Journal articles: 'DNA Aptamer-based biosensing'

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Hou, Ting, Wei Li, Lianfang Zhang, and Feng Li. "A versatile and highly sensitive homogeneous electrochemical strategy based on the split aptamer binding-induced DNA three-way junction and exonuclease III-assisted target recycling." Analyst 140, no. 16 (2015): 5748–53. http://dx.doi.org/10.1039/c5an01176k.

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A versatile and highly sensitive homogeneous electrochemical biosensing platform has been developed for an ATP assay based on split aptamer binding-induced DNA three-way junction formation and Exo III-assisted target recycling.

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Zhou, Dejian. "Quantum dot–nucleic acid/aptamer bioconjugate-based fluorimetric biosensors." Biochemical Society Transactions 40, no. 4 (July 20, 2012): 635–39. http://dx.doi.org/10.1042/bst20120059.

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Over the last 10 years, fluorescent semiconductor QD (quantum dot)–biomolecule conjugates have emerged as a powerful new sensing platform showing great potential in a wide range of applications in biosensing, environmental monitoring and disease diagnosis. The present mini-review is a brief account of the recent developments in QD–NA (nucleic acid), particularly NA aptamer, conjugate-based biosensors using the FRET (Förster resonance energy transfer) readout mechanism. It starts with a brief introduction to the NA aptamer and QD-FRET, followed by example approaches to compact QD–DNA conjugates, target readout strategies and sensing performance, and concludes with challenges and outlook for the QD–NA/aptamer bioconjugate sensors.

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Lam, Sin Yu, Hill Lam Lau, and Chun Kit Kwok. "Capture-SELEX: Selection Strategy, Aptamer Identification, and Biosensing Application." Biosensors 12, no. 12 (December 7, 2022): 1142. http://dx.doi.org/10.3390/bios12121142.

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Small-molecule contaminants, such as antibiotics, pesticides, and plasticizers, have emerged as one of the substances most detrimental to human health and the environment. Therefore, it is crucial to develop low-cost, user-friendly, and portable biosensors capable of rapidly detecting these contaminants. Antibodies have traditionally been used as biorecognition elements. However, aptamers have recently been applied as biorecognition elements in aptamer-based biosensors, also known as aptasensors. The systematic evolution of ligands by exponential enrichment (SELEX) is an in vitro technique used to generate aptamers that bind their targets with high affinity and specificity. Over the past decade, a modified SELEX method known as Capture-SELEX has been widely used to generate DNA or RNA aptamers that bind small molecules. In this review, we summarize the recent strategies used for Capture-SELEX, describe the methods commonly used for detecting and characterizing small-molecule–aptamer interactions, and discuss the development of aptamer-based biosensors for various applications. We also discuss the challenges of the Capture-SELEX platform and biosensor development and the possibilities for their future application.

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Trunzo, Nevina E., and Ka Lok Hong. "Recent Progress in the Identification of Aptamers Against Bacterial Origins and Their Diagnostic Applications." International Journal of Molecular Sciences 21, no. 14 (July 18, 2020): 5074. http://dx.doi.org/10.3390/ijms21145074.

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Aptamers have gained an increasing role as the molecular recognition element (MRE) in diagnostic assay development, since their first conception thirty years ago. The process to screen for nucleic acid-based binding elements (aptamers) was first described in 1990 by the Gold Laboratory. In the last three decades, many aptamers have been identified for a wide array of targets. In particular, the number of reports on investigating single-stranded DNA (ssDNA) aptamer applications in biosensing and diagnostic platforms have increased significantly in recent years. This review article summarizes the recent (2015 to 2020) progress of ssDNA aptamer research on bacteria, proteins, and lipids of bacterial origins that have implications for human infections. The basic process of aptamer selection, the principles of aptamer-based biosensors, and future perspectives will also be discussed.

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Hu, Yingxin, Zhiyu Wang, Zhekun Chen, and Linqiang Pan. "Switching the activity of Taq polymerase using clamp-like triplex aptamer structure." Nucleic Acids Research 48, no. 15 (July 9, 2020): 8591–600. http://dx.doi.org/10.1093/nar/gkaa581.

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Abstract In nature, allostery is the principal approach for regulating cellular processes and pathways. Inspired by nature, structure-switching aptamer-based nanodevices are widely used in artificial biotechnologies. However, the canonical aptamer structures in the nanodevices usually adopt a duplex form, which limits the flexibility and controllability. Here, a new regulating strategy based on a clamp-like triplex aptamer structure (CLTAS) was proposed for switching DNA polymerase activity via conformational changes. It was demonstrated that the polymerase activity could be regulated by either adjusting structure parameters or dynamic reactions including strand displacement or enzymatic digestion. Compared with the duplex aptamer structure, the CLTAS possesses programmability, excellent affinity and high discrimination efficiency. The CLTAS was successfully applied to distinguish single-base mismatches. The strategy expands the application scope of triplex structures and shows potential in biosensing and programmable nanomachines.

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Li, Sen, Defu He, Shuning Li, Ruipeng Chen, Yuan Peng, Shuang Li, Dianpeng Han, et al. "Magnetic Halloysite Nanotube-Based SERS Biosensor Enhanced with Au@Ag Core–Shell Nanotags for Bisphenol A Determination." Biosensors 12, no. 6 (June 2, 2022): 387. http://dx.doi.org/10.3390/bios12060387.

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Bisphenol A (BPA) has emerged as a contaminant of concern because long-term exposure may affect the human endocrine system. Herein, a novel aptamer sensor based on magnetic separation and surface-enhanced Raman scattering (SERS) is proposed for the extremely sensitive and specific detection of trace BPA. Moreover, the capture unit was prepared by immobilizing thiolated (SH)-BPA aptamer complementary DNA on AuNP-coated magnetic halloysite nanotubes (MNTs@AuNPs), and SH-BPA aptamer-modified Au@4-MBA@Ag core–shell SERS nanotags acted as signal units. By the complementary pairing of the BPA aptamer and the corresponding DNA, MNTs@AuNPs and Au@4-MBA@AgCS were linked together through hybridization-ligation, which acted as the SERS substrate. In the absence of BPA, the constructed aptamer sensor generated electromagnetic enhancement and plasmon coupling to improve the sensitivity of SERS substrates. Owing to the high affinity between BPA and the aptamer, the aptamer probe bound to BPA was separated from the capture unit by an externally-induced magnetic field. Thus, the Raman intensity of the MNTs@AuNP-Ag@AuCS core–satellite assemblies was negatively correlated with the BPA concentration. High sensitivity measurements of BPA might be performed by determining the decline in SERS signal strength together with concentration variations. The proposed aptasensor is a promising biosensing platform for BPA detection.

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Zhang, Song Bai, Pei Zhen Han, Ping Lu, Xia Hu, Li Ying Zheng, Xue Wen Liu, Guang Yu Shen, Ji Lin Lu, Li Ping Qiu, and Shi Biao Zhou. "Reusable Electrochemical Aptasensor for Sensitive Detection of Small Molecules Based on Structure-Switching Hairpin Probe." Advanced Materials Research 791-793 (September 2013): 988–91. http://dx.doi.org/10.4028/www.scientific.net/amr.791-793.988.

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A reusable electrochemical biosensing strategy based on structure-switching hairpin probe for the detection of small molecules is proposed using cocaine as the model analyte. Aptamer probe hybridized with the immobilized signal probe to form DNA duplex. When target small molecule was added, competition between target molecule and the signal probe with the aptamer probe happened, which induced the signal probe from stretched duplex to hairpin structure. By measuring ac current voltammetry, the target molecule can be sensitively detected in a linear dynamic range from 1 nM-1000 nM with a low detection limit of 0.7 nM. In particular, the biosensor can be easily regenerated by melting in hot water, making it reusable.

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Hsieh, Pi-Chou, Hui-Ting Lin, Wen-Yih Chen, Jeffrey J. P. Tsai, and Wen-Pin Hu. "The Combination of Computational and Biosensing Technologies for Selecting Aptamer against Prostate Specific Antigen." BioMed Research International 2017 (2017): 1–11. http://dx.doi.org/10.1155/2017/5041683.

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Herein, we report a method of combining bioinformatics and biosensing technologies to select aptamers against prostate specific antigen (PSA). The main objective of this study is to select DNA aptamers with higher binding affinity for PSA by using the proposed method. Based on the five known sequences of PSA-binding aptamers, we adopted the functions of reproduction and crossover in the genetic algorithm to produce next-generation sequences for the computational and experimental analysis. RNAfold web server was utilized to analyze the secondary structures, and the 3-dimensional molecular models of aptamer sequences were generated by using RNAComposer web server. ZRANK scoring function was used to rerank the docking predictions from ZDOCK. The biosensors, the quartz crystal microbalance (QCM) and a surface plasmon resonance (SPR) instrument, were used to verify the binding ability of selected aptamer for PSA. By carrying out the simulations and experiments after two generations, we obtain one aptamer that can have the highest binding affinity with PSA, which generates almost 2-fold and 3-fold greater measured signals than the responses produced by the best known DNA sequence in the QCM and SPR experiments, respectively.

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Xu, Ruiting, Leixin Ouyang, Heyi Chen, Ge Zhang, and Jiang Zhe. "Recent Advances in Biomolecular Detection Based on Aptamers and Nanoparticles." Biosensors 13, no. 4 (April 13, 2023): 474. http://dx.doi.org/10.3390/bios13040474.

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The fast, accurate detection of biomolecules, ranging from nucleic acids and small molecules to proteins and cellular secretions, plays an essential role in various biomedical applications. These include disease diagnostics and prognostics, environmental monitoring, public health, and food safety. Aptamer recognition (DNA or RNA) has gained extensive attention for biomolecular detection due to its high selectivity, affinity, reproducibility, and robustness. Concurrently, biosensing with nanoparticles has been widely used for its high carrier capacity, stability and feasibility of incorporating optical and catalytic activity, and enhanced diffusivity. Biosensors based on aptamers and nanoparticles utilize the combination of their advantages and have become a promising technology for detecting of a wide variety of biomolecules with high sensitivity, reliability, specificity, and detection speed. Via various sensing mechanisms, target biomolecules have been quantified in terms of optical (e.g., colorimetric and fluorometric), magnetic, and electrical signals. In this review, we summarize the recent advances in and compare different aptamer–nanoparticle-based biosensors by nanoparticle types and detection mechanisms. We also share our views on the highlights and challenges of the different nanoparticle-aptamer-based biosensors.

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Grechkin, Yaroslav A., Svetlana L. Grechkina, Emil A. Zaripov, Svetlana V. Fedorenko, Asiya R. Mustafina, and Maxim V. Berezovski. "Aptamer-Conjugated Tb(III)-Doped Silica Nanoparticles for Luminescent Detection of Leukemia Cells." Biomedicines 8, no. 1 (January 13, 2020): 14. http://dx.doi.org/10.3390/biomedicines8010014.

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DNA aptamers have many benefits for cell imaging, such as high affinity and specificity, easiness of chemical functionalization, and low cost of production. Among known aptamers, Sgc8-aptamer was selected against acute lymphoblastic leukemia cells with a dissociation constant in a nanomolar range. The aptamer was previously used for the covalent coupling with fluorescent and magnetic nanoparticles, as well as for the fabrication of aptamer-based biosensors. Among commonly used fluorescent tags, lanthanide nanoparticles offer stable luminescence with narrow, well-resolved emission peaks and the absence of photoblinking. In other words, lanthanide nanoparticles could serve as luminescence reporters and be used in biosensing. In our study, we conjugated amino- and carboxyl-modified silica-coated terbium (III) thiacalix[4]arenesulfonate luminescent nanoparticles with Sgc8-aptamer and showed the ability of the aptamer-conjugated nanoparticles to detect leukemia cells using fluorescence microscopy. In addition, we conducted a cell viability assay and confirmed that the nanoparticles do not induce spontaneous cell apoptosis or necrosis and could be potentially used for bioimaging applications.

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Wang, Wenxiao, Lei Ge, Ximei Sun, Ting Hou, and Feng Li. "Graphene-Assisted Label-Free Homogeneous Electrochemical Biosensing Strategy based on Aptamer-Switched Bidirectional DNA Polymerization." ACS Applied Materials & Interfaces 7, no. 51 (December 17, 2015): 28566–75. http://dx.doi.org/10.1021/acsami.5b09932.

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Hong, Ka Lok, and Letha J. Sooter. "Single-Stranded DNA Aptamers against Pathogens and Toxins: Identification and Biosensing Applications." BioMed Research International 2015 (2015): 1–31. http://dx.doi.org/10.1155/2015/419318.

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Molecular recognition elements (MREs) can be short sequences of single-stranded DNA, RNA, small peptides, or antibody fragments. They can bind to user-defined targets with high affinity and specificity. There has been an increasing interest in the identification and application of nucleic acid molecular recognition elements, commonly known as aptamers, since they were first described in 1990 by the Gold and Szostak laboratories. A large number of target specific nucleic acids MREs and their applications are currently in the literature. This review first describes the general methodologies used in identifying single-stranded DNA (ssDNA) aptamers. It then summarizes advancements in the identification and biosensing application of ssDNA aptamers specific for bacteria, viruses, their associated molecules, and selected chemical toxins. Lastly, an overview of the basic principles of ssDNA aptamer-based biosensors is discussed.

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Torelli, Emanuela, Ben Shirt-Ediss, Silvia A. Navarro, Marisa Manzano, Priya Vizzini, and Natalio Krasnogor. "Light-Up Split Broccoli Aptamer as a Versatile Tool for RNA Assembly Monitoring in Cell-Free TX-TL Systems, Hybrid RNA/DNA Origami Tagging and DNA Biosensing." International Journal of Molecular Sciences 24, no. 10 (May 9, 2023): 8483. http://dx.doi.org/10.3390/ijms24108483.

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Binary light-up aptamers are intriguing and emerging tools with potential in different fields. Herein, we demonstrate the versatility of a split Broccoli aptamer system able to turn on the fluorescence signal only in the presence of a complementary sequence. First, an RNA three-way junction harbouring the split system is assembled in an E. coli-based cell-free TX-TL system where the folding of the functional aptamer is demonstrated. Then, the same strategy is introduced into a ‘bio-orthogonal’ hybrid RNA/DNA rectangle origami characterized by atomic force microscopy: the activation of the split system through the origami self-assembly is demonstrated. Finally, our system is successfully used to detect the femtomoles of a Campylobacter spp. DNA target sequence. Potential applications of our system include the real-time monitoring of the self-assembly of nucleic-acid-based devices in vivo and of the intracellular delivery of therapeutic nanostructures, as well as the in vitro and in vivo detection of different DNA/RNA targets.

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Zhang, Xiaojuan, Yun Gao, Bowen Deng, Bo Hu, Luming Zhao, Han Guo, Chengfang Yang, et al. "Selection, Characterization, and Optimization of DNA Aptamers against Challenging Marine Biotoxin Gymnodimine-A for Biosensing Application." Toxins 14, no. 3 (March 5, 2022): 195. http://dx.doi.org/10.3390/toxins14030195.

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Gymnodimines (GYMs), belonging to cyclic imines (CIs), are characterized as fast-acting toxins, and may pose potential risks to human health and the aquaculture industry through the contamination of sea food. The existing detection methods of GYMs have certain defects in practice, such as ethical problems or the requirement of complicated equipment. As novel molecular recognition elements, aptamers have been applied in many areas, including the detection of marine biotoxins. However, GYMs are liposoluble molecules with low molecular weight and limited numbers of chemical groups, which are considered as “challenging” targets for aptamers selection. In this study, Capture-SELEX was used as the main strategy in screening aptamers targeting gymnodimine-A (GYM-A), and an aptamer named G48nop, with the highest KD value of 95.30 nM, was successfully obtained by screening and optimization. G48nop showed high specificity towards GYM-A. Based on this, a novel aptasensor based on biolayer interferometry (BLI) technology was established in detecting GYM-A. This aptasensor showed a detection range from 55 to 1400 nM (linear range from 55 to 875 nM) and a limit of detection (LOD) of 6.21 nM. Spiking experiments in real samples indicated the recovery rate of this aptasensor, ranging from 96.65% to 109.67%. This is the first study to report an aptamer with high affinity and specificity for the challenging marine biotoxin GYM-A, and the new established aptasensor may be used as a reliable and efficient tool for the detection and monitoring of GYMs in the future.

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Kooshki, Hamid, Roya Abbaszadeh, Reza Heidari, Mostafa Akbariqomi, Mohamadali Mazloumi, Shilan Shafei, Moloud Absalan, and Gholamreza Tavoosidana. "Developing a DNA aptamer-based approach for biosensing cystatin-c in serum: An alternative to antibody-based methods." Analytical Biochemistry 584 (November 2019): 113386. http://dx.doi.org/10.1016/j.ab.2019.113386.

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Geng, Weifu, Yan Feng, Yu Chen, Xin Zhang, Haoyi Zhang, Fanfan Yang, and Xiuzhong Wang. "Interactions of Amino Group Functionalized Tetraphenylvinyl and DNA: A Label-Free “On-Off-On” Fluorescent Aptamer Sensor toward Ampicillin." Biosensors 13, no. 5 (April 27, 2023): 504. http://dx.doi.org/10.3390/bios13050504.

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As a type of aggregation-induced emission (AIE) fluorescent probe, tetraphenylvinyl (TPE) or its derivatives are widely used in chemical imaging, biosensing and medical diagnosis. However, most studies have focused on molecular modification and functionalization of AIE to enhance the fluorescence emission intensity. There are few studies on the interaction between aggregation-induced emission luminogens (AIEgens) and nucleic acids, which was investigated in this paper. Experimental results showed the formation of a complex of AIE/DNA, leading to the quenching of the fluorescence of AIE molecules. Fluorescent test experiments with different temperatures proved that the quenching type was static quenching. The quenching constants, binding constants and thermodynamic parameters demonstrated that electrostatic and hydrophobic interactions promoted the binding process. Then, a label-free “on-off-on” fluorescent aptamer sensor for the detection of ampicillin (AMP) was constructed based on the interaction between the AIE probe and the aptamer of AMP. Linear range of the sensor is 0.2–10 nM with a limit of detection 0.06 nM. This fluorescent sensor was applied to detect AMP in real samples.

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Li, Zhanhong, Mona A. Mohamed, A. M. Vinu Mohan, Zhigang Zhu, Vinay Sharma, Geetesh K. Mishra, and Rupesh K. Mishra. "Application of Electrochemical Aptasensors toward Clinical Diagnostics, Food, and Environmental Monitoring: Review." Sensors 19, no. 24 (December 10, 2019): 5435. http://dx.doi.org/10.3390/s19245435.

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Aptamers are synthetic bio-receptors of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) origin selected by the systematic evolution of ligands (SELEX) process that bind a broad range of target analytes with high affinity and specificity. So far, electrochemical biosensors have come up as a simple and sensitive method to utilize aptamers as a bio-recognition element. Numerous aptamer based sensors have been developed for clinical diagnostics, food, and environmental monitoring and several other applications are under development. Aptasensors are capable of extending the limits of current analytical techniques in clinical diagnostics, food, and environmental sample analysis. However, the potential applications of aptamer based electrochemical biosensors are unlimited; current applications are observed in the areas of food toxins, clinical biomarkers, and pesticide detection. This review attempts to enumerate the most representative examples of research progress in aptamer based electrochemical biosensing principles that have been developed in recent years. Additionally, this account will discuss various current developments on aptamer-based sensors toward heavy metal detection, for various cardiac biomarkers, antibiotics detection, and also on how the aptamers can be deployed to couple with antibody-based assays as a hybrid sensing platform. Aptamers can be used in various applications, however, this account will focus on the recent advancements made toward food, environmental, and clinical diagnostic application. This review paper compares various electrochemical aptamer based sensor detection strategies that have been applied so far and used as a state of the art. As illustrated in the literature, aptamers have been utilized extensively for environmental, cancer biomarker, biomedical application, and antibiotic detection and thus have been extensively discussed in this article.

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Gavrilaș, Simona, Claudiu Ștefan Ursachi, Simona Perța-Crișan, and Florentina-Daniela Munteanu. "Recent Trends in Biosensors for Environmental Quality Monitoring." Sensors 22, no. 4 (February 15, 2022): 1513. http://dx.doi.org/10.3390/s22041513.

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The monitoring of environmental pollution requires fast, reliable, cost-effective and small devices. This need explains the recent trends in the development of biosensing devices for pollutant detection. The present review aims to summarize the newest trends regarding the use of biosensors to detect environmental contaminants. Enzyme, whole cell, antibody, aptamer, and DNA-based biosensors and biomimetic sensors are discussed. We summarize their applicability to the detection of various pollutants and mention their constructive characteristics. Several detection principles are used in biosensor design: amperometry, conductometry, luminescence, etc. They differ in terms of rapidity, sensitivity, profitability, and design. Each one is characterized by specific selectivity and detection limits depending on the sensitive element. Mimetic biosensors are slowly gaining attention from researchers and users due to their advantages compared with classical ones. Further studies are necessary for the development of robust biosensing devices that can successfully be used for the detection of pollutants from complex matrices without prior sample preparation.

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Xing, Hu, Yiting Zhang, Markus Krämer, Ann-Kathrin Kissmann, Marius Henkel, Tanja Weil, Uwe Knippschild, and Frank Rosenau. "A Polyclonal Selex Aptamer Library Directly Allows Specific Labelling of the Human Gut Bacterium Blautia producta without Isolating Individual Aptamers." Molecules 27, no. 17 (September 3, 2022): 5693. http://dx.doi.org/10.3390/molecules27175693.

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Recent studies have demonstrated that changes in the abundance of the intestinal bacterium Blautia producta, a potential probiotic, are closely associated with the development of various diseases such as obesity, diabetes, some neurodegenerative diseases, and certain cancers. However, there is still a lack of an effective method to detect the abundance of B. producta in the gut rapidly. Especially, DNA aptamers are now widely used as biometric components for medical testing due to their unique characteristics, including high chemical stability, low production cost, ease of chemical modification, low immunogenicity, and fast reproducibility. We successfully obtained a high-affinity nucleic acid aptamer library (B.p-R14) after 14 SELEX rounds, which efficiently discriminates B. producta in different analysis techniques including fluorometric suspension assays or fluorescence microscopy from other major gut bacteria in complex mixtures and even in human stool samples. These preliminary findings will be the basis towards aptamer-based biosensing applications for the fast and reliable monitoring of B. producta in the human gut microbiome.

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Goldsworthy, Victoria, Geneva LaForce, Seth Abels, and Emil Khisamutdinov. "Fluorogenic RNA Aptamers: A Nano-platform for Fabrication of Simple and Combinatorial Logic Gates." Nanomaterials 8, no. 12 (November 28, 2018): 984. http://dx.doi.org/10.3390/nano8120984.

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RNA aptamers that bind non-fluorescent dyes and activate their fluorescence are highly sensitive, nonperturbing, and convenient probes in the field of synthetic biology. These RNA molecules, referred to as light-up aptamers, operate as molecular nanoswitches that alter folding and fluorescence function in response to ligand binding, which is important in biosensing and molecular computing. Herein, we demonstrate a conceptually new generation of smart RNA nano-devices based on malachite green (MG)-binding RNA aptamer, which fluorescence output controlled by addition of short DNA oligonucleotides inputs. Four types of RNA switches possessing AND, OR, NAND, and NOR Boolean logic functions were created in modular form, allowing MG dye binding affinity to be changed by altering 3D conformation of the RNA aptamer. It is essential to develop higher-level logic circuits for the production of multi-task nanodevices for data processing, typically requiring combinatorial logic gates. Therefore, we further designed and synthetized higher-level half adder logic circuit by “in parallel” integration of two logic gates XOR and AND within a single RNA nanoparticle. The design utilizes fluorescence emissions from two different RNA aptamers: MG-binding RNA aptamer (AND gate) and Broccoli RNA aptamer that binds DFHBI dye (XOR gate). All computationally designed RNA devices were synthesized and experimentally tested in vitro. The ability to design smart nanodevices based on RNA binding aptamers offers a new route to engineer “label-free” ligand-sensing regulatory circuits, nucleic acid detection systems, and gene control elements.

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Khan, Niazul I., and Edward Song. "Detection of an IL-6 Biomarker Using a GFET Platform Developed with a Facile Organic Solvent-Free Aptamer Immobilization Approach." Sensors 21, no. 4 (February 13, 2021): 1335. http://dx.doi.org/10.3390/s21041335.

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Aptamer-immobilized graphene field-effect transistors (GFETs) have become a well-known detection platform in the field of biosensing with various biomarkers such as proteins, bacteria, virus, as well as chemicals. A conventional aptamer immobilization technique on graphene involves a two-step crosslinking process. In the first step, a pyrene derivative is anchored onto the surface of graphene and, in the second step, an amine-terminated aptamer is crosslinked to the pyrene backbone with EDC/NHS (1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride/N-hydroxysuccinimide) chemistry. However, this process often requires the use of organic solvents such as dimethyl formamide (DMF) or dimethyl sulfoxide (DMSO) which are typically polar aprotic solvents and hence dissolves both polar and nonpolar compounds. The use of such solvents can be especially problematic in the fabrication of lab-on-a-chip or point-of-care diagnostic platforms as they can attack vulnerable materials such as polymers, passivation layers and microfluidic tubing leading to device damage and fluid leakage. To remedy such challenges, in this work, we demonstrate the use of pyrene-tagged DNA aptamers (PTDA) for performing a one-step aptamer immobilization technique to implement a GFET-based biosensor for the detection of Interleukin-6 (IL-6) protein biomarker. In this approach, the aptamer terminal is pre-tagged with a pyrene group which becomes soluble in aqueous solution. This obviates the need for using organic solvents, thereby enhancing the device integrity. In addition, an external electric field is applied during the functionalization step to increase the efficiency of aptamer immobilization and hence improved coverage and density. The results from this work could potentially open up new avenues for the use of GFET-based BioMEMS platforms by broadening the choice of materials used for device fabrication and integration.

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Zhang, Qingqing, Tingting Hao, Dandan Hu, Zhiyong Guo, Sui Wang, and Yufang Hu. "RNA aptamer-driven ECL biosensing for tracing histone acetylation based on nano-prism substrate and cascade DNA amplification strategy." Electrochimica Acta 356 (October 2020): 136828. http://dx.doi.org/10.1016/j.electacta.2020.136828.

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WANG, LIHUA, YANYAN WANG, JIE ZOU, BIN LIU, and CHUNHAI FAN. "AMPLIFIED BIOSENSING STRATEGIES FOR THE DETECTION OF BIOLOGICALLY RELATED MOLECULES WITH SILICA NANOPARTICLES AND CONJUGATED POLYELECTROLYTES." COSMOS 06, no. 02 (December 2010): 207–19. http://dx.doi.org/10.1142/s0219607710000565.

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Development of rapid, field-portable and cost-effective sensors with high sensitivity and selectivity is of great importance for biomedical diagnostics, food safety and environmental monitoring. Silica nanoparticles (SiNPs) have great potential in sensor application due to their biocompatibility, controllable surface modification, excellent chemical stability and high specific surface area. On the other hand, conjugated polyelectrolytes (CPEs) have been widely used in sensor design due to their efficient Förster resonance energy transfer (FRET) to dyes and unique interaction with biomolecules. In this contribution, we briefly summarize the recent development of silica-related NP-based assays that incorporate CPEs as the signal amplifier or reporter. The silica-related NPs are used for probe immobilization, target recognition and separation, while CPEs provide amplified fluorescence signals and high sensitivity. These assays have been proven efficient for the detection of DNA, proteins, and small molecules through specific biorecognition events, such as DNA hybridization, antibody–antigen recognition and target–aptamer binding.

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Ogurcovs, Andrejs, Kevon Kadiwala, Eriks Sledevskis, Marina Krasovska, Ilona Plaksenkova, and Edgars Butanovs. "Effect of DNA Aptamer Concentration on the Conductivity of a Water-Gated Al:ZnO Thin-Film Transistor-Based Biosensor." Sensors 22, no. 9 (April 29, 2022): 3408. http://dx.doi.org/10.3390/s22093408.

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Field-effect transistor-based biosensors (bio-FETs) are promising candidates for the rapid high-sensitivity and high-selectivity sensing of various analytes in healthcare, clinical diagnostics, and the food industry. However, bio-FETs still have several unresolved problems that hinder their technological transfer, such as electrical stability. Therefore, it is important to develop reliable, efficient devices and establish facile electrochemical characterization methods. In this work, we have fabricated a flexible biosensor based on an Al:ZnO thin-film transistor (TFT) gated through an aqueous electrolyte on a polyimide substrate. In addition, we demonstrated techniques for establishing the operating range of such devices. The Al:ZnO-based devices with a channel length/width ratio of 12.35 and a channel thickness of 50 nm were produced at room temperature via magnetron sputtering. These Al:ZnO-based devices exhibited high field-effect mobility (μ = 6.85 cm2/Vs) and threshold voltage (Vth = 654 mV), thus showing promise for application on temperature-sensitive substrates. X-ray photoelectron spectroscopy was used to verify the chemical composition of the deposited films, while the morphological aspects of the films were assessed using scanning electron and atomic force microscopies. The gate–channel electric capacitance of 40 nF/cm2 was determined using electrochemical impedance spectroscopy, while the electrochemical window of the gate–channel system was determined as 1.8 V (from −0.6 V to +1.2 V) using cyclic voltammetry. A deionized water solution of 10 mer (CCC AAG GTC C) DNA aptamer (molar weight −2972.9 g/mol) in a concentration ranging from 1–1000 pM/μL was used as an analyte. An increase in aptamer concentration caused a proportional decrease in the TFT channel conductivity. The techniques demonstrated in this work can be applied to optimize the operating parameters of various semiconductor materials in order to create a universal detection platform for biosensing applications, such as multi-element FET sensor arrays based on various composition nanostructured films, which use advanced neural network signal processing.

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Zheng, Yue, Xiaoyu Wang, Shengquan He, Zehua Gao, Ya Di, Kunling Lu, Kun Li, and Jidong Wang. "Aptamer-DNA concatamer-quantum dots based electrochemical biosensing strategy for green and ultrasensitive detection of tumor cells via mercury-free anodic stripping voltammetry." Biosensors and Bioelectronics 126 (February 2019): 261–68. http://dx.doi.org/10.1016/j.bios.2018.09.076.

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Shamsipur, Mojtaba, Karam Molaei, Fatemeh Molaabasi, Saman Hosseinkhani, Avat Taherpour, Morteza Sarparast, Seyyed Ebrahim Moosavifard, and Ali Barati. "Aptamer-Based Fluorescent Biosensing of Adenosine Triphosphate and Cytochrome c via Aggregation-Induced Emission Enhancement on Novel Label-Free DNA-Capped Silver Nanoclusters/Graphene Oxide Nanohybrids." ACS Applied Materials & Interfaces 11, no. 49 (November 13, 2019): 46077–89. http://dx.doi.org/10.1021/acsami.9b14487.

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Shamsipur, Mojtaba, Karam Molaei, Fatemeh Molaabasi, Saman Hosseinkhani, Avat Taherpour, Morteza Sarparast, Seyyed Ebrahim Moosavifard, and Ali Barati. "Correction to “Aptamer-Based Fluorescent Biosensing of Adenosine Triphosphate and Cytochrome c via Aggregation-Induced Emission Enhancement on Novel Label-Free DNA-Capped Silver Nanoclusters/Graphene Oxide Nanohybrids”." ACS Applied Materials & Interfaces 12, no. 33 (August 5, 2020): 37806. http://dx.doi.org/10.1021/acsami.0c13350.

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Palma, Matteo. "(Invited) Controlling CNT-Biomolecule Interfaces -and Their Orientation- to Tune Electrostatic Gating in CNT-Based Biosensing Devices." ECS Meeting Abstracts MA2022-01, no. 8 (July 7, 2022): 679. http://dx.doi.org/10.1149/ma2022-018679mtgabs.

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The development of novel bioelectronics interfaces via the bottom-up assembly of platforms capable of monitoring and exploiting biomolecular interactions with nanoscale control is a central challenge in nanobiotechnology. Biomolecular interactions can be used to electrostatically gate conductance in nanomaterials-based field effect transistors (FETs), but this can be exploited far more effectively than currently done by defining the interface between the biomolecule and the transducer. This strategy forms the basis of greatly improved electrical-based biosensors and offers great potential for building next generation biosensing devices. We will first present different approaches to control the assembly of carbon nanotube (CNT)-protein interfaces towards the fabrication of bioelectronic devices, with a particular focus on the development of real-time biosensors with engineered protein interfacing. We will report the construction of nanoscale protein-based sensing devices designed to present proteins in defined orientations; this allowed us to control the local electrostatic surface presented within the Debye length, and thus modulate the conductance gating effect upon binding incoming protein targets.[1] We systematically tested how protein orientation dictates current response through a CNT-FET device by defining the interface site on the capture protein. Presentation of different protein-protein electrostatic surfaces within the Debye length led either to increase or decrease in conductance: defined and homogenous attachment allows distinctive conductance profiles to be sampled based on the unique electrostatic features of individual proteins, and can support the identification of preferred proteins orientations for optimal sensing. In our case this was done for the detection of a range of concentrations of a class b-lactamase enzymes, that degrade antibiotics, in the context of investigating antimicrobial resistance (AMR). Additionally, we will present the controlled assembly of CNT–GFP hybrids employing DNA as a linker, with protein attachment occurring predominantly at the terminal ends of the nanotubes, as designed.[2] The electronic coupling of the proteins to the nanotubes was confirmed via in-solution fluorescence spectroscopy, that revealed an increase in the emission intensity of GFP when linked to the CNTs. The strategies presented here are of general applicability for the controlled assembly of CNT-protein interfaces toward biosensing and optoelectronics applications. Finally, we will report the tuning of electrostatically gated conductance changes in CNT-aptamer biosensing FETs. We have developed diverse strategies for the construction of such nanoscale devices via in-solution assembly and (self)organization on surfaces. We will discuss how this can lead to distinct conformational changes of the CNT-bound aptamers upon biomarker recognition , leading to opposite electrical response of our biosensors , i.e. increase or decrease in current.[3] These studies highlight the need to define CNT-biomolecule interfaces in order to control and tune by design the electrostatic gating in CNT-based devices, toward the construction of optimized biosensors. [1] Angew. Chem. Int. Ed. 2021, 60, 20184 –20189 [2] Biomolecules 2021, 11(7), 955 [3] in preparation

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Easley, Christopher J. "(Invited) Fast and Generalizable Electrochemical Sensing of Small Molecules, Peptides, and Proteins Using a Nucleic Acid Nanostructure with Analyte-DNA Conjugates." ECS Meeting Abstracts MA2022-01, no. 53 (July 7, 2022): 2233. http://dx.doi.org/10.1149/ma2022-01532233mtgabs.

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Sensors based on electrochemical (EC) readout offer low cost, miniaturization, and adaptability to the point-of-care (POC). Nonetheless, most EC sensors are specialized to a particular target, and there remains a need for a robust EC biosensor platform for the multitude of biomarkers that are not EC-active, do not undergo enzymatic conversion, or are not suited for potentiometry [1,2]. Impressively, aptamer-based EC sensors have been proven for sensing in living animals with temporal resolution as low as a few seconds [3], yet most method development has been target-focused, lacking generalizability [4]. Presently, the clinical EC toolbox is a conglomerate of targeted methods, and there is a pressing need to develop an EC platform amenable to rapid, generalizable, quantitative readout of multiple classes of clinically relevant targets. Direct EC sensing without added reagents or amplification steps should be ideal for this purpose. For example, the Kelley group recently developed a reagentless “molecular pendulum” EC sensor for a broad range of protein analytes [5]. Our group has been working to address this need and expand to more analyte classes for several years, and in 2019 we designed a versatile DNA-nanostructure architecture attached to gold electrode surfaces [6]. Initially, our sensors were validated with biotechnology controls, antibodies, and with a small molecule immunomodulatory drug in human serum. In this presentation, we discuss the expansion of the generalizability of our sensor platform, chiefly through custom synthesis of varied DNA-analyte bioconjugates to incorporate within the DNA-nanostructure. For peptide sensing, DNA-peptide conjugates were synthesized, purified, then ligated to the DNA-nanostructure. Sensors were validated for quantifying exendin-4 (4.2 kDa)—a human glucagon-like peptide-1 receptor agonist important in diabetes therapy—for the first time using direct EC methods, with an LOD of 6 nM [7]. Sensors for larger proteins were made using DNA-epitope conjugates. The antibody-binding epitope of creatine kinase MM (CK-MM) was conjugated into the nanostructure, allowing CK-MM sensing in the 10 to 100 nM range. Finally, DNA-steroid bioconjugates have been incorporated into the sensors. Sensing of testosterone throughout the clinically relevant range (for males) was accomplished from 1 to 50 nM (LOD of 0.9 nM), and cortisol could be easily detected in the 1 to 100 nM range, well below the 90 – 550 nM range in blood and nicely encompassing the 6 – 75 nM range in saliva. All of these sensors were functional in 98% human serum, and several detection ranges overlap with the clinical/therapeutic ranges, boding well for future applications in biosensing or therapeutic drug monitoring. Overall, this new DNA nanostructure platform provides a generalizable sensor with minimal workflow, direct-readout, and the capability to expand EC sensing to a wide variety of clinically important analytes. References: Turner, A. P., Chemical Society Reviews 2013, 42 (8), 3184-96. Wilson, G. S.; Johnson, M. A., Chem. Reviews 2008, 108 (7), 2462-81. Idili, A.; Gerson, J.; Kippin, T.; Plaxco, K. W., Anal. Chem. 2021, 93, 4023-32. Labib, M.; Sargent, E. H.; Kelley, S. O., Chem. Reviews 2016, 116 (16), 9001-90. Das, J.; Gomis, S.; Chen, J. B.; Yousefi, H.; Ahmed, S.; Mahmud, A.; Zhou, W.; Sargent, E. H.; Kelley, S. O., Nature Chem. 2021, 13 (5), 428-434. Somasundaram, S.; Easley, C. J., J. Am. Chem. Soc. 2019, 141, 11721-11726. Khuda, N; Somasundaram, S.; Easley, C. J., ACS Sensors 2021, under revision.

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Onaş, Andra Mihaela, Constanţa Dascălu, Matei D. Raicopol, and Luisa Pilan. "Critical Design Factors for Electrochemical Aptasensors Based on Target-Induced Conformational Changes: The Case of Small-Molecule Targets." Biosensors 12, no. 10 (October 1, 2022): 816. http://dx.doi.org/10.3390/bios12100816.

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Nucleic-acid aptamers consisting in single-stranded DNA oligonucleotides emerged as very promising biorecognition elements for electrochemical biosensors applied in various fields such as medicine, environmental, and food safety. Despite their outstanding features, such as high-binding affinity for a broad range of targets, high stability, low cost and ease of modification, numerous challenges had to be overcome from the aptamer selection process on the design of functioning biosensing devices. Moreover, in the case of small molecules such as metabolites, toxins, drugs, etc., obtaining efficient binding aptamer sequences proved a challenging task given their small molecular surface and limited interactions between their functional groups and aptamer sequences. Thus, establishing consistent evaluation standards for aptamer affinity is crucial for the success of these aptamers in biosensing applications. In this context, this article will give an overview on the thermodynamic and structural aspects of the aptamer-target interaction, its specificity and selectivity, and will also highlight the current methods employed for determining the aptamer-binding affinity and the structural characterization of the aptamer-target complex. The critical aspects regarding the generation of aptamer-modified electrodes suitable for electrochemical sensing, such as appropriate bioreceptor immobilization strategy and experimental conditions which facilitate a convenient anchoring and stability of the aptamer, are also discussed. The review also summarizes some effective small molecule aptasensing platforms from the recent literature.

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Jolly, Pawan, Nello Formisano, and Pedro Estrela. "DNA aptamer-based detection of prostate cancer." Chemical Papers 69, no. 1 (January 1, 2015). http://dx.doi.org/10.1515/chempap-2015-0025.

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AbstractThe use of aptamers in biosensing has attracted considerable attention as an alternative to antibodies because of their unique properties such as long-term stability, cost-effectiveness and adjustability to various applications. Among cancers, the early diagnosis of prostate cancer (PCa) is one of the greatest concerns for ageing men worldwide. One of the most commonly used biomarkers for PCa is prostate-specific antigen (PSA), which can be found in elevated levels in patients with cancer. This review presents the gradual transition of research from antibody-based to aptamerbased biosensors, specifically for PSA. A brief description on aptamer-based biosensing for other PCa biomarkers is also presented. Special attention is given to electrochemical methods as analytical techniques for the development of simple, sensitive and cost-effective biosensors. The review also focuses on the different surface chemistries exploited for fabrication and their applications in clinical samples. The use of aptamers represents a promising tool for the development of point-ofcare biosensors for the early detection of prostate cancer. In view of the unmatched upper hand of aptamers, future prospects are also discussed, not only in the point-of-care format but also in other novel applications.

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Li, Yusi, Xia Li, Fang Yang, Ruo Yuan, and Yun Xiang. "Target-induced activation of polymerase activity for recycling signal amplification cascades for sensitive aptamer-based detection of biomarkers." Analyst, 2021. http://dx.doi.org/10.1039/d0an02288h.

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Kolm, Claudia, Isabella Cervenka, Ulrich J. Aschl, Niklas Baumann, Stefan Jakwerth, Rudolf Krska, Robert L. Mach, et al. "DNA aptamers against bacterial cells can be efficiently selected by a SELEX process using state-of-the art qPCR and ultra-deep sequencing." Scientific Reports 10, no. 1 (December 2020). http://dx.doi.org/10.1038/s41598-020-77221-9.

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AbstractDNA aptamers generated by cell-SELEX against bacterial cells have gained increased interest as novel and cost-effective affinity reagents for cell labelling, imaging and biosensing. Here we describe the selection and identification of DNA aptamers for bacterial cells using a combined approach based on cell-SELEX, state-of-the-art applications of quantitative real-time PCR (qPCR), next-generation sequencing (NGS) and bioinformatic data analysis. This approach is demonstrated on Enterococcus faecalis (E. faecalis), which served as target in eleven rounds of cell-SELEX with multiple subtractive counter-selections against non-target species. During the selection, we applied qPCR-based analyses to evaluate the ssDNA pool size and remelting curve analysis of qPCR amplicons to monitor changes in pool diversity and sequence enrichment. Based on NGS-derived data, we identified 16 aptamer candidates. Among these, aptamer EF508 exhibited high binding affinity to E. faecalis cells (KD-value: 37 nM) and successfully discriminated E. faecalis from 20 different Enterococcus and non-Enterococcus spp. Our results demonstrate that this combined approach enabled the rapid and efficient identification of an aptamer with both high affinity and high specificity. Furthermore, the applied monitoring and assessment techniques provide insight into the selection process and can be highly useful to study and improve experimental cell-SELEX designs to increase selection efficiency.

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Emami, Neda, and Reza Ferdousi. "AptaNet as a deep learning approach for aptamer–protein interaction prediction." Scientific Reports 11, no. 1 (March 16, 2021). http://dx.doi.org/10.1038/s41598-021-85629-0.

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AbstractAptamers are short oligonucleotides (DNA/RNA) or peptide molecules that can selectively bind to their specific targets with high specificity and affinity. As a powerful new class of amino acid ligands, aptamers have high potentials in biosensing, therapeutic, and diagnostic fields. Here, we present AptaNet—a new deep neural network—to predict the aptamer–protein interaction pairs by integrating features derived from both aptamers and the target proteins. Aptamers were encoded by using two different strategies, including k-mer and reverse complement k-mer frequency. Amino acid composition (AAC) and pseudo amino acid composition (PseAAC) were applied to represent target information using 24 physicochemical and conformational properties of the proteins. To handle the imbalance problem in the data, we applied a neighborhood cleaning algorithm. The predictor was constructed based on a deep neural network, and optimal features were selected using the random forest algorithm. As a result, 99.79% accuracy was achieved for the training dataset, and 91.38% accuracy was obtained for the testing dataset. AptaNet achieved high performance on our constructed aptamer-protein benchmark dataset. The results indicate that AptaNet can help identify novel aptamer–protein interacting pairs and build more-efficient insights into the relationship between aptamers and proteins. Our benchmark dataset and the source codes for AptaNet are available in: https://github.com/nedaemami/AptaNet.

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Ma, Wenjuan, Yuxi Zhan, Yuxin Zhang, Chenchen Mao, Xueping Xie, and Yunfeng Lin. "The biological applications of DNA nanomaterials: current challenges and future directions." Signal Transduction and Targeted Therapy 6, no. 1 (October 8, 2021). http://dx.doi.org/10.1038/s41392-021-00727-9.

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AbstractDNA, a genetic material, has been employed in different scientific directions for various biological applications as driven by DNA nanotechnology in the past decades, including tissue regeneration, disease prevention, inflammation inhibition, bioimaging, biosensing, diagnosis, antitumor drug delivery, and therapeutics. With the rapid progress in DNA nanotechnology, multitudinous DNA nanomaterials have been designed with different shape and size based on the classic Watson–Crick base-pairing for molecular self-assembly. Some DNA materials could functionally change cell biological behaviors, such as cell migration, cell proliferation, cell differentiation, autophagy, and anti-inflammatory effects. Some single-stranded DNAs (ssDNAs) or RNAs with secondary structures via self-pairing, named aptamer, possess the ability of targeting, which are selected by systematic evolution of ligands by exponential enrichment (SELEX) and applied for tumor targeted diagnosis and treatment. Some DNA nanomaterials with three-dimensional (3D) nanostructures and stable structures are investigated as drug carrier systems to delivery multiple antitumor medicine or gene therapeutic agents. While the functional DNA nanostructures have promoted the development of the DNA nanotechnology with innovative designs and preparation strategies, and also proved with great potential in the biological and medical use, there is still a long way to go for the eventual application of DNA materials in real life. Here in this review, we conducted a comprehensive survey of the structural development history of various DNA nanomaterials, introduced the principles of different DNA nanomaterials, summarized their biological applications in different fields, and discussed the current challenges and further directions that could help to achieve their applications in the future.

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Journal articles on the topic 'DNA Aptamer-based biosensing'

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