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Awawdeh K, Buttkewitz MA, Bahnemann J, Segal E. Enhancing the performance of porous silicon biosensors: the interplay of nanostructure design and microfluidic integration. MICROSYSTEMS & NANOENGINEERING 2024; 10:100. [PMID: 39021530 PMCID: PMC11252414 DOI: 10.1038/s41378-024-00738-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/08/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024]
Abstract
This work presents the development and design of aptasensor employing porous silicon (PSi) Fabry‒Pérot thin films that are suitable for use as optical transducers for the detection of lactoferrin (LF), which is a protein biomarker secreted at elevated levels during gastrointestinal (GI) inflammatory disorders such as inflammatory bowel disease and chronic pancreatitis. To overcome the primary limitation associated with PSi biosensors-namely, their relatively poor sensitivity due to issues related to complex mass transfer phenomena and reaction kinetics-we employed two strategic approaches: First, we sought to optimize the porous nanostructure with respect to factors including layer thickness, pore diameter, and capture probe density. Second, we leveraged convection properties by integrating the resulting biosensor into a 3D-printed microfluidic system that also had one of two different micromixer architectures (i.e., staggered herringbone micromixers or microimpellers) embedded. We demonstrated that tailoring the PSi aptasensor significantly improved its performance, achieving a limit of detection (LOD) of 50 nM-which is >1 order of magnitude lower than that achieved using previously-developed biosensors of this type. Moreover, integration into microfluidic systems that incorporated passive and active micromixers further enhanced the aptasensor's sensitivity, achieving an additional reduction in the LOD by yet another order of magnitude. These advancements demonstrate the potential of combining PSi-based optical transducers with microfluidic technology to create sensitive label-free biosensing platforms for the detection of GI inflammatory biomarkers.
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Affiliation(s)
- Kayan Awawdeh
- Faculty of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, 320003 Haifa, Israel
| | - Marc A. Buttkewitz
- Institute of Technical Chemistry, Leibniz Universität Hannover, 30167 Hannover, Germany
| | - Janina Bahnemann
- Institute of Physics, University of Augsburg, 86159 Augsburg, Germany
- Centre for Advanced Analytics and Predictive Sciences (CAAPS), University of Augsburg, 86159 Augsburg, Germany
| | - Ester Segal
- Faculty of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, 320003 Haifa, Israel
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Ferreira L, Flanagan SP, Fogel R, Limson JL. Generation of epitope-specific hCG aptamers through a novel targeted selection approach. PLoS One 2024; 19:e0295673. [PMID: 38394285 PMCID: PMC10890750 DOI: 10.1371/journal.pone.0295673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/28/2023] [Indexed: 02/25/2024] Open
Abstract
Human chorionic gonadotropin (hCG) is a glycoprotein hormone used as a biomarker for several medical conditions, including pregnancy, trophoblastic and nontrophoblastic cancers. Most commercial hCG tests rely on a combination of antibodies, one of which is usually specific to the C-terminal peptide of the β-subunit. However, cleavage of this region in many hCG degradation variants prevents rapid diagnostic tests from quantifying all hCG variants in serum and urine samples. An epitope contained within the core fragment, β1, represents an under-researched opportunity for developing immunoassays specific to most variants of hCG. In the study described here, we report on a SELEX procedure tailored towards the identification of two pools of aptamers, one specific to the β-subunit of hCG and another to the β1 epitope within it. The described SELEX procedure utilized antibody-blocked targets, which is an underutilized strategy to exert negative selection pressure and in turn direct aptamer enrichment to a specific epitope. We report on the first aptamers, designated as R4_64 and R6_5, each capable of recognising two distinct sites of the hCG molecule-the β-subunit and the (presumably) β1-epitope, respectively. This study therefore presents a new SELEX approach and the generation of novel aptamer sequences that display potential hCG-specific biorecognition.
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Affiliation(s)
- Lauren Ferreira
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, Eastern Cape, South Africa
| | - Shane Patrick Flanagan
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, Eastern Cape, South Africa
| | - Ronen Fogel
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, Eastern Cape, South Africa
| | - Janice Leigh Limson
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, Eastern Cape, South Africa
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Li H, Li R, He S, Wang Y, Fang W, Jin Y, Yang R, Liu Y, Ye Q, Peng X. An Aptamer-Embedded Two-Dimensional DNA Nanoscale Material with the Property of Cells Recruitment. NANO LETTERS 2023; 23:8399-8405. [PMID: 37339058 DOI: 10.1021/acs.nanolett.3c01240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Stem cells possess exceptional proliferation and differentiation abilities, making them highly promising for targeted recruitment research in tissue engineering and other clinical applications. DNA is a naturally water-soluble, biocompatible, and highly editable material that is widely used in cell recruitment research. However, DNA nanomaterials face challenges, such as poor stability, complex synthesis processes, and demanding storage conditions, which limit their potential applications. In this study, we designed a highly stable DNA nanomaterial that embeds nucleic acid aptamers in the single strand region. This material has the ability to specifically bind, recruit, and capture human mesenchymal stem cells. The synthesis process involves rolling circle amplification and topological isomerization, and it can be stored for extended periods under varying temperatures and humidity conditions. This DNA material offers high specificity, ease of fabrication, simple preservation, and low cost, providing a novel approach to stem cell recruitment strategies.
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Affiliation(s)
- Hongshu Li
- School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Rui Li
- School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Songlin He
- School of Medicine, Nankai University, Tianjin, 300071, P. R. China
- Institute of Orthopedics, the First Medical Center, Chinese PLA General Hospital; Beijing Key Lab of Regenerative Medicine in Orthopedics, Key Laboratory of Musculoskeletal Trauma & War Injuries PLA, Beijing 100853, P. R. China
| | - Yu Wang
- School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Wenya Fang
- School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Yufeng Jin
- School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Rui Yang
- School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Yin Liu
- School of Medicine, Nankai University, Tianjin, 300071, P. R. China
- Nankai University Eye Institute, Nankai University, Tianjin 300071, P. R. China
| | - Qing Ye
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, P. R. China
- Nankai University Eye Institute, Nankai University, Tianjin 300071, P. R. China
| | - Xi Peng
- School of Medicine, Nankai University, Tianjin, 300071, P. R. China
- Nankai University Eye Institute, Nankai University, Tianjin 300071, P. R. China
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Multivalent Aptamer Approach: Designs, Strategies, and Applications. MICROMACHINES 2022; 13:mi13030436. [PMID: 35334728 PMCID: PMC8956053 DOI: 10.3390/mi13030436] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/26/2022] [Accepted: 03/10/2022] [Indexed: 12/04/2022]
Abstract
Aptamers are short and single-stranded DNA or RNA molecules with highly programmable structures that give them the ability to interact specifically with a large variety of targets, including proteins, cells, and small molecules. Multivalent aptamers refer to molecular constructs that combine two or more identical or different types of aptamers. Multivalency increases the avidity of aptamers, a particularly advantageous feature that allows for significantly increased binding affinities in comparison with aptamer monomers. Another advantage of multivalency is increased aptamer stabilities that confer improved performances under physiological conditions for various applications in clinical settings. The current study aims to review the most recent developments in multivalent aptamer research. The review will first discuss structures of multivalent aptamers. This is followed by detailed discussions on design strategies of multivalent aptamer approaches. Finally, recent developments of the multivalent aptamer approach in biosensing and biomedical applications are highlighted.
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Assays to Estimate the Binding Affinity of Aptamers. Talanta 2022; 238:122971. [PMID: 34857318 DOI: 10.1016/j.talanta.2021.122971] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 02/07/2023]
Abstract
Aptamers have become coming-of-age molecular recognition elements in both diagnostic and therapeutic applications. Generated by SELEX, the 'quality control' of aptamers, which involves the validation of their binding affinity against their respective targets is pivotal to ascertain their potency prior to use in any downstream assays or applications. Several aptamers have been isolated thus far, however, the usage of inappropriate validation assays renders some of these aptamers dubitable in terms of their binding capabilities. Driven by this need, we provide an up-to-date critical review of the various strategies used to determine the aptamer-target binding affinity with the aim of providing researchers a better comprehension of the different analytical approaches in respect to the molecular properties of aptamers and their intended targets. The techniques reported have been classified as label-based techniques such as fluorescence intensity, fluorescence anisotropy, filter-binding assays, gel shift assays, ELISA; and label-free techniques such as UV-Vis spectroscopy, circular dichroism, isothermal titration calorimetry, native electrospray ionization-mass spectrometry, quartz crystal microbalance, surface plasmon resonance, NECEEM, backscattering interferometry, capillary electrophoresis, HPLC, and nanoparticle aggregation assays. Hybrid strategies combining the characteristics of both categories such as microscale thermophoresis have been also additionally emphasized. The fundamental principles, complexity, benefits, and challenges under each technique are elaborated in detail.
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Arshavsky‐Graham S, Heuer C, Jiang X, Segal E. Aptasensors versus immunosensors—Which will prevail? Eng Life Sci 2022; 22:319-333. [PMID: 35382545 PMCID: PMC8961048 DOI: 10.1002/elsc.202100148] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 12/11/2022] Open
Abstract
Since the invention of the first biosensors 70 years ago, they have turned into valuable and versatile tools for various applications, ranging from disease diagnosis to environmental monitoring. Traditionally, antibodies have been employed as the capture probes in most biosensors, owing to their innate ability to bind their target with high affinity and specificity, and are still considered as the gold standard. Yet, the resulting immunosensors often suffer from considerable limitations, which are mainly ascribed to the antibody size, conjugation chemistry, stability, and costs. Over the past decade, aptamers have emerged as promising alternative capture probes presenting some advantages over existing constraints of immunosensors, as well as new biosensing concepts. Herein, we review the employment of antibodies and aptamers as capture probes in biosensing platforms, addressing the main aspects of biosensor design and mechanism. We also aim to compare both capture probe classes from theoretical and experimental perspectives. Yet, we highlight that such comparisons are not straightforward, and these two families of capture probes should not be necessarily perceived as competing but rather as complementary. We, thus, elaborate on their combined use in hybrid biosensing schemes benefiting from the advantages of each biorecognition element.
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Affiliation(s)
- Sofia Arshavsky‐Graham
- Faculty of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
| | - Christopher Heuer
- Faculty of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
- Institute of Technical Chemistry Leibniz University Hannover Hannover Germany
| | - Xin Jiang
- Faculty of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
| | - Ester Segal
- Faculty of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
- Russell Berrie Nanotechnology Institute Technion ‐ Israel Institute of Technology Haifa Israel
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Daems E, Moro G, Campos R, De Wael K. Mapping the gaps in chemical analysis for the characterisation of aptamer-target interactions. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116311] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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In situ rolling circle amplification surface modifications to improve E. coli O157:H7 capturing performances for rapid and sensitive microfluidic detection applications. Anal Chim Acta 2021; 1150:338229. [PMID: 33583552 DOI: 10.1016/j.aca.2021.338229] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/01/2021] [Accepted: 01/14/2021] [Indexed: 11/24/2022]
Abstract
We investigated the application of rolling circle amplification (RCA) to modify microfluidic channels for potential sensitive detection applications. To this end, a novel in situ capturing RCA (cRCA) strategy was used to modify the inner surfaces of microfluidic channels with cRCA products that featured repeating tandem capturing aptamers specific for E. coli O157:H7 cells. We showed that the in situ cRCA reaction modified microfluidic channels demonstrated significantly enhanced capturing efficiency in a wide range of flow rates when compared with the unit-aptamer approach. We demonstrated for the first time that microfluidic surfaces modified with the in situ cRCA products showed peak capturing performances both in terms of target capturing efficiency and specificity, and this was likely due to unexpected base-pairing that resulted in altered secondary structures of the capturing aptamers. Our data suggest that the in situ cRCA surface modification is a promising strategy to improve capturing performances in microfluidic devices in sensitive detection applications that also require high throughput. However, cRCA reaction conditions, particularly reaction time and concentrations of initial circular template, must be carefully investigated before the potentials of the in situ cRCA surface modification approach can be fully realized.
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Developing a dual-RCA microfluidic platform for sensitive E. coli O157:H7 whole-cell detections. Anal Chim Acta 2020; 1127:79-88. [DOI: 10.1016/j.aca.2020.06.046] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 02/08/2023]
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Wang M, Wu H, Li Q, Yang Y, Che F, Wang G, Zhang L. Novel Aptamer-Functionalized Nanoparticles Enhances Bone Defect Repair By Improving Stem Cell Recruitment. Int J Nanomedicine 2019; 14:8707-8724. [PMID: 31806966 PMCID: PMC6847998 DOI: 10.2147/ijn.s223164] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 10/01/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The restoration and repair method in the clinic of delayed fracture healing and non-union after comminuted fractures are urgently needed to improve the prognosis of patients. The recruitment of endogenous stem cells has been considered a promising approach in bone defect repair. PROPOSE The aim of this study was to generate a de novel MSCs aptamer and developed the first, feasible, economical, bio-compatible, and functional MSCs aptamer-directed nanoparticles without complex manufacture to recruit mesenchymal stem cells (MSCs) for bone defect regeneration. METHODS Whole-cell SELEX was used to generate a de novel MSCs aptamer. Flow cytometry was applied to assess the binding specificities, affinities and sorting abilities of the aptamers. Nano-Aptamer Ball (NAB) was constructed by NHS/EDC reaction. The diameter and zeta of NAB were assessed by dynamic light scattering. CCK8 assay was utilized to evaluate whether NAB could cause non-specific cytotoxicity and induce cell proliferation. To evaluate the bone repair capacity of NAB, histomorphological staining, alizarin red and micro X-ray were used to observe the repair degree of defect in vivo. ELISA was used to detect osteopontin (OPN), osteocalcin (BGP) by, and alkaline phosphatase (ALP) in peripheral blood. RESULTS MSCs aptamer termed as HM69 could bind with MSCs with high specificity and Kd of 9.67 nM, while has minimal cross-reactivities to other negative cells. HM69 could capture MSCs with a purity of >89%. In vitro, NAB could bind and capture MSCs effectively, whereas did not cause obvious cytotoxicity. In vivo, serum OPN, BGP, and ALP levels in the NAB group of rats were increased at both 2 and 4 weeks, indicating the repair and osteogenesis generation. The healing of bone defects in the NAB group was significantly better than control groups, the defects became blurred, and local trabecular bone growth could be observed in X-ray. The organized hematoma and cell growth in the bone marrow of the NAB group were more vigorous in bone sections staining. CONCLUSION These suggested that HM69 and HM69-functionalized nanoparticles NAB exhibited the ability to recruit MSCs both in vitro and in vivo and achieved a better outcome of bone defect repair in a rat model. The findings demonstrate a promising strategy of using aptamer-functionalized bio-nanoparticles for the restoration of bone defects via aptamer-introduced homing of MSCs.
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Affiliation(s)
- Meng Wang
- Department of Orthopaedics, The NO. 946 Hospital of PLA, YiNing, XinJiang86-835000, People’s Republic of China
| | - Haibin Wu
- Shaanxi Institute of Pediatric Diseases, Xi’an Children’s Hospital, Xi’an, Shaanxi86-710003, People’s Republic of China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi86-710061, People’s Republic of China
| | - Qiao Li
- Clinical Laboratory, Xi’an Children’s Hospital, Xi’an, Shaanxi86-710003, People’s Republic of China
| | - Ying Yang
- Shaanxi Institute of Pediatric Diseases, Xi’an Children’s Hospital, Xi’an, Shaanxi86-710003, People’s Republic of China
| | - Fengyu Che
- Shaanxi Institute of Pediatric Diseases, Xi’an Children’s Hospital, Xi’an, Shaanxi86-710003, People’s Republic of China
| | - Guoxia Wang
- Shaanxi Institute of Pediatric Diseases, Xi’an Children’s Hospital, Xi’an, Shaanxi86-710003, People’s Republic of China
| | - Liyu Zhang
- Shaanxi Institute of Pediatric Diseases, Xi’an Children’s Hospital, Xi’an, Shaanxi86-710003, People’s Republic of China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi86-710061, People’s Republic of China
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