1
|
Hasanzadeh A, Ebadati A, Saeedi S, Kamali B, Noori H, Jamei B, Hamblin MR, Liu Y, Karimi M. Nucleic acid-responsive smart systems for controlled cargo delivery. Biotechnol Adv 2024; 74:108393. [PMID: 38825215 DOI: 10.1016/j.biotechadv.2024.108393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
Stimulus-responsive delivery systems allow controlled, highly regulated, and efficient delivery of various cargos while minimizing side effects. Owing to the unique properties of nucleic acids, including the ability to adopt complex structures by base pairing, their easy synthesis, high specificity, shape memory, and configurability, they have been employed in autonomous molecular motors, logic circuits, reconfigurable nanoplatforms, and catalytic amplifiers. Moreover, the development of nucleic acid (NA)-responsive intelligent delivery vehicles is a rapidly growing field. These vehicles have attracted much attention in recent years due to their programmable, controllable, and reversible properties. In this work, we review several types of NA-responsive controlled delivery vehicles based on locks and keys, including DNA/RNA-responsive, aptamer-responsive, and CRISPR-responsive, and summarize their advantages and limitations.
Collapse
Affiliation(s)
- Akbar Hasanzadeh
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Arefeh Ebadati
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Department of Molecular and Cell Biology, University of California, Merced, Merced, USA
| | - Sara Saeedi
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Babak Kamali
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Noori
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Behnam Jamei
- Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
| | - Yong Liu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China.
| | - Mahdi Karimi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Oncopathology Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran; Research Center for Science and Technology in Medicine, Tehran University of Medical Sciences, Tehran, Iran; Applied Biotechnology Research Centre, Tehran Medical Science, Islamic Azad University, Tehran, Iran.
| |
Collapse
|
2
|
Guo X. Research progress on the detection of foodborne pathogens based on aptamer recognition. Mikrochim Acta 2024; 191:318. [PMID: 38727855 DOI: 10.1007/s00604-024-06375-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/20/2024] [Indexed: 05/15/2024]
Abstract
Foodborne diseases caused by bacterial contamination are a serious threat to food safety and human health. The classical plate culture method has the problems of long detection cycle, low sensitivity and specificity, and complicated operation, which cannot meet the growing demand for rapid quantitative detection of pathogenic bacteria. The frequent outbreak of foodborne diseases has put forward higher requirements for rapid and simple detection technology of foodborne pathogens. Aptamer is a kind of oligonucleotide fragment that can recognize targets with the advantages of high affinity and good specificity. The target can be range from proteins, small molecules, cells bacteria, and even viruses. Herein, the latest advances in sensitive and rapid detection of foodborne pathogens based on aptamer recognition was reviewed. Special attention has been paid to the obtained sequences of aptamers to various foodborne pathogens, the optimization of sequences, and the mechanism of aptamer recognition. Then, the research progress of biosensors for the detection of pathogenic bacteria based on aptamer recognition were summarized. Some challenges and prospects for the detection of foodborne pathogens based on aptamer recognition were prospected. In summary, with the further deepening of aptamer research and improvement of detection technology, aptamer-based recognition can meet the needs of rapid, sensitive, and accurate detection in practical applications.
Collapse
Affiliation(s)
- Xianglin Guo
- School of Food Science and Technology, Hunan Agricultural University, Changsha, 410128, Hunan, China.
| |
Collapse
|
3
|
Li J, Xu T, Zheng Y, Liu D, Zhang C, Li J, Wang ZA, Du Y. In Silico Study on a Binding Mechanism of ssDNA Aptamers Targeting Glycosidic Bond-Containing Small Molecules. Anal Chem 2024; 96:5056-5064. [PMID: 38497564 DOI: 10.1021/acs.analchem.4c00927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Aptamer-based detection targeting glycoconjugates has attracted significant attention for its remarkable potential in identifying structural changes in saccharides in different stages of various diseases. However, the challenges in screening aptamers for small carbohydrates or glycoconjugates, which contain highly flexible and diverse glycosidic bonds, have hindered their application and commercialization. In this study, we investigated the binding conformations between three glycosidic bond-containing small molecules (GlySMs; glucose, N-acetylneuraminic acid, and neomycin) and their corresponding aptamers in silico, and analyzed factors contributing to their binding affinities. Based on the findings, a novel binding mechanism was proposed, highlighting the central role of the stem structure of the aptamer in binding and recognizing GlySMs and the auxiliary role of the mismatched bases in the adjacent loop. Guided by this binding mechanism, an aptamer with a higher 6'-sialyllactose binding affinity was designed, achieving a KD value of 4.54 ± 0.64 μM in vitro through a single shear and one mutation. The binding mechanism offers crucial guidance for designing high-affinity aptamers, enhancing the virtual screening efficiency for GlySMs. This streamlined workflow filters out ineffective binding sites, accelerating aptamer development and providing novel insights into glycan-nucleic acid interactions.
Collapse
Affiliation(s)
- Jiaqing Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Tong Xu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yalan Zheng
- Key Laboratory for Animal Disease-Resistant Nutrition of the Ministry of Education of China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Dongdong Liu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
| | - Chen Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
| | - Jianjun Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
| | - Zhuo A Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
| | - Yuguang Du
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
| |
Collapse
|
4
|
Argoubi W, Algethami FK, Raouafi N. Enhanced sensitivity in electrochemical detection of ochratoxin A within food samples using ferrocene- and aptamer-tethered gold nanoparticles on disposable electrodes. RSC Adv 2024; 14:8007-8015. [PMID: 38454949 PMCID: PMC10918640 DOI: 10.1039/d3ra08567h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/01/2024] [Indexed: 03/09/2024] Open
Abstract
Ensuring food security is crucial for public health, and the presence of mycotoxins, produced by fungi in improperly stored processed or unprocessed food, poses a significant threat. This research introduces a novel approach - a disposable aptasensing platform designed for the detection of ochratoxin A (OTA). The platform employs gold-nanostructured screen-printed carbon electrodes functionalized with a ferrocene derivative, serving as an integrated faradaic transducing system, and an anti-OTA aptamer as a bioreceptor site. Detection relies on the ferrocene electrochemical signal changes induced by the aptamer folding in the presence of the target molecule. Remarkably sensitive, the platform detects OTA within the range of 0.5 to 70 ng mL-1 and a detection limit of 11 pg mL-1. This limit is approximately 200 times below the levels stipulated by the European Commission for agricultural commodities. Notably, the sensing device exhibits efficacy in detecting OTA in complex media, such as roasted coffee beans and wine, without the need for sample pretreatment, yielding accurate recoveries. Furthermore, while label-free electrochemical aptasensors have proliferated, this study addresses a gap in understanding the binding mechanisms of some aptasensors. To enhance the experimental findings, a theoretical study was conducted to underscore the specificity of the anti-OTA aptamer as a donor for OTA detection. The molecular docking technique was employed to unveil the key binding region of the aptamer, providing valuable insights into the aptasensor specificity.
Collapse
Affiliation(s)
- Wicem Argoubi
- Sensors and Biosensors Group, ACE-Lab (LR99ES15), Faculty of Science, University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Faisal K Algethami
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU) P.O. Box 90950 Riyadh 11623 Saudi Arabia
| | - Noureddine Raouafi
- Sensors and Biosensors Group, ACE-Lab (LR99ES15), Faculty of Science, University of Tunis El Manar 2092 Tunis El Manar Tunisia
| |
Collapse
|
5
|
Martin DR, Mutombwera AT, Madiehe AM, Onani MO, Meyer M, Cloete R. Molecular modeling and simulation studies of SELEX-derived high-affinity DNA aptamers to the Ebola virus nucleoprotein. J Biomol Struct Dyn 2024:1-18. [PMID: 38217874 DOI: 10.1080/07391102.2024.2302922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
Ebola viral disease (EVD) is a highly infectious and potentially fatal illness with a case fatality rate ranging from 25% to 90%. To effectively control its spread, there is a need for rapid, reliable and lowcost point-of-care (P OC) diagnostic tests. While various EVD diagnostic tests exist, few are P OC tests, and many are not cost-effective. The use of antibodies in these tests has limitations, prompting the exploration of aptamers as potential alternatives. Various proteins from the Ebola virus (EBOV) proteome, including EBOV nucleoprotein (NP), are considered viable targets for diagnostic assays. A previous study identified three aptamers (Apt1. Apt2 and Apt3) with high affinity for EBOV NP using systemic evolution of ligands by exponential enrichment (SELEX). This study aimed to employ in silico methods, such as Phyre2, RNAfold, RNAComposer, HADDOCK and GROMACS, to model the structures of EBOV NP and the aptamers, and to investigate their binding. The in silico analysis revealed successful binding of all the three aptamers to EBOV NP, with a suggested ranking of Apt1 > Apt2 > Apt3 based on binding affinity. Microscale thermophoresis (MST) analysis confirmed the binding, providing dissociation constants of 25 ± 2.84, 56 ± 2.76 and 140 ±3.69 nM for Apt1, Apt2 and Apt3, respectively. The study shows that the findings of the in silico analysis was in agreement with the MST analysis. Inclusion of these in silico approaches in diagnostic assay development can expedite the selection of candidate aptamers, potentially overcoming challenges associated with aptamer application in diagnostics.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- D R Martin
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute (SANBI), University of the Western Cape, Bellville, South Africa Cape Town, South Africa
| | - A T Mutombwera
- Department of Biochemistry and Microbiology, Nelson Mandela University, Port Elizabeth, South Africa
| | - A M Madiehe
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
- Nanobiotechnology Research Group, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - M O Onani
- Department of Chemistry, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - M Meyer
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - R Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute (SANBI), University of the Western Cape, Bellville, South Africa Cape Town, South Africa
| |
Collapse
|
6
|
Stuber A, Douaki A, Hengsteler J, Buckingham D, Momotenko D, Garoli D, Nakatsuka N. Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores. ACS NANO 2023; 17:19168-19179. [PMID: 37721359 PMCID: PMC10569099 DOI: 10.1021/acsnano.3c05377] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/08/2023] [Indexed: 09/19/2023]
Abstract
Aptamers that undergo conformational changes upon small-molecule recognition have been shown to gate the ionic flux through nanopores by rearranging the charge density within the aptamer-occluded orifice. However, mechanistic insight into such systems where biomolecular interactions are confined in nanoscale spaces is limited. To understand the fundamental mechanisms that facilitate the detection of small-molecule analytes inside structure-switching aptamer-modified nanopores, we correlated experimental observations to theoretical models. We developed a dopamine aptamer-functionalized nanopore sensor with femtomolar detection limits and compared the sensing behavior with that of a serotonin sensor fabricated with the same methodology. When these two neurotransmitters with comparable mass and equal charge were detected, the sensors showed an opposite electronic behavior. This distinctive phenomenon was extensively studied using complementary experimental techniques such as quartz crystal microbalance with dissipation monitoring, in combination with theoretical assessment by the finite element method and molecular dynamic simulations. Taken together, our studies demonstrate that the sensing behavior of aptamer-modified nanopores in detecting specific small-molecule analytes correlates with the structure-switching mechanisms of individual aptamers. We believe that such investigations not only improve our understanding of the complex interactions occurring in confined nanoscale environments but will also drive further innovations in biomimetic nanopore technologies.
Collapse
Affiliation(s)
- Annina Stuber
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Ali Douaki
- Instituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Julian Hengsteler
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Denis Buckingham
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Dmitry Momotenko
- Department
of Chemistry, Carl von Ossietzky University
of Oldenburg, Oldenburg D-26129, Germany
| | - Denis Garoli
- Instituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Nako Nakatsuka
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| |
Collapse
|
7
|
Ruiz-Ciancio D, Lin LH, Veeramani S, Barros MN, Sanchez D, Di Bartolo AL, Masone D, Giangrande PH, Mestre MB, Thiel WH. Selection of a novel cell-internalizing RNA aptamer specific for CD22 antigen in B cell acute lymphoblastic leukemia. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:698-712. [PMID: 37662970 PMCID: PMC10469072 DOI: 10.1016/j.omtn.2023.07.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 07/25/2023] [Indexed: 09/05/2023]
Abstract
Despite improvements in B cell acute lymphoblastic leukemia (B-ALL) treatment, a significant number of patients experience relapse of the disease, resulting in poor prognosis and high mortality. One of the drawbacks of current B-ALL treatments is the high toxicity associated with the non-specificity of chemotherapeutic drugs. Targeted therapy is an appealing strategy to treat B-ALL to mitigate these toxic off-target effects. One such target is the B cell surface protein CD22. The restricted expression of CD22 on the B-cell lineage and its ligand-induced internalizing properties make it an attractive target in cases of B cell malignancies. To target B-ALL and the CD22 protein, we performed cell internalization SELEX (Systematic Evolution of Ligands by EXponential enrichment) followed by molecular docking to identify internalizing aptamers specific for B-ALL cells that bind the CD22 cell-surface receptor. We identified two RNA aptamers, B-ALL1 and B-ALL2, that target human malignant B cells, with B-ALL1 the first documented RNA aptamer interacting with the CD22 antigen. These B-ALL-specific aptamers represent an important first step toward developing novel targeted therapies for B cell malignancy treatments.
Collapse
Affiliation(s)
- Dario Ruiz-Ciancio
- Instituto de Ciencias Biomédicas (ICBM), Facultad de Ciencias Médicas, Universidad Católica de Cuyo, Av. José Ignacio de la Roza 1516, Rivadavia, San Juan 5400, Argentina
- National Council of Scientific and Technical Research (CONICET), Godoy Cruz 2290, Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
| | - Li-Hsien Lin
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52246, USA
| | - Suresh Veeramani
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52246, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA
| | - Maya N. Barros
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52246, USA
| | - Diego Sanchez
- Instituto de Medicina y Biología Experimental de Cuyo (IMBECU), CONICET, CCT-Mendoza 5500, Argentina
| | - Ary Lautaro Di Bartolo
- Instituto de Histología y Embriología de Mendoza (IHEM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), Mendoza M5502JMA, Argentina
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), Mendoza M5502JMA, Argentina
| | - Paloma H. Giangrande
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52246, USA
- VP Platform Discovery Sciences, Biology, Wave Life Sciences, 733 Concord Avenue, Cambridge, MA 02138, USA
| | - María Belén Mestre
- Instituto de Ciencias Biomédicas (ICBM), Facultad de Ciencias Médicas, Universidad Católica de Cuyo, Av. José Ignacio de la Roza 1516, Rivadavia, San Juan 5400, Argentina
- National Council of Scientific and Technical Research (CONICET), Godoy Cruz 2290, Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
| | - William H. Thiel
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52246, USA
| |
Collapse
|
8
|
Ding Y, Xie Y, Li AZ, Huang PJJ, Liu J. Cross-Binding of Four Adenosine/ATP Aptamers to Caffeine, Theophylline, and Other Methylxanthines. Biochemistry 2023; 62:2280-2288. [PMID: 37433121 DOI: 10.1021/acs.biochem.3c00260] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
The classical DNA aptamer for adenosine and ATP was selected twice using ATP as the target in 1995 and 2005, respectively. In 2022, this motif appeared four more times from selections using adenosine, ATP, theophylline, and caffeine as targets, suggesting that this aptamer can also bind methylxanthines. In this work, using thioflavin T fluorescence spectroscopy, this classical DNA aptamer showed Kd values for adenosine, theophylline, and caffeine of 9.5, 101, and 131 μM, respectively, and similar Kd values were obtained using isothermal titration calorimetry. Binding to the methylxanthines was also observed for the newly selected Ade1301 aptamer but not for the Ade1304 aptamer. The RNA aptamer for ATP also had no binding to the methylxanthines. Molecular dynamics simulations were performed using the classical DNA and RNA aptamers based on their NMR structures, and the simulation results were consistent with the experimental observations, explaining the selectivity profiles. This study suggests that a broader range of target analogues need to be tested for aptamers. For the detection of adenosine and ATP, the Ade1304 aptamer is a better choice due to its better selectivity.
Collapse
Affiliation(s)
- Yuzhe Ding
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Yachen Xie
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Albert Zehan Li
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| |
Collapse
|
9
|
Li J, Liu Y, Liu D, Xu T, Zhang C, Li J, Wang ZA, Du Y. In Silico Selection and Validation of High-Affinity ssDNA Aptamers Targeting Paromomycin. Anal Chem 2023. [PMID: 37384819 DOI: 10.1021/acs.analchem.3c01575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Glycans are promising for disease diagnosis since glycan biosynthesis is significantly affected by disease states, and glycosylation changes are probably more pronounced than protein expression during the transformation to the diseased condition. Glycan-specific aptamers can be developed for challenging applications such as cancer targeting; however, the high flexibility of glycosidic bonds and scarcity of studies on glycan-aptamer binding mechanisms increased the difficulty of screening. In this work, the model of interactions between glycans and ssDNA aptamers synthesized based on the sequence of rRNA genes was developed. Our simulation-based approach revealed that paromomycin as a representative example of glycans is preferred to bind base-restricted stem structures of aptamers because they are more critical in stabilizing the flexible structures of glycans. Combined experiments and simulations have identified two optimal mutant aptamers. Our work would provide a potential strategy that the glycan-binding rRNA genes could act as the initial aptamer pools to accelerate aptamer screening. In addition, this in silico workflow would be potentially applied in the more extensive in vitro development and application of RNA-templated ssDNA aptamers targeting glycans.
Collapse
Affiliation(s)
- Jiaqing Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North 2nd Street, Zhongguancun, Haidian District, 100190 Beijing, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, 100049 Beijing, China
| | - Yangyang Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Dongdong Liu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North 2nd Street, Zhongguancun, Haidian District, 100190 Beijing, China
| | - Tong Xu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North 2nd Street, Zhongguancun, Haidian District, 100190 Beijing, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, 100049 Beijing, China
| | - Chen Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North 2nd Street, Zhongguancun, Haidian District, 100190 Beijing, China
| | - Jianjun Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North 2nd Street, Zhongguancun, Haidian District, 100190 Beijing, China
| | - Zhuo A Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North 2nd Street, Zhongguancun, Haidian District, 100190 Beijing, China
| | - Yuguang Du
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North 2nd Street, Zhongguancun, Haidian District, 100190 Beijing, China
| |
Collapse
|
10
|
Mulyani DE, Maksum IP. Detection of Biomarker Using Aptasensors to Determine the Type of Diabetes. Diagnostics (Basel) 2023; 13:2035. [PMID: 37370930 DOI: 10.3390/diagnostics13122035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/04/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Diabetes mellitus (DM) is a metabolic disorder characterized by elevated blood glucose levels. This disease is so serious that many experts refer to it as the "silent killer". The early detection of diabetes mellitus, whether type 1, type 2 or mitochondrial, is crucial because it can improve the success of treatment and the quality of life for patients. Aptamer-based biosensor diagnosis methods have been widely developed because they have high sensitivity and selectivity in detecting biomarkers of various diseases. Aptamers are short sequences of oligonucleotides or proteins that recognize specific ligands and bind to various target molecules, ranging from small ions to large proteins. They are promising diagnostic molecules due to their high sensitivity and selectivity, ease of modification, low toxicity, and high stability. This article aims to summarize the progress of detection methods, including detection principles, sensitivity, selectivity, and the performance of detection devices, to distinguish between types of diabetes mellitus using electrochemical aptasensors with biomarkers such as glucose, insulin, HbA1c, GHSA, and ATP.
Collapse
Affiliation(s)
- Dinda Exelsa Mulyani
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, Indonesia
| | - Iman Permana Maksum
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, Indonesia
| |
Collapse
|
11
|
Ma P, Guo H, Ye H, Zhang Y, Wang Z. Structural insights into the AFB 1 aptamer coupled with a rationally designed CRISPR/Cas12a-Exo III aptasensor for AFB 1 detection. Int J Biol Macromol 2023; 225:1164-1171. [PMID: 36414074 DOI: 10.1016/j.ijbiomac.2022.11.177] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 11/21/2022]
Abstract
Aflatoxin B1 (AFB1) is a typical food contaminant. A truncated DNA aptamer of AFB1 was reported by our team in previous work. However, the recognition mechanism between aptamer and AFB1 was lacking, which was crucial for the design of related aptasensor. Herein, the binding of aptamer to AFB1 was systematically studied and found that it was an exothermic process and the conformation of aptamer changed during the recognition process. Loop bases in the secondary structure of aptamer formed a special binding pocket to recognize AFB1. Van der Waals and electrostatic interaction were the main driving forces. By blocking the stem bases guided by the structural investigation, a rationally designed CRISPR/Cas12a-Exo III aptasensor for AFB1 detection was constructed, and the sensitivity was improved by target recycling. Under optimal conditions, the linear detection range for AFB1 was 0.01-20 ng/mL, and AFB1 was accurately determined in corn and wheat samples. This work laid a theoretical foundation for the design of AFB1 aptasensor, and the developed detection model came up with new ideas for the development of CRISPR/Cas12a-based aptasensor.
Collapse
Affiliation(s)
- Pengfei Ma
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Hualin Guo
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Hua Ye
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China
| | - Yin Zhang
- Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu 610106, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China; School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China.
| |
Collapse
|
12
|
Ramasanoff RR, Sokolov PA. The binding model of adenosine-specific DNA aptamer: Umbrella sampling study. J Mol Graph Model 2023; 118:108338. [PMID: 36201878 DOI: 10.1016/j.jmgm.2022.108338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 11/25/2022]
Abstract
We report a novel model of the selective binding mechanism of adenosine-specific DNA aptamer. Our theoretical investigations of AMP (Adenosine monophosphate) dissociation from aptamer-AMP complexes reveals new details of aptamer molecular specificity and stabilisation factors. Umbrella sampling MD calculations using parmbsc1 force field shows that the disordered structure of the internal loop of the unbound aptamer hairpin has a characteristic packing of guanines, which prevents barrier-free penetration of ligands into the site cavity. Also, this disordered structure of the unbound aptamer has a network of hydrogen bonds stabilising the cavity near the target guanines within the binding sites during the whole binding process. We suggested that the first AMP molecule binds to the disordered structure of the site closest to the aptamer hairpin stem and spends some free energy on ordering of the internal loop. Then the second AMP molecule binds to the ordered site closest to the aptamer hairpin loop with a lower energy gain. As a result, the induced-fit binding model is the most applicable for this aptamer and does not contradict the modern experimental NMR and calorimetry data.
Collapse
Affiliation(s)
- Ruslan R Ramasanoff
- Sevastopol State University, Universitetskaya 33, 299053, Sevastopol, Russia.
| | - Petr A Sokolov
- Sevastopol State University, Universitetskaya 33, 299053, Sevastopol, Russia; Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034, Saint Petersburg, Russia
| |
Collapse
|
13
|
Kou Q, Wang L, Zhang L, Ma L, Fu S, Su X. Simulation-Assisted Localized DNA Logical Circuits for Cancer Biomarkers Detection and Imaging. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2205191. [PMID: 36287076 DOI: 10.1002/smll.202205191] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/30/2022] [Indexed: 06/16/2023]
Abstract
DNA-based nanodevices equipped with localized modules have been promising probes for biomarker detection. Such devices heavily rely on the intramolecular hybridization reaction. However, there is a lack of mechanistic insights into this reaction that limits the sensing speed and sensitivity. A coarse-grained model is utilized to simulate the intramolecular hybridization of localized DNA circuits (LDCs) not only optimizing the performance, but also providing mechanistic insights into the hybridization reaction. The simulation guided-LDCs enable the detection of multiple biomarkers with high sensitivity and rapid speed showing good consistency with the simulation. Fluorescence assays demonstrate that the simulation-guided LDC shows an enhanced sensitivity up to 9.3 times higher than that of the same probes without localization. The detection limits of ATP, miRNA, and APE1 reach 0.14 mM, 0.68 pM, and 0.0074 U mL-1 , respectively. The selected LDC is operated in live cells with good success in simultaneously detecting the biomarkers and discriminating between cancer cells and normal cells. LDC is successfully applied to detect the biomarkers in cancer tissues from patients, allowing the discrimination of cancer/adjacent/normal tissues. This work herein presents a design workflow for DNA nanodevices holding great potential for expanding the applications of DNA nanotechnology in diagnostics and therapeutics.
Collapse
Affiliation(s)
- Qiaoni Kou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Lei Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Linghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Liang Ma
- Clinical Laboratory, China-Japan Friendship Hospital, Beijing, 100029, P. R. China
| | - Shengnan Fu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| |
Collapse
|
14
|
Wang SD, Zhang RB, Eriksson LA. Markov state models elucidate the stability of DNA influenced by the chiral 5S-Tg base. Nucleic Acids Res 2022; 50:9072-9082. [PMID: 35979954 PMCID: PMC9458442 DOI: 10.1093/nar/gkac691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/15/2022] [Accepted: 07/30/2022] [Indexed: 12/24/2022] Open
Abstract
The static and dynamic structures of DNA duplexes affected by 5S-Tg (Tg, Thymine glycol) epimers were studied using MD simulations and Markov State Models (MSMs) analysis. The results show that the 5S,6S-Tg base caused little perturbation to the helix, and the base-flipping barrier was determined to be 4.4 kcal mol-1 through the use of enhanced sampling meta-eABF calculations, comparable to 5.4 kcal mol-1 of the corresponding thymine flipping. Two conformations with the different hydrogen bond structures between 5S,6R-Tg and A19 were identified in several independent MD trajectories. The 5S,6R-Tg:O6HO6•••N1:A19 hydrogen bond is present in the high-energy conformation displaying a clear helical distortion, and near barrier-free Tg base flipping. The low-energy conformation always maintains Watson-Crick base pairing between 5S,6R-Tg and A19, and 5S-Tg base flipping is accompanied by a small barrier of ca. 2.0 KBT (T = 298 K). The same conformations are observed in the MSMs analysis. Moreover, the transition path and metastable structures of the damaged base flipping are for the first time verified through MSMs analysis. The data clearly show that the epimers have completely different influence on the stability of the DNA duplex, thus implying different enzymatic mechanisms for DNA repair.
Collapse
Affiliation(s)
- Shu-dong Wang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, South Street No. 5, Zhongguancun, Haidan District, 100081 Beijing, China
| | - Ru-bo Zhang
- Correspondence may also be addressed to Ru-bo Zhang.
| | - Leif A Eriksson
- To whom correspondence should be addressed. Tel: +46 31 786 9117;
| |
Collapse
|
15
|
Ma P, Ye H, Guo H, Ma X, Yue L, Wang Z. Aptamer truncation strategy assisted by molecular docking and sensitive detection of T-2 toxin using SYBR Green I as a signal amplifier. Food Chem 2022; 381:132171. [DOI: 10.1016/j.foodchem.2022.132171] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 12/26/2022]
|
16
|
Chen J, Liu Z, Yang R, Liu M, Feng H, Li N, Jin M, Zhang M, Shui L. A liquid crystal-based biosensor for detection of insulin driven by conformational change of an aptamer at aqueous-liquid crystal interface. J Colloid Interface Sci 2022; 628:215-222. [DOI: 10.1016/j.jcis.2022.07.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/14/2022] [Accepted: 07/09/2022] [Indexed: 11/28/2022]
|
17
|
A novel fluorescent aptasensor based on mesoporous silica nanoparticles for the selective detection of sulfadiazine in edible tissue. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104067] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
18
|
Wang SD, Eriksson LA, Zhang RB. Dynamics of 5R-Tg Base Flipping in DNA Duplexes Based on Simulations─Agreement with Experiments and Beyond. J Chem Inf Model 2022; 62:386-398. [PMID: 34994562 PMCID: PMC8790752 DOI: 10.1021/acs.jcim.1c01169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Damaged or mismatched
DNA bases are normally thought to be able
to flip out of the helical stack, providing enzymes with access to
the faulty genetic information otherwise hidden inside the helix.
Thymine glycol (Tg) is one of the most common products of nucleic
acid damage. However, the static and dynamic structures of DNA duplexes
affected by 5R-Tg epimers are still not clearly understood, including
the ability of these to undergo spontaneous base flipping. Structural
effects of the 5R-Tg epimers on the duplex DNA are herein studied
using molecular dynamics together with reliable DFT based calculations.
In comparison with the corresponding intact DNA, the cis-5R,6S-Tg epimer base causes little perturbation to the duplex DNA,
and a barrier of 4.9 kcal mol–1 is obtained by meta-eABF
for cis-5R,6S-Tg base flipping out of the duplex
DNA, comparable to the 5.4 kcal mol–1 obtained for
the corresponding thymine flipping in intact DNA. For the trans-5R,6R-Tg epimer, three stable local structures were
identified, of which the most stable disrupts the Watson–Crick
hydrogen-bonded G5/C20 base pair, leading to conformational distortion
of the duplex. Interestingly, the relative barrier height of the 5R-Tg
flipping is only 1.0 kcal mol–1 for one of these trans-5R,6R-Tg epimers. Water bridge interactions were identified
to be essential for 5R-Tg flipping. The study clearly demonstrates
the occurrence of partial trans-5R,6R-Tg epimer flipping
in solution.
Collapse
Affiliation(s)
- Shu Dong Wang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, South Street no 5, Zhongguancun, Haidian District, 100081 Beijing, China
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9c, 405 30 Göteborg, Sweden
| | - Ru Bo Zhang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, South Street no 5, Zhongguancun, Haidian District, 100081 Beijing, China
| |
Collapse
|
19
|
Wen J, Jiang D, Shan X, Wang W, Xu F, Shiigi H, Chen Z. Ternary electrochemiluminescence biosensor based on black phosphorus quantum dots doped perylene derivative and metal organic frameworks as a coreaction accelerator for the detection of chloramphenicol. Microchem J 2022. [DOI: 10.1016/j.microc.2021.106927] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
20
|
Li J, Jiang J, Su Y, Liang Y, Zhang C. A novel cloth-based supersandwich electrochemical aptasensor for direct, sensitive detection of pathogens. Anal Chim Acta 2021; 1188:339176. [PMID: 34794578 DOI: 10.1016/j.aca.2021.339176] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/04/2021] [Accepted: 10/13/2021] [Indexed: 01/07/2023]
Abstract
Traditional detection methods for food-borne pathogens are usually expensive and laborious, so there is an urgent need for an economical, facile and sensitive method. In this work, a novel cloth-based supersandwich electrochemical aptasensor (CSEA) is firstly developed for direct detection of pathogens. Carbon ink- and wax-based screen-printing is used to make cloth-based electrodes and hydrophilic/hydrophobic regions respectively to fabricate the sensing devices. Two well-designed, specific single-stranded DNA sequences arise a cascade hybridization reaction to form the DNA supersandwich (DSS) whose grooves can be inserted by methylene blue (MB), which effectively amplifies the current signal to greatly improve the detection sensitivity. Taking the detection of Salmonella typhimurium (S. typhimurium) as an example, the aptamers bind to S. typhimurium to form the target-aptamers complex, which can simultaneously bind to the capture probe and DSS, resulting in detection of S. typhimurium. Moreover, the addition of tail sequences of aptamer makes the proposed CSEA versatile. Under optimized conditions, the electrochemical signal increases linearly with the logarithm of S. typhimurium concentration over the range from 102 to 108 CFU mL-1, with a limit of detection of 16 CFU mL-1. Additionally, the CSEA efficiently determined the levels of S. typhimurium in milk samples. Experimental results illustrate that the fabricated CSEA is sensitive, specific, reproducible and stable. Moreover, when Ru(bpy)32+ replaces MB, the electrochemiluminescence (ECL) can be performed. Thus, for the proposed sensing strategy, the dual-mode detection of electrochemistry and ECL is easily realized.
Collapse
Affiliation(s)
- Jie Li
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China; Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Jun Jiang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China; Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Yan Su
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China; Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Yi Liang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China; Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Chunsun Zhang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China; Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China.
| |
Collapse
|
21
|
Kozlovskii I, Popov P. Structure-based deep learning for binding site detection in nucleic acid macromolecules. NAR Genom Bioinform 2021; 3:lqab111. [PMID: 34859211 PMCID: PMC8633674 DOI: 10.1093/nargab/lqab111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/14/2021] [Accepted: 11/09/2021] [Indexed: 12/30/2022] Open
Abstract
Structure-based drug design (SBDD) targeting nucleic acid macromolecules, particularly RNA, is a gaining momentum research direction that already resulted in several FDA-approved compounds. Similar to proteins, one of the critical components in SBDD for RNA is the correct identification of the binding sites for putative drug candidates. RNAs share a common structural organization that, together with the dynamic nature of these molecules, makes it challenging to recognize binding sites for small molecules. Moreover, there is a need for structure-based approaches, as sequence information only does not consider conformation plasticity of nucleic acid macromolecules. Deep learning holds a great promise to resolve binding site detection problem, but requires a large amount of structural data, which is very limited for nucleic acids, compared to proteins. In this study we composed a set of ∼2000 nucleic acid-small molecule structures comprising ∼2500 binding sites, which is ∼40-times larger than previously used one, and demonstrated the first structure-based deep learning approach, BiteNetN, to detect binding sites in nucleic acid structures. BiteNetN operates with arbitrary nucleic acid complexes, shows the state-of-the-art performance, and can be helpful in the analysis of different conformations and mutant variants, as we demonstrated for HIV-1 TAR RNA and ATP-aptamer case studies.
Collapse
Affiliation(s)
- Igor Kozlovskii
- iMolecule, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Petr Popov
- iMolecule, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| |
Collapse
|
22
|
Ma P, Guo H, Duan N, Ma X, Yue L, Gu Q, Wang Z. Label free structure-switching fluorescence polarization detection of chloramphenicol with truncated aptamer. Talanta 2021; 230:122349. [PMID: 33934798 DOI: 10.1016/j.talanta.2021.122349] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 03/02/2021] [Accepted: 03/18/2021] [Indexed: 12/18/2022]
Abstract
In this study, the original chloramphenicol aptamer containing 80 bases was truncated to 30 bases with high affinity by the SYBR Green I assay. It was found that the ionic strength and type affect the recognition of aptamers, especially magnesium ion played a vital role in the binding process. Furthermore, the binding performance of aptamer, including binding mode, key binding sites and conformational changes were further investigated by circular dichroism spectroscopy, UV-vis absorption spectrum and molecular docking. Based on these research data, we inferred that chloramphenicol bound to the minor groove region in the aptamer double helix. Finally, the optimized aptamer LLR10 was used to develop a novel label free fluorescence polarization assay to detect chloramphenicol within SYBR Green I as the source of fluorescence polarization signal. Under optimal conditions, the designed method showed a linear detection range of 0.1-10 nM with a detection limit of 0.06 nM. Additionally, the aptasensor exhibited a high accuracy to the detection of chloramphenicol in milk samples with a recovery rate from 93.7% to 98.4%. Therefore, the developed label free fluorescence polarization aptasensor provides a new idea for the rapid, reliable and sensitive detection of chloramphenicol, which can be applied to food safety control.
Collapse
Affiliation(s)
- Pengfei Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Hualin Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Nuo Duan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Lin Yue
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Qianhui Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Three Squirrels Inc., Wuhu, 241000, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China; Collaborative Innovation Center of Food Safety and Quality Control of Jiangsu Province, Jiangnan University, Wuxi, 214122, China.
| |
Collapse
|
23
|
Joshi K, Kaur S, Kumar R. Cytochrome P450 2C19 gene polymorphisms (CYP2C19*2 and CYP2C19*3) in chronic myeloid leukemia patients: in vitro and in silico studies. J Biomol Struct Dyn 2021; 40:9389-9402. [PMID: 34060427 DOI: 10.1080/07391102.2021.1929491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polymorphisms in the CYP2C19 have a huge impact on drug processing, out of which CYP2C19*2 and CYP2C19*3 are the most common variants associated with reduced metabolism of drugs. Mechanism by which two variants contribute in poor metabolization of drugs and cancer is not well understood. Here, we hypothesized that the mutations in CYP2C19 gene might affect the risk of chronic myeloid leukemia patients (CML). Present study has two main objectives: first to investigate the allele frequencies of CYP2C19*2 and CYP2C19*3 associated gene polymorphisms in CML patients and to elucidate the structural stability, conformation and functions of protein encoded by such variants. Genotyping of CYP2C19 was performed in 103 CML patients and 103 matched healthy controls. Heterozygous genotype of CYP2C19*2 was higher in CML patients (13.59%) than the controls (4.85%). Whereas, CYP2C19*3 allele frequency was not observed in cases as well as in controls. Furthermore, molecular dynamics (MD) simulation was applied to monitor the structural and conformational effect of above mutants. MD simulation results demonstrated that these mutants formed unstable proteins with distorted conformations, altered residues network and affected drug binding site which led to malfunction of mutant proteins. Hence, the study provides the role of CYP2C19 gene polymorphisms in susceptibility to CML population and explored the molecular basis of malignancies caused which may aid in the development of precise medicine or adjusting the drug dosages so as to reduce the chemotherapeutic side effects.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Kaishiv Joshi
- Department of Human Genetics, Punjabi University, Patiala, India
| | - Satbir Kaur
- Department of Human Genetics, Punjabi University, Patiala, India
| | - Rakesh Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
24
|
Zhu M, Wang S. Functional Nucleic‐Acid‐Decorated Spherical Nanoparticles: Preparation Strategies and Current Applications in Cancer Therapy. SMALL SCIENCE 2021. [DOI: 10.1002/smsc.202000056] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Min Zhu
- Department of Pharmaceutical Engineering College of Chemistry and Chemical Engineering Central South University No. 932 South Lushan Rd Changsha Hunan 410083 P. R. China
| | - Shan Wang
- Department of Pharmaceutical Engineering College of Chemistry and Chemical Engineering Central South University No. 932 South Lushan Rd Changsha Hunan 410083 P. R. China
| |
Collapse
|
25
|
Torabi R, Rezvanipour AA, Heiat M. A challenging choice of aptamer for the selective enrichment of ochratoxin A. J Sep Sci 2020; 44:903-907. [PMID: 33289273 DOI: 10.1002/jssc.202001044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 11/23/2020] [Accepted: 11/27/2020] [Indexed: 12/11/2022]
Abstract
In a recent study, the adenosine monophosphate-specific aptamer has been applied for the rapid extraction of ochratoxin A. Although several publications have already reported the selection of adenosine monophosphate, adenosine triphosphate, and adenosine, there is no report on the detection of ochratoxin A using this aptamer. The data of the previous study are surprising since its aptamer-based magnetic metal-organic framework has shown a high selectivity with a very low detection limit for the selection of ochratoxin A. However, numerous studies have demonstrated that each aptamer can specifically bind to a target by folding into a unique structure and can differentiate molecules that differ by only one functional group. This study aimed to deal with the possibility of recognizing ochratoxin A and adenosine monophosphate by adenosine monophosphate-specific aptamer. The procedure was performed by determining structural similarity and alignment, docking adenosine monophosphate and ochratoxin A on aptamer, and monitoring the interactions between ochratoxin A and adenosine monophosphate specific aptamer complex. The results indicated not only the lack of structural similarity between adenosine monophosphate and ochratoxin A but also the little possibility for strong bonds between the ochratoxin A and aptamer.
Collapse
Affiliation(s)
- Raheleh Torabi
- Laboratory of Bioanalysis, Institute of Biochemistry & Biophysics, University of Tehran, Tehran, Iran
| | - Abbas Ali Rezvanipour
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Heiat
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran
| |
Collapse
|
26
|
Structure-switching fluorescence aptasensor for sensitive detection of chloramphenicol. Mikrochim Acta 2020; 187:505. [PMID: 32815083 DOI: 10.1007/s00604-020-04471-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 08/02/2020] [Indexed: 01/09/2023]
Abstract
The performance of chloramphenicol aptamer, including binding thermodynamics, structure switching, and binding domain, was investigated by isothermal titration calorimetry, circular dichroism, and molecular docking. Then, a new fluorescence aptasensor was developed with signal amplification mediated by exonuclease I-catalyzed reaction and hybridization chain reaction (HCR) for chloramphenicol detection. In this system, the aptamer-binding domain is blocked by the initiator of HCR, the aptamer undergoes structure switching in the presence of chloramphenicol, and DNA dissociation occurs. The released aptamer is subsequently recognized and cleaved by Exo I to set free chloramphenicol. With the Exo I-assisted chloramphenicol recycling, an increasing number of initiators were exposed from the digestion of the initiator-aptamer complex. Then, the chain-like assembly of FAM labeled H1 and H2 through HCR was triggered by the initiator, generating a long DNA polymer. Under optimum conditions, the aptasensor exhibited a log-linear range from 0.001 to 100 nM of chloramphenicol and a detection limit of 0.3 pM. Additionally, the designed biosensing platform was applied to determine chloramphenicol in milk and lake water with high accuracy. The current approach provides a new avenue to develop sensitive aptasensors with the assistance of binding mechanism between aptamer and target compounds. Graphical abstract.
Collapse
|