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McKenzie LK, Flamme M, Felder PS, Karges J, Bonhomme F, Gandioso A, Malosse C, Gasser G, Hollenstein M. A ruthenium-oligonucleotide bioconjugated photosensitizing aptamer for cancer cell specific photodynamic therapy. RSC Chem Biol 2022; 3:85-95. [PMID: 35128412 PMCID: PMC8729177 DOI: 10.1039/d1cb00146a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/31/2021] [Indexed: 12/15/2022] Open
Abstract
Ruthenium complexes have emerged as a promising class of compounds for use as photosensitizers (PSs) in photodynamic therapy (PDT) due to their attractive photophysical properties and relative ease of chemical alteration. While promising, they generally are not inherently targeting to disease sites and may therefore be prone to side effects and require higher doses. Aptamers are short oligonucleotides that bind specific targets with high affinity. One such aptamer is AS1411, a nucleolin targeting, G-quadruplex forming, DNA aptamer. Here we present the first example of direct conjugation of a Ru(ii) polypyridyl complex-based PS to an aptamer and an assessment of its in vitro cancer cell specific photosensitization including discussion of the challenges faced.
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Affiliation(s)
- Luke K McKenzie
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523 28 rue du Docteur Roux 75724 Paris Cedex 15 France https://research.pasteur.fr/en/team/bioorganic-chemistry-of-nucleic-acids/ +33 1 44 38 94 66
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology 75005 Paris France www.gassergroup.com +33 1 85 78 41 51
| | - Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523 28 rue du Docteur Roux 75724 Paris Cedex 15 France https://research.pasteur.fr/en/team/bioorganic-chemistry-of-nucleic-acids/ +33 1 44 38 94 66
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology 75005 Paris France www.gassergroup.com +33 1 85 78 41 51
- Université de Paris 12 rue de l'École de Médecine 75006 Paris France
| | - Patrick S Felder
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology 75005 Paris France www.gassergroup.com +33 1 85 78 41 51
| | - Johannes Karges
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology 75005 Paris France www.gassergroup.com +33 1 85 78 41 51
| | - Frederic Bonhomme
- Institut Pasteur, Department of Structural Biology and Chemistry, Unité de Chimie Biologique Epigénétique, UMR CNRS 3523 28 rue du Docteur Roux 75724 Paris Cedex 15 France
| | - Albert Gandioso
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology 75005 Paris France www.gassergroup.com +33 1 85 78 41 51
| | - Christian Malosse
- Institut Pasteur, Mass Spectrometry for Biology Unit 28 rue du Docteur Roux 75724 Paris Cedex 15 France
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology 75005 Paris France www.gassergroup.com +33 1 85 78 41 51
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523 28 rue du Docteur Roux 75724 Paris Cedex 15 France https://research.pasteur.fr/en/team/bioorganic-chemistry-of-nucleic-acids/ +33 1 44 38 94 66
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102
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Wang J, Wang DX, Liu B, Jing X, Chen DY, Tang AN, Cui YX, Kong DM. Recent advances in constructing high-order DNA structures. Chem Asian J 2022; 17:e202101315. [PMID: 34989140 DOI: 10.1002/asia.202101315] [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: 11/22/2021] [Revised: 01/04/2022] [Indexed: 11/07/2022]
Abstract
Molecular self-assembly is widely used in the fields of biosensors, molecular devices, efficient catalytic materials, and medical biomaterials. As the carrier of genetic information, DNA is a kind of biomacromolecule composed of deoxyribonucleotide units. DNA nanotechnology extends DNA of its original properties as a molecule that stores and transmits genetic information from its biological environment. By taking advantage of its unique base pairing and inherent biocompatibility to produce structurally-defined supramolecular structures. With the continuously development of DNA technology, the assembly method of DNA nanostructures is not only limited on the basis of DNA hybridization but also other biochemical interactions. In this review, we summarize the latest methods used to construct high-order DNA nanostructures. The problems of DNA nanostructures are discussed and the future directions in this field are provided.
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Affiliation(s)
- Jing Wang
- Nankai University, Department of Chemistry, CHINA
| | | | - Bo Liu
- Nankai University, College of Chemistry, CHINA
| | - Xiao Jing
- Nankai University, College of Chemistry, CHINA
| | - Dan-Ye Chen
- Nankai University, College of Chemistry, CHINA
| | - An-Na Tang
- Nankai University, College of Chemistry, CHINA
| | - Yun-Xi Cui
- Nankai University, College of Chemistry, CHINA
| | - De Ming Kong
- Nankai University, Key Laboratory of Functional Polymer Materials, Weijin road 94, 30071, Tianjin, CHINA
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103
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Slyusarenko M, Shalaev S, Valitova A, Zabegina L, Nikiforova N, Nazarova I, Rudakovskaya P, Vorobiev M, Lezov A, Filatova L, Yevlampieva N, Gorin D, Krzhivitsky P, Malek A. AuNP Aptasensor for Hodgkin Lymphoma Monitoring. BIOSENSORS 2022; 12:23. [PMID: 35049651 PMCID: PMC8774100 DOI: 10.3390/bios12010023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
A liquid biopsy based on circulating small extracellular vesicles (SEVs) has not yet been used in routine clinical practice due to the lack of reliable analytic technologies. Recent studies have demonstrated the great diagnostic potential of nanozyme-based systems for the detection of SEV markers. Here, we hypothesize that CD30-positive Hodgkin and Reed-Sternberg (HRS) cells secrete CD30 + SEVs; therefore, the relative amount of circulating CD30 + SEVs might reflect classical forms of Hodgkin lymphoma (cHL) activity and can be measured by using a nanozyme-based technique. A AuNP aptasensor analytics system was created using aurum nanoparticles (AuNPs) with peroxidase activity. Sensing was mediated by competing properties of DNA aptamers to attach onto surface of AuNPs inhibiting their enzymatic activity and to bind specific markers on SEVs surface. An enzymatic activity of AuNPs was evaluated through the color reaction. The study included characterization of the components of the analytic system and its functionality using transmission and scanning electron microscopy, nanoparticle tracking analysis (NTA), dynamic light scattering (DLS), and spectrophotometry. AuNP aptasensor analytics were optimized to quantify plasma CD30 + SEVs. The developed method allowed us to differentiate healthy donors and cHL patients. The results of the CD30 + SEV quantification in the plasma of cHL patients were compared with the results of disease activity assessment by positron emission tomography/computed tomography (PET-CT) scanning, revealing a strong positive correlation. Moreover, two cycles of chemotherapy resulted in a statistically significant decrease in CD30 + SEVs in the plasma of cHL patients. The proposed AuNP aptasensor system presents a promising new approach for monitoring cHL patients and can be modified for the diagnostic testing of other diseases.
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Affiliation(s)
- Maria Slyusarenko
- Subcellular Technology Laboratory, Department of Hematology and Chemotherapy and Department of Radionuclide Diagnostics, N.N. Petrov National Medical Research Center of Oncology, 197758 St. Petersburg, Russia; (M.S.); (S.S.); (A.V.); (L.Z.); (N.N.); (I.N.); (L.F.); (P.K.)
- The Faculty of Physics and Center for Molecular and Cell Technologies, Saint-Petersburg State University, 199034 St. Petersburg, Russia; (M.V.); (A.L.); (N.Y.)
| | - Sergey Shalaev
- Subcellular Technology Laboratory, Department of Hematology and Chemotherapy and Department of Radionuclide Diagnostics, N.N. Petrov National Medical Research Center of Oncology, 197758 St. Petersburg, Russia; (M.S.); (S.S.); (A.V.); (L.Z.); (N.N.); (I.N.); (L.F.); (P.K.)
| | - Alina Valitova
- Subcellular Technology Laboratory, Department of Hematology and Chemotherapy and Department of Radionuclide Diagnostics, N.N. Petrov National Medical Research Center of Oncology, 197758 St. Petersburg, Russia; (M.S.); (S.S.); (A.V.); (L.Z.); (N.N.); (I.N.); (L.F.); (P.K.)
| | - Lidia Zabegina
- Subcellular Technology Laboratory, Department of Hematology and Chemotherapy and Department of Radionuclide Diagnostics, N.N. Petrov National Medical Research Center of Oncology, 197758 St. Petersburg, Russia; (M.S.); (S.S.); (A.V.); (L.Z.); (N.N.); (I.N.); (L.F.); (P.K.)
| | - Nadezhda Nikiforova
- Subcellular Technology Laboratory, Department of Hematology and Chemotherapy and Department of Radionuclide Diagnostics, N.N. Petrov National Medical Research Center of Oncology, 197758 St. Petersburg, Russia; (M.S.); (S.S.); (A.V.); (L.Z.); (N.N.); (I.N.); (L.F.); (P.K.)
| | - Inga Nazarova
- Subcellular Technology Laboratory, Department of Hematology and Chemotherapy and Department of Radionuclide Diagnostics, N.N. Petrov National Medical Research Center of Oncology, 197758 St. Petersburg, Russia; (M.S.); (S.S.); (A.V.); (L.Z.); (N.N.); (I.N.); (L.F.); (P.K.)
| | - Polina Rudakovskaya
- Center for Photonics and Quantum Materials, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (P.R.); (D.G.)
| | - Maxim Vorobiev
- The Faculty of Physics and Center for Molecular and Cell Technologies, Saint-Petersburg State University, 199034 St. Petersburg, Russia; (M.V.); (A.L.); (N.Y.)
| | - Alexey Lezov
- The Faculty of Physics and Center for Molecular and Cell Technologies, Saint-Petersburg State University, 199034 St. Petersburg, Russia; (M.V.); (A.L.); (N.Y.)
| | - Larisa Filatova
- Subcellular Technology Laboratory, Department of Hematology and Chemotherapy and Department of Radionuclide Diagnostics, N.N. Petrov National Medical Research Center of Oncology, 197758 St. Petersburg, Russia; (M.S.); (S.S.); (A.V.); (L.Z.); (N.N.); (I.N.); (L.F.); (P.K.)
| | - Natalia Yevlampieva
- The Faculty of Physics and Center for Molecular and Cell Technologies, Saint-Petersburg State University, 199034 St. Petersburg, Russia; (M.V.); (A.L.); (N.Y.)
| | - Dmitry Gorin
- Center for Photonics and Quantum Materials, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (P.R.); (D.G.)
| | - Pavel Krzhivitsky
- Subcellular Technology Laboratory, Department of Hematology and Chemotherapy and Department of Radionuclide Diagnostics, N.N. Petrov National Medical Research Center of Oncology, 197758 St. Petersburg, Russia; (M.S.); (S.S.); (A.V.); (L.Z.); (N.N.); (I.N.); (L.F.); (P.K.)
| | - Anastasia Malek
- Subcellular Technology Laboratory, Department of Hematology and Chemotherapy and Department of Radionuclide Diagnostics, N.N. Petrov National Medical Research Center of Oncology, 197758 St. Petersburg, Russia; (M.S.); (S.S.); (A.V.); (L.Z.); (N.N.); (I.N.); (L.F.); (P.K.)
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105
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Qi S, Duan N, Khan IM, Dong X, Zhang Y, Wu S, Wang Z. Strategies to manipulate the performance of aptamers in SELEX, post-SELEX and microenvironment. Biotechnol Adv 2022; 55:107902. [DOI: 10.1016/j.biotechadv.2021.107902] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/21/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023]
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106
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Zhu BC, He J, Xia XY, Jiang J, Liu W, Liu LY, Liang BB, Yao HG, Ke Z, Xia W, Mao ZW. Solution structure of thrombin binding aptamer complex with a non-planar platinum(II) compound. Chem Sci 2022; 13:8371-8379. [PMID: 35919711 PMCID: PMC9297526 DOI: 10.1039/d2sc01196d] [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: 02/27/2022] [Accepted: 05/29/2022] [Indexed: 11/21/2022] Open
Abstract
Thrombin Binding Aptamer (TBA) is a monomolecular well-defined two G-tetrads antiparallel G-quadruplex DNA that inhibits the activity of human α-thrombin. In this report, we synthesized a quasi-cross-shaped platinum(II) compound (L'2LPt)...
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Affiliation(s)
- Bo-Chen Zhu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University Guangzhou 510275 China
| | - Juan He
- School of Pharmaceutical and Chemical Engineering, Guangdong Pharmaceutical University Zhongshan 528458 China
| | - Xiao-Yu Xia
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University Guangzhou 510275 China
| | - Jingxing Jiang
- School of Materials Science and Engineering, PCFM Lab, School of Chemistry, Sun Yat-sen University Guangzhou 510275 China
| | - Wenting Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University Guangzhou 510275 China
| | - Liu-Yi Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University Guangzhou 510275 China
| | - Bing-Bing Liang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University Guangzhou 510275 China
| | - Hua-Gang Yao
- School of Pharmaceutical and Chemical Engineering, Guangdong Pharmaceutical University Zhongshan 528458 China
| | - Zhuofeng Ke
- School of Materials Science and Engineering, PCFM Lab, School of Chemistry, Sun Yat-sen University Guangzhou 510275 China
| | - Wei Xia
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University Guangzhou 510275 China
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University Guangzhou 510275 China
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107
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Yang C, Zhao H, Sun Y, Wang C, Geng X, Wang R, Tang L, Han D, Liu J, Tan W. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3083-3095. [PMID: 35293579 PMCID: PMC8989545 DOI: 10.1093/nar/gkac156] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 01/24/2022] [Accepted: 02/19/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | | | - Cheng Wang
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xinyao Geng
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Ruowen Wang
- To whom correspondence should be addressed. Tel: +86 02168385698; Fax:+86 02168385698;
| | - Lumin Tang
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Da Han
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jianjun Liu
- Correspondence may also be addressed to Jianjun Liu.
| | - Weihong Tan
- Correspondence may also be addressed to Weihong Tan.
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108
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Ding Y, Zhang M, Li C, Xie B, Zhao G, Sun Y. RETRACTED ARTICLE: A reusable aptasensor based on the dual signal amplification of Ce@AuNRs-PAMAM-Fc and DNA walker for ultrasensitive detection of TNF-α. J Solid State Electrochem 2022. [DOI: 10.1007/s10008-020-04885-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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109
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Zhu C, Li L, Yang G, Qu F. Investigating the Influences of Random-Region Length on Aptamer Selection Efficiency Based on Capillary Electrophoresis-SELEX and High-Throughput Sequencing. Anal Chem 2021; 93:17030-17035. [PMID: 34908408 DOI: 10.1021/acs.analchem.1c03661] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
For aptamer selection, the random-region length of an ssDNA library was generally taken in a relatively arbitrary fashion, which may lead to failure for unsuitable target binding. Herein, we coupled high-efficiency capillary electrophoresis (CE)-SELEX and high-throughput sequencing (HTS) to investigate the influences of random-region length. First, one round of selection against programmed cell death-ligand 1 (PD-L1) was performed using ssDNA libraries with random-region lengths of 15, 30, 40, and 60 nt, respectively. A good correlation was observed between candidates' random-region lengths and dissociation constant (Kd), in which the longer sequences presented higher affinity, and the picked Seq 60-1 after one round notably presented a similar affinity toward a reported aptamer through eight rounds. Molecular dynamics (MD) simulation suggested, for PD-L1, the long sequence could supply more noncovalent bonds including hydrogen bonds, electrostatic interactions, and hydrophobic interactions to form a stable protein/aptamer complex. Besides, four other proteins with selective binding performances validated the importance of random-region length. To further investigate how random-region length affects the selection efficiency, a mixed library with random-region lengths ranging from 10 to 50 nt was employed for six rounds of selection against Piezo2. Sequence variations were tracked by HTS, showing the preferential evolution and PCR uncertainty with even higher impact were the main causes. This study suggested random-region length plays a crucial factor, and a mixed library with different random-region sequences can be a worthy choice for increasing the speed of high-affinity aptamer selection. Moreover, the PCR process should be given particular attention in aptamer selection.
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Affiliation(s)
- Chao Zhu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.,Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Linsen Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Ge Yang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Feng Qu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
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110
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Xu J, Zhang X, Yan C, Qin P, Yao L, Wang Q, Chen W. Trigging Isothermal Circular Amplification-Based Tuning of Rigorous Fluorescence Quenching into Complete Restoration on a Multivalent Aptamer Probe Enables Ultrasensitive Detection of Salmonella. Anal Chem 2021; 94:1357-1364. [PMID: 34963277 DOI: 10.1021/acs.analchem.1c04638] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Detection of pathogenic bacteria is of vital significance for combating and preventing infectious diseases. In this work, we developed a multivalent aptamer probe (Multi-VAP)-based trigging isothermal circular amplification (TICA) for rapidly and ultrasensitively detecting Salmonella. In this sensing system, the fluorescence of Multi-VAP was strongly quenched via the dual effect of FRET. Introduction of Salmonella to the system forced the configuration change of Multi-VAP, leading to the occurrence of a TICA responsible for tuning all of the fluorescence-quenched Multi-VAP into a complete restoration state. This prominent feature allows the reasonable combination of a strong background restraint and great target signal amplification into one sensing system, which in turn benefits the improvement of the signal-to-noise ratio to ensure that the system has an ultrahigh sensitivity. Combined with the employment of an aptamer to ensure that it has excellent specificity, the Salmonella can be quantitatively and qualitatively analyzed even from human serum. The total processing merely requires sample addition and incubation. The turnaround time of the complete analysis from "sample-to-result" was within 30 min. With the method to decrease the time to detect and simplify the process to operate, the assay was successfully used as a sensing platform for specific detection of as few as 9 CFU/mL Salmonella.
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Affiliation(s)
- Jianguo Xu
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Xinlei Zhang
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Chao Yan
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China.,Anhui Province Institute of Product Quality Supervision & Inspection, Hefei 230051, P. R. China
| | - Panzhu Qin
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei 230032, China
| | - Li Yao
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Qi Wang
- Key Laboratory of Embryo Development and Reproductive Regulation, Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, Anhui 236037, P. R. China
| | - Wei Chen
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
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111
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Keijzer JF, Albada B. DNA-assisted site-selective protein modification. Biopolymers 2021; 113:e23483. [PMID: 34878181 PMCID: PMC9285461 DOI: 10.1002/bip.23483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/09/2022]
Abstract
Protein modification is important for various types of biomedical research, including proteomics and therapeutics. Many methodologies for protein modification exist, but not all possess the required level of efficiency and site selectivity. This review focuses on the use of DNA to achieve the desired conversions and levels of accuracy in protein modification by using DNA (i) as a template to help concentrate dilute reactants, (ii) as a guidance system to achieve selectivity by binding specific proteins, and (iii) even as catalytic entity or construct to enhance protein modification reactions.
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Affiliation(s)
- Jordi F Keijzer
- Laboratory of Organic Chemistry, Wageningen University and Research, Wageningen, The Netherlands
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University and Research, Wageningen, The Netherlands
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112
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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.
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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
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113
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Zhang X, Xu J, Yan C, Yao L, Shang H, Chen W. A Short- and Long-Range Fluorescence Resonance Energy Transfer-Cofunctionalized Fluorescence Quenching Collapsar Probe Regulates Amplified and Accelerated Detection of Salmonella. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:14294-14301. [PMID: 34797054 DOI: 10.1021/acs.jafc.1c05780] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Accurate and rapid quantification of foodborne pathogens is of great significance for food safety and human health. In this work, we have successfully constructed a fluorescence quenching collapsar probe (FQCP) on the basis of a conventional aptamer-encoded molecular beacon (AEMB) and applied it for the detection of Salmonella. In structure, the FQCP is assembled by AEMBs in fours via specific streptavidin and biotin binding. Such a simple format makes the FQCP cofunctionalized with short- and long-range fluorescence resonance energy transfer (FRET) effects, thereby leading to a significantly suppressed inherent background fluorescence that is much lower than that of the conventional AEMB. Moreover, the FQCP exhibits superior biostability because of the blocking of its 3' terminal. The reaction kinetics of the FQCP for Salmonella recognition is obviously improved since the probe designed with four binding sites increases the probability to react with Salmonella. As a result, the FQCP-based sensing platform can rapidly output the target detection signal within 30 min associated with a greatly improved signal-to-noise ratio up to 32.4. The system was also demonstrated with a well antimatrix effect for ultrasensitive detection of Salmonella from tap water, milk, red bull, green tea, orange juice, and Coca-Cola. Our study provides insights into the facile tailoring of functional nucleic acids for amplified and mix-to-answer detection of foodborne pathogens, which could become a powerful analytical tool for straightforward sensing of pathogens in the fields of food safety analysis, clinical diagnostics, and environmental monitoring.
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Affiliation(s)
- Xinlei Zhang
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jianguo Xu
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Chao Yan
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
- Anhui Province Institute of Product Quality Supervision & Inspection, Hefei 230051, P.R. China
| | - Li Yao
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Huijie Shang
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Wei Chen
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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Yu Y, Wang X, Jia X, Feng Z, Zhang L, Li H, He J, Shen G, Ding X. Aptamer Probes Labeled with Lanthanide-Doped Carbon Nanodots Permit Dual-Modal Fluorescence and Mass Cytometric Imaging. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2102812. [PMID: 34719883 PMCID: PMC8693039 DOI: 10.1002/advs.202102812] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/07/2021] [Indexed: 05/11/2023]
Abstract
High-dimensional imaging mass cytometry (IMC) enables simultaneous quantification of over 35 biomarkers on one tissue section. However, its limited resolution and ultralow acquisition speed remain major issues for general clinical application. Meanwhile, conventional immunofluorescence microscopy (IFM) allows sub-micrometer resolution and rapid identification of the region of interest (ROI), but only operates with low multiplicity. Herein, a series of lanthanide-doped blue-, green-, and red-fluorescent carbon nanodots (namely, B-Cdots(Ln1 ), G-Cdots(Ln2 ), and R-Cdots(Ln3 )) as fluorescence and mass dual-modal tags are developed. Coupled with aptamers, B-Cdots(159 Tb)-A10-3.2, G-Cdots(165 Ho)-AS1411, and R-Cdots(169 Tm)-SYL3C dual-functional aptamer probes, which are then multiplexed with commercially available Maxpar metal-tagged antibodies for analyzing clinical formalin-fixed, paraffin-embedded (FFPE) prostatic adenocarcinoma (PaC) tissue, are further synthesized. The rapid identification of ROI with IFM using fluorescence signals and subsequent multiplexed detection of in situ ROI with IMC using the same tissue section is demonstrated. Dual-modal probes save up to 90% IMC blind scanning time for a standard 3.5 mm × 3.5 mm overall image. Meanwhile, the IFM provides refined details and topological spatial distributions for the functional proteins at optical resolution, which compensates for the low resolution of the IMC imaging.
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Affiliation(s)
- Youyi Yu
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xin Wang
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xiaolong Jia
- Department of UrologyNingbo First HospitalNingbo Hospital of Zhejiang UniversityNingboZhejiang Province315700China
| | - Zijian Feng
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Lulu Zhang
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Hongxia Li
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Jie He
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Guangxia Shen
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
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115
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DNA nanotechnology-facilitated ligand manipulation for targeted therapeutics and diagnostics. J Control Release 2021; 340:292-307. [PMID: 34748871 DOI: 10.1016/j.jconrel.2021.11.004] [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: 08/13/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 11/21/2022]
Abstract
Ligands, mostly binding to proteins to form complexes and catalyze chemical reactions, can serve as drug and probe molecules, as well as sensing elements. DNA nanotechnology can integrate the high editability of DNA nanostructures and the biological activity of ligands into functionalized DNA nanostructures in a manner of controlled ligand stoichiometry, type, and arrangement, which provides significant advantages for targeted therapeutics and diagnostics. As therapeutic agents, multiple- and multivalent-ligands functionalized DNA nanostructures increase ligand-receptor affinity and activate multivalent ligand-receptor interactions, enabling improved regulation of cell signaling and enhanced control of cell behavior. As diagnostic agents, multiple ligands interaction via DNA nanostructures endows DNA nanosensors with high sensitivity and excellent signal transduction capability. Herein, we review the principles and advantages of using DNA nanostructures to manipulate ligands for targeted therapeutics and diagnostics and provide future perspectives.
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A replacement-type electrochemiluminescent aptasensor for lysozyme based on full-electric modification electrode coupled to silica-coated Ru(bpy) 32+/silver nanospheres. Anal Bioanal Chem 2021; 413:7411-7419. [PMID: 34731261 DOI: 10.1007/s00216-021-03696-8] [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: 08/10/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 10/19/2022]
Abstract
This research proposed a replacement-type electrochemiluminescent (ECL) aptasensor for lysozyme (LYZ) detection at trace levels based on a full-electric modification electrode (FEMG) coupled to silica-coated Ru(bpy)32+/silver nanospheres (Ru/SNs@SiO2). The multi-walled carbon nanotubes-doped-thionine (MWCNTs/PTn) electropolymerized modified electrode was decorated with electrodeposited gold nanoparticles (GNs) to form the FEMG. Then, the FEMG was utilized as sensing substrates for the immobilization of the anti-lysozyme aptamer (LA); the stability and number of LA attaching onto the FEMG were dramatically increased. The ECL measurement was used to evaluate the hybridization reaction of LA and the Ru/SNs@SiO2 marked DNA probe, and it was noted as Ia. After the combination of the LA with the LYZ, the target-triggered replacement of the DNA probe was actualized and the ECL measurement descended to Ib. The ECL difference (ΔIECL = Ia - Ib) before and after the replacement event was utilized for quantitation of LYZ. As a result, the fabricated aptasensor with great sensitivity and specificity achieved a wide linear range (10 fM-10 pM) and a low limit of detection (5 fM). It obtained satisfactory recovery for the detection of LYZ in human serum, and the results were identified with the LYZ ELISA kit. Therefore, the proposed ECL sensor is expected to become a promising approach in the field of biomolecule detection.
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118
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Berdnikova DV. Photoswitches for controllable RNA binding: a future approach in the RNA-targeting therapy. Chem Commun (Camb) 2021; 57:10819-10826. [PMID: 34585681 DOI: 10.1039/d1cc04241f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA is an emerging drug target that opens new perspectives in the treatment of viral and bacterial infections, cancer and a range of so far incurable genetic diseases. Among the various strategies towards the design and development of selective and efficient ligands for targeting and detection of therapeutically relevant RNA, photoswitchable RNA binders represent a very promising approach due to the possibility to control the ligand-RNA and protein-RNA interactions by light with high spatiotemporal resolution. However, the field of photoswitchable RNA binders still remains underexplored due to challenging design of lead structures that should combine high RNA binding selectivity with efficient photochemical performance. The aim of this highlight article is to describe the development of photoswitchable noncovalent RNA binders and to outline the current situation and perspectives of this emerging interdisciplinary field.
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Affiliation(s)
- Daria V Berdnikova
- Universität Siegen, Organische Chemie II, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany.
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119
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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120
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Pérez de Carvasal K, Riccardi C, Russo Krauss I, Cavasso D, Vasseur JJ, Smietana M, Morvan F, Montesarchio D. Charge-Transfer Interactions Stabilize G-Quadruplex-Forming Thrombin Binding Aptamers and Can Improve Their Anticoagulant Activity. Int J Mol Sci 2021; 22:9510. [PMID: 34502432 PMCID: PMC8430690 DOI: 10.3390/ijms22179510] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/24/2021] [Accepted: 08/27/2021] [Indexed: 02/07/2023] Open
Abstract
In the search for optimized thrombin binding aptamers (TBAs), we herein describe the synthesis of a library of TBA analogues obtained by end-functionalization with the electron-rich 1,5-dialkoxy naphthalene (DAN) and the electron-deficient 1,8,4,5-naphthalenetetra-carboxylic diimide (NDI) moieties. Indeed, when these G-rich oligonucleotides were folded into the peculiar TBA G-quadruplex (G4) structure, effective donor-acceptor charge transfer interactions between the DAN and NDI residues attached to the extremities of the sequence were induced, providing pseudo-cyclic structures. Alternatively, insertion of NDI groups at both extremities produced TBA analogues stabilized by π-π stacking interactions. All the doubly-modified TBAs were characterized by different biophysical techniques and compared with the analogues carrying only the DAN or NDI residue and unmodified TBA. These modified TBAs exhibited higher nuclease resistance, and their G4 structures were markedly stabilized, as evidenced by increased Tm values compared to TBA. These favorable properties were also associated with improved anticoagulant activity for one DAN/NDI-modified TBA, and for one NDI/NDI-modified TBA. Our results indicated that TBA pseudo-cyclic structuring by ad hoc designed end-functionalization represents an efficient approach to improve the aptamer features, while pre-organizing and stabilizing the G4 structure but allowing sufficient flexibility to the aptamer folding, which is necessary for optimal thrombin recognition.
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Affiliation(s)
- Kévan Pérez de Carvasal
- Institut des Biomolécules Max Mousseron, University Montpellier, CNRS, ENSCM, 34095 Montpellier, France; (K.P.d.C.); (J.-J.V.); (M.S.)
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Naples, Italy; (C.R.); (I.R.K.); (D.C.)
| | - Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Naples, Italy; (C.R.); (I.R.K.); (D.C.)
- CSGI—Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Domenico Cavasso
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Naples, Italy; (C.R.); (I.R.K.); (D.C.)
- CSGI—Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, University Montpellier, CNRS, ENSCM, 34095 Montpellier, France; (K.P.d.C.); (J.-J.V.); (M.S.)
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron, University Montpellier, CNRS, ENSCM, 34095 Montpellier, France; (K.P.d.C.); (J.-J.V.); (M.S.)
| | - François Morvan
- Institut des Biomolécules Max Mousseron, University Montpellier, CNRS, ENSCM, 34095 Montpellier, France; (K.P.d.C.); (J.-J.V.); (M.S.)
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Naples, Italy; (C.R.); (I.R.K.); (D.C.)
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121
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Liu L, Jiang J, Liu G, Jia X, Zhao J, Chen L, Yang P. Hexameric to Trimeric Lanthanide-Included Selenotungstates and Their 2D Honeycomb Organic-Inorganic Hybrid Films Used for Detecting Ochratoxin A. ACS APPLIED MATERIALS & INTERFACES 2021; 13:35997-36010. [PMID: 34288662 DOI: 10.1021/acsami.1c10012] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Two types of organic-inorganic hybrid structure-related lanthanide (Ln)-included selenotungstates (Ln-SeTs) [H2N(CH3)2]11Na7[Ce4(H2PTCA)2(H2O)12(HICA)]2[SeW4O17]2[W2O5]4[SeW9O33]4·64H2O (1, H3PTCA = 1,2,3-propanetricarboxylic acid, H2ICA = itaconic acid) and [H2N(CH3)2]6Na4[Ln4SeW8(H2O)14(H2PTCA)2O28] [SeW9O33]2·31H2O [Ln = Pr3+ (2), Nd3+ (3)] were obtained by Ln nature control. The primary frameworks of 1-3 are composed of trivacant Keggin-type [B-α-SeW9O33]8- and [SeW4Om]n- [Ln = Ce3+ (1), m = 17, n = 6; Ln = Pr3+ (2), Nd3+ (3), m = 18, n = 8] fragments bridged by organic ligands and Ln clusters. Intriguingly, Ln nature results in the degradation of hexameric 1 to trimeric 2-3. Besides, 1@DMDSA and 3@DMDSA composites (DMDSA·Cl = dimethyl distearylammonium chloride) were prepared through the cation exchange method, which were then reorganized to form two-dimensional (2D) honeycomb thin films by the breath figure method. Using these honeycomb thin films as electrode materials, the aptasensors were further established by utilizing methylene blue as an indicator and cDNA and Au nanoparticles as signal amplifiers to enhance the response signal so as to realize the purpose of ochratoxin A (OTA) detection. This work provides a new platform for detecting OTA and explores the application potential of POM-based composites in biological and clinical analyses.
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Affiliation(s)
- Lulu Liu
- Henan Key Laboratory of Polyoxometalate Chemistry, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, People's Republic of China
| | - Jun Jiang
- Henan Key Laboratory of Polyoxometalate Chemistry, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, People's Republic of China
| | - Guoping Liu
- Henan Key Laboratory of Polyoxometalate Chemistry, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, People's Republic of China
| | - Xiaodan Jia
- Henan Key Laboratory of Polyoxometalate Chemistry, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, People's Republic of China
| | - Junwei Zhao
- Henan Key Laboratory of Polyoxometalate Chemistry, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, People's Republic of China
| | - Lijuan Chen
- Henan Key Laboratory of Polyoxometalate Chemistry, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, People's Republic of China
| | - Peng Yang
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, People's Republic of China
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122
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Shen L, Wang P, Ke Y. DNA Nanotechnology-Based Biosensors and Therapeutics. Adv Healthc Mater 2021; 10:e2002205. [PMID: 34085411 DOI: 10.1002/adhm.202002205] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/19/2021] [Indexed: 12/19/2022]
Abstract
Over the past few decades, DNA nanotechnology engenders a vast variety of programmable nanostructures utilizing Watson-Crick base pairing. Due to their precise engineering, unprecedented programmability, and intrinsic biocompatibility, DNA nanostructures cannot only interact with small molecules, nucleic acids, proteins, viruses, and cancer cells, but also can serve as nanocarriers to deliver different therapeutic agents. Such addressability innate to DNA nanostructures enables their use in various fields of biomedical applications such as biosensors and cancer therapy. This review is begun with a brief introduction of the development of DNA nanotechnology, followed by a summary of recent applications of DNA nanostructures in biosensors and therapeutics. Finally, challenges and opportunities for practical applications of DNA nanotechnology are discussed.
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Affiliation(s)
- Luyao Shen
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Pengfei Wang
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
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123
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Ji D, Lyu K, Zhao H, Kwok CK. Circular L-RNA aptamer promotes target recognition and controls gene activity. Nucleic Acids Res 2021; 49:7280-7291. [PMID: 34233000 PMCID: PMC8287958 DOI: 10.1093/nar/gkab593] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/22/2021] [Accepted: 06/28/2021] [Indexed: 12/18/2022] Open
Abstract
Rational design of aptamers to incorporate unnatural nucleotides and special chemical moieties can expand their functional complexity and diversity. Spiegelmer (L-RNA aptamer) is a unique class of aptamer that is composed of unnatural L-RNA nucleotides, and so far there are limited L-RNA aptamer candidates and applications being reported. Moreover, the target binding properties of current L-RNA aptamers require significant improvement. Here, using L-Apt.4-1c as an example, we develop a simple and robust strategy to generate the first circular L-RNA aptamer, cycL-Apt.4-1c, quantitatively, demonstrate substantial enhancement in binding affinity and selectivity toward its target, and notably report novel applications of circular L-RNA aptamer in controlling RNA-protein interaction, and gene activity including telomerase activity and gene expression. Our approach and findings will be applicable to any L-RNA aptamers and open up a new avenue for diverse applications.
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Affiliation(s)
- Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Kaixin Lyu
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Haizhou Zhao
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
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124
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Matsunaga KI, Kimoto M, Lim VW, Tan HP, Wong YQ, Sun W, Vasoo S, Leo YS, Hirao I. High-affinity five/six-letter DNA aptamers with superior specificity enabling the detection of dengue NS1 protein variants beyond the serotype identification. Nucleic Acids Res 2021; 49:11407-11424. [PMID: 34169309 PMCID: PMC8599795 DOI: 10.1093/nar/gkab515] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/24/2021] [Accepted: 06/04/2021] [Indexed: 12/25/2022] Open
Abstract
Genetic alphabet expansion of DNA by introducing unnatural bases (UBs), as a fifth letter, dramatically augments the affinities of DNA aptamers that bind to target proteins. To determine whether UB-containing DNA (UB-DNA) aptamers obtained by affinity selection could spontaneously achieve high specificity, we have generated a series of UB-DNA aptamers (KD: 27-182 pM) targeting each of four dengue non-structural protein 1 (DEN-NS1) serotypes. The specificity of each aptamer is remarkably high, and the aptamers can recognize the subtle variants of DEN-NS1 with at least 96.9% amino acid sequence identity, beyond the capability of serotype identification (69-80% sequence identities). Our UB-DNA aptamers specifically identified two major variants of dengue serotype 1 with 10-amino acid differences in the DEN-NS1 protein (352 aa) in Singaporeans' clinical samples. These results suggest that the high-affinity UB-DNA aptamers generated by affinity selection also acquire high target specificity. Intriguingly, one of the aptamers contained two different UBs as fifth and sixth letters, which are essential for the tight binding to the target. These two types of unnatural bases with distinct physicochemical properties profoundly expand the potential of DNA aptamers. Detection methods incorporating the UB-DNA aptamers will facilitate precise diagnoses of viral infections and other diseases.
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Affiliation(s)
- Ken-Ichiro Matsunaga
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - Michiko Kimoto
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - Vanessa Weixun Lim
- National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore 308442, Singapore
| | - Hui Pen Tan
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - Yu Qian Wong
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - William Sun
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Shawn Vasoo
- National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore 308442, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore 308433, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Dr., Experimental Medicine Building, Singapore 636921, Singapore
| | - Yee Sin Leo
- National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore 308442, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore 308433, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Dr., Experimental Medicine Building, Singapore 636921, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, #10-01, Singapore 117549, Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
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125
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Wada M, Endo T, Hisamoto H, Sueyoshi K. Fractionation of Single-stranded DNAs with/without Stable Preorganized Structures Using Capillary Sieving Electrophoresis for Aptamer Selection. ANAL SCI 2021; 37:799-802. [PMID: 33952863 DOI: 10.2116/analsci.21c003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Aptamers, single-stranded DNAs/RNAs with a strong and specific interaction towards a target molecule, have wide applications in the fields of medicine and biosensors. In conventional aptamer selection methods, it is difficult to obtain "preorganized" and/or "induced-fit" type of aptamers selectively. In this study, separation and fractionation of single-stranded DNAs with/without stable preorganized structures were carried out using capillary sieving electrophoresis. The fractionated DNAs showed different mobilities and thermodynamic stabilities of their secondary structures; this outcome is deemed to be necessary for the synthesis of novel aptasensors with a desirable sensing mechanism.
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Affiliation(s)
- Masahide Wada
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University
| | - Tatsuro Endo
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University
| | - Hideaki Hisamoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University
| | - Kenji Sueyoshi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University.,PRESTO, Japan Science and Technology Agency
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126
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Multifunctional nanoparticles as optical biosensing probe for breast cancer detection: A review. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2021; 127:112249. [PMID: 34225888 DOI: 10.1016/j.msec.2021.112249] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 05/11/2021] [Accepted: 06/05/2021] [Indexed: 12/15/2022]
Abstract
Optical biosensors show attractive performance in medical sensing in the event of using different nanoparticles in their design. Owing to their unique optical characteristics and biological compatibility, gold nanoparticles (GNPs), silver nanoparticles (AgNPs), bimetallic nanoparticles and magnetic nanoparticles have been broadly implemented in making sensing tools. The functionalization of these nanoparticles with different components provides an excellent opportunity to assemble selective and sensitive sensing materials to detect various biological molecules related to breast cancer. This review summarizes the recent application of optical biosensing devices based on nanomaterials and discusses their pros and cons to improve breast cancer detection in real samples. In particular, the main constituent elements of these optical biosensors including recognition and transducer elements, types of applied nanostructures, analytical sensing procedures, sensor detection ranges and limit of detection (LOD), are expressed in detail.
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127
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Yu C, Li L, Ding Y, Liu H, Cui H, Zhang F, Lin J, Duan Y. A sensitive molecularly imprinted electrochemical aptasensor for highly specific determination of melamine. Food Chem 2021; 363:130202. [PMID: 34304106 DOI: 10.1016/j.foodchem.2021.130202] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/19/2021] [Accepted: 05/22/2021] [Indexed: 12/29/2022]
Abstract
An electrochemical aptamer sensor based on gold nanoparticles (AuNPs) was developed for highly specific sensing of melamine (MEL), which combines molecularly imprinted polymers (MIPs) and aptamers. AuNPs were synthesized by simple reduction of sodium citrate and characterized by transmission electron microscopy. The MIP membranes with particular recognition sites were formed by electropolymerization of dopamine (DA) with polythymine (poly T) aptamers as functional monomers and melamine as template molecules. Under optimal experimental conditions, this molecularly imprinted electrochemical aptamer sensor (MIEAS) exhibits a linear relationship between 10-12 M and 10-4 M for detecting MEL with the detection limit of 6.7 × 10-13 M. Moreover, this sensor displays excellent selectivity, reproducibility and stability. The milk samples analysis has confirmed the potential application of this MIEAS to quantitative detection of melamine.
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Affiliation(s)
- Chenhong Yu
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Li Li
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, PR China.
| | - Yaping Ding
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, PR China.
| | - Huajie Liu
- School of Chemical Science and Engineering, Tongji University, Shanghai 200092, PR China.
| | - Hanyue Cui
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Fenfen Zhang
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, PR China
| | - Jiaxin Lin
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Yingchun Duan
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, PR China
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128
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Abbasi H, Rahbar N, Kouchak M, Khalil Dezfuli P, Handali S. Functionalized liposomes as drug nanocarriers for active targeted cancer therapy: a systematic review. J Liposome Res 2021; 32:195-210. [PMID: 33729077 DOI: 10.1080/08982104.2021.1903035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cancer is a broad term used to describe a group of diseases that have more than 270 types. Today, due to the suffering of patients from the side effects of existing methods in the treatment of cancer such as chemotherapy and radiotherapy, the employment of targeted methods in the treatment of this disease has been received much consideration. In recent years, nanoparticles have revolutionized in the treatment of many diseases such as cancer. Among these nanoparticles, liposomes are more considerable. Active targeted liposomes show an important role in the selective action of the drug on cancer cells. Until now, a variety of anti-cancer agents have been reported for targeted delivery to cancer cells using liposomes. The results of in vitro and studies in vivo have been shown that selective action of the targeted liposomes is increased with reduced side effects and toxicity compared with free drugs or non-targeted liposomes. This systematic review expresses the reports of this type of drug delivery system. Search terms were searched through several online databases including PubMed, Scopus, and Science Direct from 1990 to 2019 and the quality evaluation was performed. Out of 11,676 published articles, 196 articles met the inclusion criteria. The current report reviews developments in the liposomes targeted with aptamer, transferrin, folate, and monoclonal antibodies.
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Affiliation(s)
- Hanieh Abbasi
- Nanotechnology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Nadereh Rahbar
- Nanotechnology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Medicinal Chemistry, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Maryam Kouchak
- Nanotechnology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Pharmaceutics, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Parna Khalil Dezfuli
- School of Pharmacy Library, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Somayeh Handali
- Medical Biomaterial Research Center (MBRC), Tehran University of Medical Sciences, Tehran, Iran
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129
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Niederlender S, Fontaine JJ, Karadjian G. Potential applications of aptamers in veterinary science. Vet Res 2021; 52:79. [PMID: 34078451 PMCID: PMC8172000 DOI: 10.1186/s13567-021-00948-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/23/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers are small nucleic acids that fold in a three-dimensional conformation allowing them to bind specifically to a target. This target can be an organic molecule, free or carried in cells or tissues, or inorganic components, such as metal ions. Analogous to monoclonal antibodies, aptamers however have certain advantages over the latter: e.g., high specificity for their target, no to low immunogenicity and easy in vitro selection. Since their discovery more than 30 years ago, aptamers have led to various applications, although mainly restricted to basic research. This work reviews the applications of aptamers in veterinary science to date. First, we present aptamers, how they are selected and their properties, then we give examples of applications in food and environmental safety, as well as in diagnosis and medical treatment in the field of veterinary medicine. Because examples of applications in veterinary medicine are scarce, we explore the potential avenues for future applications based on discoveries made in human medicine. Aptamers may offer new possibilities for veterinarians to diagnose certain diseases—particularly infectious diseases—more rapidly or “at the patient’s bedside”. All the examples highlight the growing interest in aptamers and the premises of a potential market. Aptamers may benefit animals as well as their owners, breeders and even public health in a “One Health” approach.
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Affiliation(s)
- Solène Niederlender
- École Nationale Vétérinaire d'Alfort, Université Paris-Est Sup, 7 avenue du Général de Gaulle, 94700, Maisons-Alfort, France
| | - Jean-Jacques Fontaine
- UMR BIPAR 956, ANSES, INRAE, École Nationale Vétérinaire d'Alfort, Université Paris-Est Sup, 7 avenue du Général de Gaulle, 94700, Maisons-Alfort, France
| | - Grégory Karadjian
- UMR BIPAR, Laboratoire de Santé Animale, ANSES, INRAE, École Nationale Vétérinaire d'Alfort, Université Paris-Est Sup, 94700, Maisons-Alfort, France.
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130
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Li Z, Fu X, Huang J, Zeng P, Huang Y, Chen X, Liang C. Advances in Screening and Development of Therapeutic Aptamers Against Cancer Cells. Front Cell Dev Biol 2021; 9:662791. [PMID: 34095130 PMCID: PMC8170048 DOI: 10.3389/fcell.2021.662791] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/21/2021] [Indexed: 01/10/2023] Open
Abstract
Cancer has become the leading cause of death in recent years. As great advances in medical treatment, emerging therapies of various cancers have been developed. Current treatments include surgery, radiotherapy, chemotherapy, immunotherapy, and targeted therapy. Aptamers are synthetic ssDNA or RNA. They can bind tightly to target molecules due to their unique tertiary structure. It is easy for aptamers to be screened, synthesized, programmed, and chemically modified. Aptamers are emerging targeted drugs that hold great potentials, called therapeutic aptamers. There are few types of therapeutic aptamers that have already been approved by the US Food and Drug Administration (FDA) for disease treatment. Now more and more therapeutic aptamers are in the stage of preclinical research or clinical trials. This review summarized the screening and development of therapeutic aptamers against different types of cancer cells.
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Affiliation(s)
- Zheng Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Xuekun Fu
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Jie Huang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Peiyuan Zeng
- Department of Biochemistry, University of Victoria, Victoria, BC, Canada
| | - Yuhong Huang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Xinxin Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Chao Liang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
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131
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Liu M, Xi L, Tan T, Jin L, Wang Z, He N. A novel aptamer-based histochemistry assay for specific diagnosis of clinical breast cancer tissues. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2020.11.072] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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132
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Zhang H, Yao S, Song X, Xu K, Wang J, Li J, Zhao C, Jin M. One-step colorimetric detection of Staphylococcus aureus based on target-induced shielding against the peroxidase mimicking activity of aptamer-functionalized gold-coated iron oxide nanocomposites. Talanta 2021; 232:122448. [PMID: 34074432 DOI: 10.1016/j.talanta.2021.122448] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 04/04/2021] [Accepted: 04/18/2021] [Indexed: 12/30/2022]
Abstract
Staphylococcus aureus (S. aureus) is one of the most threatened food-borne pathogens. Thus, it is necessary to establish fast, portable and reliable tools to realize the identification of S. aureus. Herein, the authors describe an effective colorimetric-based biosensor for the detection of S. aureus in multiple types of samples. Initially, a nanozyme composed of gold and iron oxide nanoparticles was synthesized and further modified with S. aureus-specific aptamer via Au-S bond. By utilizing the intrinsic peroxidase-like activity of the above magnetic conjugates, 3,3',5,5'-tetramethylbenzidine (TMB) can be transferred to oxTMB by oxidation of hydrogen peroxide (H2O2), resulting in a visible blue color. However, the introduction of S. aureus can turn off the UV-vis absorbance signals of TMB-H2O2 system, due to the identification property of the nanozyme probe. Consequently, the optical density of the mixed solution measured at 652 nm decreased linearly as the concentration of S. aureus increased from 10 to 106 CFU mL-1, with the visible limit of detection as low as 10 CFU mL-1. The as-prepared sensor can detect S. aureus in spiked water, milk and urine samples quantitatively during 12 min without any pre-enrichment, separation or washing steps. In our perception, the one-step colorimetric assay show promise in practical on-site detection of S. aureus.
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Affiliation(s)
- Huiwen Zhang
- School of Public Health, Jilin University, Changchun, 130021, China
| | - Shuo Yao
- School of Public Health, Jilin University, Changchun, 130021, China
| | - Xiuling Song
- School of Public Health, Jilin University, Changchun, 130021, China
| | - Kun Xu
- School of Public Health, Jilin University, Changchun, 130021, China
| | - Juan Wang
- School of Public Health, Jilin University, Changchun, 130021, China
| | - Juan Li
- School of Public Health, Jilin University, Changchun, 130021, China.
| | - Chao Zhao
- School of Public Health, Jilin University, Changchun, 130021, China.
| | - Minghua Jin
- School of Public Health, Jilin University, Changchun, 130021, China.
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133
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Luo Q, Wang W, Tan J, Yuan Q. Surface Modified Persistent Luminescence Probes for Biosensing and Bioimaging: A Review. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202000583] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Qiang Luo
- Institute of Chemical Biology and Nanomedicine (ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, Hunan University Changsha Hunan 410082 China
| | - Wenjie Wang
- Institute of Chemical Biology and Nanomedicine (ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, Hunan University Changsha Hunan 410082 China
| | - Jie Tan
- Institute of Chemical Biology and Nanomedicine (ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, Hunan University Changsha Hunan 410082 China
| | - Quan Yuan
- Institute of Chemical Biology and Nanomedicine (ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, Hunan University Changsha Hunan 410082 China
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry, College of Chemistry and Molecular Sciences Wuhan University Wuhan Hubei 430072 China
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134
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Chudinov AV, Vasiliskov VA, Kuznetsova VE, Lapa SA, Kolganova NA, Timofeev EN. Mononucleotide repeat expansions with non-natural polymerase substrates. Sci Rep 2021; 11:2423. [PMID: 33510377 PMCID: PMC7844250 DOI: 10.1038/s41598-021-82150-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 01/15/2021] [Indexed: 12/25/2022] Open
Abstract
Replicative strand slippage is a biological phenomenon, ubiquitous among different organisms. However, slippage events are also relevant to non-natural replication models utilizing synthetic polymerase substrates. Strand slippage may notably affect the outcome of the primer extension reaction with repetitive templates in the presence of non-natural nucleoside triphosphates. In the current paper, we studied the ability of Taq, Vent (exo-), and Deep Vent (exo-) polymerases to produce truncated, full size, or expanded modified strands utilizing non-natural 2′-deoxyuridine nucleotide analogues and different variants of the homopolymer template. Our data suggest that the slippage of the primer strand is dependent on the duplex fluttering, incorporation efficiency for a particular polymerase-dNTP pair, rate of non-templated base addition, and presence of competing nucleotides.
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Affiliation(s)
- Alexander V Chudinov
- W. A. Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilov St. 32, Moscow, Russia, 119991
| | - Vadim A Vasiliskov
- W. A. Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilov St. 32, Moscow, Russia, 119991
| | - Viktoriya E Kuznetsova
- W. A. Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilov St. 32, Moscow, Russia, 119991
| | - Sergey A Lapa
- W. A. Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilov St. 32, Moscow, Russia, 119991
| | - Natalia A Kolganova
- W. A. Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilov St. 32, Moscow, Russia, 119991
| | - Edward N Timofeev
- W. A. Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilov St. 32, Moscow, Russia, 119991.
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135
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Smirnov I, Kolganova N, Troisi R, Sica F, Timofeev E. Expanding the recognition interface of the thrombin-binding aptamer HD1 through modification of residues T3 and T12. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:863-871. [PMID: 33614235 PMCID: PMC7868722 DOI: 10.1016/j.omtn.2021.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/08/2021] [Indexed: 01/11/2023]
Abstract
Post-SELEX modification of DNA aptamers is an established strategy to improve their affinity or inhibitory characteristics. In this study, we examined the possibility of increasing the recognition interface between the thrombin-binding aptamer HD1 (TBA) and thrombin by adding a chemically modified side chain to selected nucleotide residues. A panel of 22 TBA variants with N3-modified residues T3 and T12 was prepared by a two-step modification procedure. Aptamers were characterized by a combination of biophysical and biochemical methods. We identified mutants with enhanced affinity and improved anticoagulant activity. The crystal structures of thrombin complexes with three selected modified variants revealed that the modified pyrimidine base invariably allocates in proximity to thrombin residues Tyr76 and Ile82 due to the directing role of the unmodified TT loop. The modifications induced an increase in the contact areas between thrombin and the modified TBAs. Comparative analysis of the structural, biochemical, and biophysical data suggests that the non-equivalent binding modes of the mutants with thrombin in the T3- and T12-modified series account for the observed systematic differences in their affinity characteristics. In this study, we show that extending the recognition surface between the protein and modified aptamers is a promising approach that may improve characteristics of aptamer ligands.
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Affiliation(s)
- Igor Smirnov
- Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
| | - Natalia Kolganova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Edward Timofeev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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136
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Saito S. SELEX-based DNA Aptamer Selection: A Perspective from the Advancement of Separation Techniques. ANAL SCI 2021; 37:17-26. [PMID: 33132238 DOI: 10.2116/analsci.20sar18] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 10/22/2020] [Indexed: 11/23/2022]
Abstract
DNA aptamers, which are short, single-stranded DNA sequences that selectively bind to target substances (proteins, cells, small molecules, metal ions), can be acquired by means of the systematic evolution of ligands by exponential enrichment (SELEX) methodology. In the SELEX procedure, one of the keys for the effective acquisition of high-affinity and functional aptamer sequences is the separation stage to isolate target-bound DNA from unbound DNA in a randomized DNA library. In this review, various remarkable advancements in separation techniques for SELEX-based aptamer selection developed in this decade, are described and discussed, including CE-, microfluidic chip-, solid phase-, and FACS-based SELEX along with other methods.
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Affiliation(s)
- Shingo Saito
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo Sakura, Saitama, 338-8570, Japan.
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137
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Zuo C, Guo Y, Li J, Peng Z, Bai S, Yang S, Wang D, Chen H, Xie G. A nanoprobe for fluorescent monitoring of microRNA and targeted delivery of drugs. RSC Adv 2021; 11:8871-8878. [PMID: 35423397 PMCID: PMC8695329 DOI: 10.1039/d1ra00154j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/19/2021] [Indexed: 12/14/2022] Open
Abstract
Multifunctional nano-materials that can be used to monitor the expression of specific biomarkers and serve as vehicles for controlled drug delivery are highly desirable. Herein, we report a new DNA-hybrid-gated core–shell upconversion nanoprobe (UCNP@MOF/DOX) for fluorescence analysis of microRNA-21 (miR-21), which also triggers the release of drug loaded in the probes for on-demand anti-cancer treatment. The nanoprobe is built on the merits of ultraviolet-visible light of upconversion nanoparticles (UCNPs) excited by near-infrared (NIR) and extraordinary loading capability of metal–organic frameworks (MOFs) for drug delivery. Controlled release of doxorubicin (DOX) from the nanoprobe by miR-21 underwent the following two-stage kinetics: a fast release stage specifically triggered by miR-21 and proportional to miR-21 concentration and a slow stage observed in both gated and ungated nanoprobes due to collapse of the UIO-66-NH2 coatings via ligand exchange with phosphates. In addition, the nanoprobe showed good selectivity, a linear response towards miR-21 ranging from 4 nM to 500 nM, and a limit of detection in 4 nM, which precluded unintended payload leakage due to low-abundance endogenous miR-21 expression in normal cells. Moreover, based on a dual-targeted delivery system constituted by AS1411-mediated recognition and responsive release of DOX, a specific cytotoxic efficacy was observed in MCF-7 cells. The present work provides a smart and robust nanoprobe for real-time detection of miRNA and dual-responsive drug delivery in tumor cells. A DNA-hybrid-gated core–shell upconversion nanoprobe is prepared for both fluorescent monitoring of miR-21 and on-demand delivery of DOX. It showed good selectivity towards miR-21 and demonstrated specific cytotoxic efficacy towards MCF-7 cells.![]()
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Affiliation(s)
- Chen Zuo
- Key Laboratory of Laboratory Medical Diagnostics
- Ministry of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
| | - Yongcan Guo
- Department of Laboratory Medicine
- Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University
- Luzhou
- P. R. China
| | - Junjie Li
- Key Laboratory of Laboratory Medical Diagnostics
- Ministry of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
| | - Zhiping Peng
- Department of Radiological Medicine and Oncology
- College of Basic Medicine
- Chongqing Medical University
- Chongqing
- P. R. China
| | - Shulian Bai
- Key Laboratory of Laboratory Medical Diagnostics
- Ministry of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
| | - Shuangshuang Yang
- Key Laboratory of Laboratory Medical Diagnostics
- Ministry of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
| | - Ding Wang
- Key Laboratory of Laboratory Medical Diagnostics
- Ministry of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
| | - Hui Chen
- Department of Laboratory Medicine
- The First Affiliated Hospital of Chongqing Medical University
- Chongqing
- P. R. China
| | - Guoming Xie
- Key Laboratory of Laboratory Medical Diagnostics
- Ministry of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
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138
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Ducongé F. Aptamers for Molecular Imaging. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00034-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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139
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McKenzie LK, El-Khoury R, Thorpe JD, Damha MJ, Hollenstein M. Recent progress in non-native nucleic acid modifications. Chem Soc Rev 2021; 50:5126-5164. [DOI: 10.1039/d0cs01430c] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.
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Affiliation(s)
- Luke K. McKenzie
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
| | | | | | | | - Marcel Hollenstein
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
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140
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Duan B, Zou S, Sun Y, Xu X. Fabrication of tumor-targeting composites based on the triple helical β-glucan through conjugation of aptamer. Carbohydr Polym 2020; 254:117476. [PMID: 33357929 DOI: 10.1016/j.carbpol.2020.117476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/31/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022]
Abstract
Herein the nucleic acid aptamers were attached to the polydeoxyadenylic acid (poly(dA)) tail for improving the tumor-targetability and cellular internalization of s-LNT/poly(dA) composite composed of two single chains of triple helical β-glucan lentinan (s-LNT) and one poly(dA) chain. The in vitro results demonstrate that the cellular uptake of s-LNT/poly(dA) composites in MCF-7 cancer cells was enhanced effectively after attaching the aptamer. The as-prepared fluorescin isothiocyanate (FITC)-labelled LNT (LNT-FITC) through grafting was used for tracing the enhanced tumor-targetability of the composites. As a result, the cellular internalization of the LNT-FITC into MCF-7 and 4T1 cancer cells was further increased by the aptamer conjugated to poly(dA). Meanwhile, the in vivo experiments further demonstrate more s-LNT/poly(dA)-aptamer composites were effectively accumulated at the tumor site compared with s-LNT alone. This work provides a novel strategy for fabricating triplex β-glucan as delivery vectors with active tumor-targetability.
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Affiliation(s)
- Bingchao Duan
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Siwei Zou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Ying Sun
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaojuan Xu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China; Hubei Engineering Center of Natural Polymers-based Medical Materials, Wuhan University, Wuhan, 430072, China.
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141
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Ondruš M, Sýkorová V, Bednárová L, Pohl R, Hocek M. Enzymatic synthesis of hypermodified DNA polymers for sequence-specific display of four different hydrophobic groups. Nucleic Acids Res 2020; 48:11982-11993. [PMID: 33152081 PMCID: PMC7708046 DOI: 10.1093/nar/gkaa999] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
A set of modified 2'-deoxyribonucleoside triphosphates (dNTPs) bearing a linear or branched alkane, indole or phenyl group linked through ethynyl or alkyl spacer were synthesized and used as substrates for polymerase synthesis of hypermodified DNA by primer extension (PEX). Using the alkyl-linked dNTPs, the polymerase synthesized up to 22-mer fully modified oligonucleotide (ON), whereas using the ethynyl-linked dNTPs, the enzyme was able to synthesize even long sequences of >100 modified nucleotides in a row. In PCR, the combinations of all four modified dNTPs showed only linear amplification. Asymmetric PCR or PEX with separation or digestion of the template strand can be used for synthesis of hypermodified single-stranded ONs, which are monodispersed polymers displaying four different substituents on DNA backbone in sequence-specific manner. The fully modified ONs hybridized with complementary strands and modified DNA duplexes were found to exist in B-type conformation (B- or C-DNA) according to CD spectral analysis. The modified DNA can be replicated with high fidelity to natural DNA through PCR and sequenced. Therefore, this approach has a promising potential in generation and selection of hypermodified aptamers and other functional polymers.
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Affiliation(s)
- Marek Ondruš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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142
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Alijani H, Noori A, Faridi N, Bathaie S, Mousavi MF. Aptamer-functionalized Fe3O4@MOF nanocarrier for targeted drug delivery and fluorescence imaging of the triple-negative MDA-MB-231 breast cancer cells. J SOLID STATE CHEM 2020. [DOI: 10.1016/j.jssc.2020.121680] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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143
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Cao J, Su J, An M, Yang Y, Zhang Y, Zuo J, Zhang N, Zhao Y. Novel DEK-Targeting Aptamer Delivered by a Hydrogel Microneedle Attenuates Collagen-Induced Arthritis. Mol Pharm 2020; 18:305-316. [PMID: 33253580 DOI: 10.1021/acs.molpharmaceut.0c00954] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DEK protein is critical to the formation of neutrophil extracellular traps (NETs) in rheumatoid arthritis (RA). Blocking DEK using the aptamer DTA via articular injection has been shown to have robust anti-inflammatory efficacy in a previous study. However, DTA is prone to nuclease degradation and renal clearance in vivo. RA is a systemic disease that involves multiple joints, and local injection is impractical in clinical settings. In this study, DTA was modified with methoxy groups on all deoxyribose sugar units and inverted deoxythymidine on the 3' end (DTA4) to enhance its stability against nuclease. DTA4 is stable for 72 h in 90% mouse serum and maintains a high binding affinity to DEK. DTA4 effectively inhibits the formation of NETs and the migration of HUVECs in vitro. DTA4 was then modified with cholesterol on its 5' end to form DTA6. DTA6 dramatically reduces DEK expression in inflammatory RAW264.7 cells. A hydrogel microneedle (hMN) was then fabricated for the transdermal delivery of DTA6. The hMN maintains morphological integrity after absorbing the aptamer solution, effectively pierces the skin, and rapidly releases DTA6 into the dermis. The DTA6-loaded hMN significantly attenuates inflammation and protects joints from cartilage/bone erosion in collagen-induced arthritis (CIA) mice.
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Affiliation(s)
- Jian Cao
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, Henan, P. R. China
| | - Jingjing Su
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, Henan, P. R. China
| | - Mengchen An
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, Henan, P. R. China
| | - Yang Yang
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, Henan, P. R. China
| | - Yi Zhang
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, Henan, P. R. China
| | - Jing Zuo
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, Henan, P. R. China
| | - Nan Zhang
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, Henan, P. R. China.,Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Henan Province, Zhengzhou 450001, Henan, P. R. China.,Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Henan Province, Zhengzhou 450001, Henan, P. R. China
| | - Yongxing Zhao
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, Henan, P. R. China.,Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Henan Province, Zhengzhou 450001, Henan, P. R. China.,Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, Henan Province, Zhengzhou 450001, Henan, P. R. China
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144
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Shatunova EA, Korolev MA, Omelchenko VO, Kurochkina YD, Davydova AS, Venyaminova AG, Vorobyeva MA. Aptamers for Proteins Associated with Rheumatic Diseases: Progress, Challenges, and Prospects of Diagnostic and Therapeutic Applications. Biomedicines 2020; 8:biomedicines8110527. [PMID: 33266394 PMCID: PMC7700471 DOI: 10.3390/biomedicines8110527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid aptamers capable of affine and specific binding to their molecular targets have now established themselves as a very promising alternative to monoclonal antibodies for diagnostic and therapeutic applications. Although the main focus in aptamers’ research and development for biomedicine is made on cardiovascular, infectious, and malignant diseases, the use of aptamers as therapeutic or diagnostic tools in the context of rheumatic diseases is no less important. In this review, we consider the main features of aptamers that make them valuable molecular tools for rheumatologists, and summarize the studies on the selection and application of aptamers for protein biomarkers associated with rheumatic diseases. We discuss the progress in the development of aptamer-based diagnostic assays and targeted therapeutics for rheumatic disorders, future prospects in the field, and issues that have yet to be addressed.
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Affiliation(s)
- Elizaveta A. Shatunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.A.S.); (A.S.D.); (A.G.V.)
| | - Maksim A. Korolev
- Research Institute of Clinical and Experimental Lymphology, Affiliated Branch of Federal Research Center of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, 630060 Novosibirsk, Russia; (M.A.K.); (V.O.O.); (Y.D.K.)
| | - Vitaly O. Omelchenko
- Research Institute of Clinical and Experimental Lymphology, Affiliated Branch of Federal Research Center of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, 630060 Novosibirsk, Russia; (M.A.K.); (V.O.O.); (Y.D.K.)
| | - Yuliya D. Kurochkina
- Research Institute of Clinical and Experimental Lymphology, Affiliated Branch of Federal Research Center of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, 630060 Novosibirsk, Russia; (M.A.K.); (V.O.O.); (Y.D.K.)
| | - Anna S. Davydova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.A.S.); (A.S.D.); (A.G.V.)
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.A.S.); (A.S.D.); (A.G.V.)
| | - Mariya A. Vorobyeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.A.S.); (A.S.D.); (A.G.V.)
- Correspondence:
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Riccardi C, Napolitano E, Musumeci D, Montesarchio D. Dimeric and Multimeric DNA Aptamers for Highly Effective Protein Recognition. Molecules 2020; 25:E5227. [PMID: 33182593 PMCID: PMC7698228 DOI: 10.3390/molecules25225227] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/14/2022] Open
Abstract
Multivalent interactions frequently occur in biological systems and typically provide higher binding affinity and selectivity in target recognition than when only monovalent interactions are operative. Thus, taking inspiration by nature, bivalent or multivalent nucleic acid aptamers recognizing a specific biological target have been extensively studied in the last decades. Indeed, oligonucleotide-based aptamers are suitable building blocks for the development of highly efficient multivalent systems since they can be easily modified and assembled exploiting proper connecting linkers of different nature. Thus, substantial research efforts have been put in the construction of dimeric/multimeric versions of effective aptamers with various degrees of success in target binding affinity or therapeutic activity enhancement. The present review summarizes recent advances in the design and development of dimeric and multimeric DNA-based aptamers, including those forming G-quadruplex (G4) structures, recognizing different key proteins in relevant pathological processes. Most of the designed constructs have shown improved performance in terms of binding affinity or therapeutic activity as anti-inflammatory, antiviral, anticoagulant, and anticancer agents and their number is certainly bound to grow in the next future.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini, 5, I-80131 Naples, Italy
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
- Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
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146
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Shrivastava G, Bakshi HA, Aljabali AA, Mishra V, Hakkim FL, Charbe NB, Kesharwani P, Chellappan DK, Dua K, Tambuwala MM. Nucleic Acid Aptamers as a Potential Nucleus Targeted Drug Delivery System. Curr Drug Deliv 2020; 17:101-111. [PMID: 31906837 DOI: 10.2174/1567201817666200106104332] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 10/04/2019] [Accepted: 11/02/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Nucleus targeted drug delivery provides several opportunities for the treatment of fatal diseases such as cancer. However, the complex nucleocytoplasmic barriers pose significant challenges for delivering a drug directly and efficiently into the nucleus. Aptamers representing singlestranded DNA and RNA qualify as next-generation highly advanced and personalized medicinal agents that successfully inhibit the expression of certain proteins; possess extraordinary gene-expression for manoeuvring the diseased cell's fate with negligible toxicity. In addition, the precisely directed aptamers to the site of action present a tremendous potential to reach the nucleus by escaping the ensuing barriers to exhibit a better drug activity and gene expression. OBJECTIVE This review epigrammatically highlights the significance of targeted drug delivery and presents a comprehensive description of the principal barriers faced by the nucleus targeted drug delivery paradigm and ensuing complexities thereof. Eventually, the progress of nucleus targeting with nucleic acid aptamers and success achieved so far have also been reviewed. METHODS Systematic literature search was conducted of research published to date in the field of nucleic acid aptamers. CONCLUSION The review specifically points out the contribution of individual aptamers as the nucleustargeting agent rather than aptamers in conjugated form.
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Affiliation(s)
- Garima Shrivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India
| | - Hamid A Bakshi
- SAAD Centre for Pharmacy and Diabetes, School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, County Londonderry BT52 1SA Northern Ireland, United Kingdom
| | - Alaa A Aljabali
- Faculty of Pharmacy, Department of Pharmaceutical Sciences, Yarmouk University, Irbid, Jordan
| | - Vijay Mishra
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara (Punjab), India
| | - Faruck L Hakkim
- Department of Mathematics and Sciences, College of Arts and Applied Sciences, Dhofar University, Salalah, Oman
| | - Nitin B Charbe
- Departamento de Quimica Organica, Facultad de Quimicay de Farmacia, Pontificia Universidad Catolica de Chile, Av. Vicuña McKenna 4860, Macul, Santiago 7820436, Chile
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Dinesh K Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Bukit Jalil 57000, Kuala Lumpur, Malaysia
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Murtaza M Tambuwala
- SAAD Centre for Pharmacy and Diabetes, School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, County Londonderry BT52 1SA Northern Ireland, United Kingdom
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147
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YANG JW, WANG CY, LUO L, GUO L, XIE JW. Applications and Prospects of Oligonucleotide Aptamers in Mass Spectrometry. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60056-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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148
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Li S, Liu X, Liu S, Guo M, Liu C, Pei M. Fluorescence sensing strategy based on aptamer recognition and mismatched catalytic hairpin assembly for highly sensitive detection of alpha-fetoprotein. Anal Chim Acta 2020; 1141:21-27. [PMID: 33248654 DOI: 10.1016/j.aca.2020.10.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/05/2020] [Accepted: 10/15/2020] [Indexed: 12/23/2022]
Abstract
At present, alpha fetoprotein (AFP) is mainly used as a serum marker of primary Hepatocellular carcinoma. A simple, enzyme-free sensing strategy is introduced for highly sensitive fluorescence detection of AFP. This detection strategy is based on aptamer recognition and mismatched catalytic hairpin assembly (MCHA). At first, Trigger is locked by aptamer before the introduction of AFP in this aptamer-MCHA system. The aptamer preferentially combines with AFP via powerful attraction in the presence of AFP. This results in the release of trigger and initiation of MCHA cycle, thus forming the H1 and H2 double chain complexes (denoted as H1@H2). Finally, H1@H2 and double chain structure containing fluorophore and its quenched group- BHQ1 (denoted as F@Q) initiated displacement reaction, which caused double chain separation and fluorescence recovery. This assay produces a wide detection range, which is from 0.1 ng mL-1 to 10 μg mL-1 and the limit of detection as 0.033 ng mL-1. The whole detection process was performed at 37 °C for 60 min. In addition, this assay had high anti-interference ability and could be used to detect AFP in clinical serum. This novel AFP detection strategy is able to screen of Hepatocellular carcinoma.
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Affiliation(s)
- Shengqiang Li
- Clinical Laboratory, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300000, China
| | - Xu Liu
- Clinical Laboratory, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300000, China
| | - Shenglin Liu
- Clinical Laboratory, Tianjin Xi Qing Hospital Tianjin, 300000, China
| | - Mei Guo
- Clinical Laboratory, Tianjin Xi Qing Hospital Tianjin, 300000, China
| | - Cuiying Liu
- Clinical Laboratory, Tianjin Xi Qing Hospital Tianjin, 300000, China.
| | - Ming Pei
- Nephrology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine Tianjin, 300000, China.
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149
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Liu M, Zhang B, Li Z, Wang Z, Li S, Liu H, Deng Y, He N. Precise discrimination of Luminal A breast cancer subtype using an aptamer in vitro and in vivo. NANOSCALE 2020; 12:19689-19701. [PMID: 32966497 DOI: 10.1039/d0nr03324c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Precise discrimination of breast cancer remains a challenge in clinical medicine, which depends on the development of novel specific molecular probes. However, the current technologies and antibodies cannot achieve precise discrimination of breast cancer subtypes very well. To address this problem, a novel truncated DNA aptamer MF3Ec was developed in this work. Aptamer MF3Ec exhibited high specificity and binding affinity against MCF-7 breast cancer cells with a Kd value of 18.95 ± 2.9 nM which is four times lower than that of the original aptamer, and could work at 4 °C, 25 °C and 37 °C with no obvious differences. Besides, aptamer MF3Ec displayed better stability in serum samples with a long existence time of about 12 h. Moreover, fluorescence imaging experiments indicated that aptamer MF3Ec was able to distinguish MCF-7 breast cancer cells from SK-BR-3, MDA-MB-231 and MCF-10A breast cancer cell subtypes, and differentiate the tumor-bearing mice and xenografted tissue sections of MCF-7 breast cancer cells from those of MDA-MB-231 and SK-BR-3 breast cancer cells in vivo and in vitro, respectively. Finally, clinical experiments indicated that aptamer MF3Ec could distinguish Luminal A breast cancer subtype from Luminal B (HER2+), HER2-enriched, and triple-negative breast cancer subtypes, para-carcinoma tissues and normal breast tissues. Collectively, all these results suggest that aptamer MF3Ec is a promising probe for precise discrimination and targeted therapy of Luminal A breast cancer molecular subtype.
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Affiliation(s)
- Mei Liu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education (Southeast University), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China.
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Han J, Gao L, Wang J, Wang J. Application and development of aptamer in cancer: from clinical diagnosis to cancer therapy. J Cancer 2020; 11:6902-6915. [PMID: 33123281 PMCID: PMC7592013 DOI: 10.7150/jca.49532] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/20/2020] [Indexed: 01/04/2023] Open
Abstract
Traditional anticancer therapies can cause serious side effects in clinical treatment due to their nonspecific of tumor cells. Aptamers, also termed as 'chemical antibodies', are short DNA or RNA oligonucleotides selected from the synthetic large random single-strand oligonucleotide library by systematic evolution of ligands by exponential enrichment (SELEX) to bind to lots of different targets, such as proteins or nucleic acid structures. Aptamers have good affinities and high specificity with target molecules, thus may be able to act as drugs themselves to directly inhibit the proliferation of tumor cells, or own great potentialities in the targeted drug delivery systems which can be used in tumor diagnosis and target specific tumor cells, thereby minimizing the toxicity to normal cells. Here we review the unique properties of aptamer represents a great opportunity when applied to the rapidly developing fields of biotechnology and discuss the recent developments in the use of aptamers as powerful tools for analytic, diagnostic and therapeutic applications for cancer.
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Affiliation(s)
- Jing Han
- Department of Reproductive Medicine, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, 046000 China
| | - Liang Gao
- Department of Dermatology, Heji Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, 046000 China
| | - Jinsheng Wang
- Department of Pathology, Changzhi Medical College, Changzhi, Shanxi, 046000 China
| | - Jia Wang
- Department of Immunology, Changzhi Medical College, Changzhi, Shanxi, 046000 China
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