efforts have been made pertaining to the detection and quantification of theophylline, especially in blood, due to its pharmaceutical relevance. [7][8][9] Our lab recently reported a series of DNA aptamers that can bind caffeine [5] and theophylline, [10] respectively. These aptamers can be used to develop biosensors for selective detection of these molecules.…”

Section: Introductionmentioning

confidence: 99%

Interactions between Caffeine, Theophylline and Derivatives with Gold Nanoparticles and Implications for Aptamer‐Based Label‐Free Colorimetric Detection

Labas

Liu

2022

ChemPlusChem

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Caffeine, theophylline, and other methylxanthines have interesting biological activities and are consumed in high quantities globally, causing health and environmental concerns. Gold nanoparticles (AuNPs) have excellent optical properties for biosensor development, although little is known about the adsorption of these xanthine derivatives to AuNPs. In this work, interactions of these compounds with AuNPs were studied. Caffeine, theophylline and theobromine are adsorbed in a manner that affords protection against salt‐induced aggregation, whereas xanthine and paraxanthine are adsorbed to destabilize and thus aggregate the AuNPs. Caffeine and theophylline are able to protect AuNPs starting at concentrations as low as 6.3 μM. Xanthine and paraxanthine induce significant AuNP aggregation at 5 μM. Adsorption was also confirmed by surface‐enhanced Raman scattering (SERS). Using two recently selected DNA aptamers for caffeine and theophylline, the label‐free colorimetric sensing method was tested; our results indicated that due to adsorption of these target molecules, this method cannot be directly used for their detection. The adsorption of these compounds to AuNPs may enable various detection methods such as SERS, but at the same time, it may complicate other detection methods.

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A DNA Aptamer for Theophylline with Ultrahigh Selectivity Reminiscent of the Classic RNA Aptamer

Cited by 26 publications

References 54 publications

General Label-Free Fluorescent Aptamer Binding Assay Using Cationic Conjugated Polymers

General Label-Free Fluorescent Aptamer Binding Assay Using Cationic Conjugated Polymers

Machine Learning Directed Aptamer Search from Conserved Primary Sequence and Secondary Structure

Interactions between Caffeine, Theophylline and Derivatives with Gold Nanoparticles and Implications for Aptamer‐Based Label‐Free Colorimetric Detection

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