» Articles » PMID: 31699984

Independent Control of the Thermodynamic and Kinetic Properties of Aptamer Switches

Overview
Journal Nat Commun
Specialty Biology
Date 2019 Nov 9
PMID 31699984
Citations 25
Authors
Affiliations
Soon will be listed here.
Abstract

Molecular switches that change their conformation upon target binding offer powerful capabilities for biotechnology and synthetic biology. Aptamers are useful as molecular switches because they offer excellent binding properties, undergo reversible folding, and can be engineered into many nanostructures. Unfortunately, the thermodynamic and kinetic properties of the aptamer switches developed to date are intrinsically coupled, such that high temporal resolution can only be achieved at the cost of lower sensitivity or high background. Here, we describe a design strategy that decouples and enables independent control over the thermodynamics and kinetics of aptamer switches. Starting from a single aptamer, we create an array of aptamer switches with effective dissociation constants ranging from 10 μM to 40 mM and binding kinetics ranging from 170 ms to 3 s. Our strategy is broadly applicable to other aptamers, enabling the development of switches suitable for a diverse range of biotechnology applications.

Citing Articles

A Review on Perception of Binding Kinetics in Affinity Biosensors: Challenges and Opportunities.

McCann B, Tipper B, Shahbeigi S, Soleimani M, Jabbari M, Nasr Esfahani M ACS Omega. 2025; 10(5):4197-4216.

PMID: 39959045 PMC: 11822510. DOI: 10.1021/acsomega.4c10040.


Generalizable Molecular Switch Designs for Continuous Biosensing.

Saunders J, Thompson I, Soh H Acc Chem Res. 2025; 58(5):703-713.

PMID: 39954262 PMC: 11883736. DOI: 10.1021/acs.accounts.4c00721.


Fluorescent aptasensor based on target-induced hairpin conformation switch coupled with nicking enzyme-assisted signal amplification for detection of beta-amyloid oligomers in cerebrospinal fluid.

Chuang W, Chen C, Duh T, Chen Y Mikrochim Acta. 2025; 192(2):70.

PMID: 39804483 DOI: 10.1007/s00604-024-06943-8.


Wearable Electrochemical Biosensors for Advanced Healthcare Monitoring.

Duan H, Peng S, He S, Tang S, Goda K, Wang C Adv Sci (Weinh). 2024; 12(2):e2411433.

PMID: 39588557 PMC: 11727287. DOI: 10.1002/advs.202411433.


Nucleic acid-based wearable and implantable electrochemical sensors.

Ye C, Lukas H, Wang M, Lee Y, Gao W Chem Soc Rev. 2024; 53(15):7960-7982.

PMID: 38985007 PMC: 11308452. DOI: 10.1039/d4cs00001c.


References
1.
Autour A, Jeng S, Cawte A, Abdolahzadeh A, Galli A, Panchapakesan S . Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells. Nat Commun. 2018; 9(1):656. PMC: 5811451. DOI: 10.1038/s41467-018-02993-8. View

2.
Harroun S, Prevost-Tremblay C, Lauzon D, Desrosiers A, Wang X, Pedro L . Programmable DNA switches and their applications. Nanoscale. 2018; 10(10):4607-4641. DOI: 10.1039/c7nr07348h. View

3.
Ferguson B, Hoggarth D, Maliniak D, Ploense K, White R, Woodward N . Real-time, aptamer-based tracking of circulating therapeutic agents in living animals. Sci Transl Med. 2013; 5(213):213ra165. PMC: 4010950. DOI: 10.1126/scitranslmed.3007095. View

4.
Hall B, Cater S, Levy M, Ellington A . Kinetic optimization of a protein-responsive aptamer beacon. Biotechnol Bioeng. 2009; 103(6):1049-59. DOI: 10.1002/bit.22355. View

5.
Hernandez F, Hernandez L, Pinto A, Schafer T, Ozalp V . Targeting cancer cells with controlled release nanocapsules based on a single aptamer. Chem Commun (Camb). 2013; 49(13):1285-7. DOI: 10.1039/c2cc37370j. View