1
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Adachi T, Nakamura S, Michishita A, Kawahara D, Yamamoto M, Hamada M, Nakamura Y. RaptGen-Assisted Generation of an RNA/DNA Hybrid Aptamer against SARS-CoV-2 Spike Protein. Biochemistry 2024; 63:906-912. [PMID: 38457656 PMCID: PMC10993888 DOI: 10.1021/acs.biochem.3c00596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/22/2024] [Accepted: 02/22/2024] [Indexed: 03/10/2024]
Abstract
Optimization of aptamers in length and chemistry is crucial for industrial applications. Here, we developed aptamers against the SARS-CoV-2 spike protein and achieved optimization with a deep-learning-based algorithm, RaptGen. We conducted a primer-less SELEX against the receptor binding domain (RBD) of the spike with an RNA/DNA hybrid library, and the resulting sequences were subjected to RaptGen analysis. Based on the sequence profiling by RaptGen, a short truncation aptamer of 26 nucleotides was obtained and further optimized by a chemical modification of relevant nucleotides. The resulting aptamer is bound to RBD not only of SARS-CoV-2 wildtype but also of its variants, SARS-CoV-1, and Middle East respiratory syndrome coronavirus (MERS-CoV). We concluded that the RaptGen-assisted discovery is efficient for developing optimized aptamers.
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Affiliation(s)
- Tatsuo Adachi
- RIBOMIC
Inc., 3-16-13 Shirokanedai,
Minato-ku, Tokyo 108-0071, Japan
| | | | - Akiya Michishita
- Graduate
School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
- Computational
Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology
(AIST), 3-4-1, Okubo
Shinjuku-ku, Tokyo 169-8555, Japan
| | - Daiki Kawahara
- RIBOMIC
Inc., 3-16-13 Shirokanedai,
Minato-ku, Tokyo 108-0071, Japan
| | - Mizuki Yamamoto
- Research
Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Michiaki Hamada
- Graduate
School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
- Computational
Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology
(AIST), 3-4-1, Okubo
Shinjuku-ku, Tokyo 169-8555, Japan
| | - Yoshikazu Nakamura
- RIBOMIC
Inc., 3-16-13 Shirokanedai,
Minato-ku, Tokyo 108-0071, Japan
- The
Institute of Medical Science, The University
of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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2
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Liu Y, Hu B, Li J, Pei X, Hu X. Perspectives and Prospects on the Application of DNA Aptamer in SARS-CoV-2. Curr Med Chem 2024; 31:273-279. [PMID: 37031389 DOI: 10.2174/0929867330666230408193030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 02/06/2023] [Accepted: 02/22/2023] [Indexed: 04/10/2023]
Affiliation(s)
- Yunyi Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Bei Hu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Juan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Xiaming Pei
- Department of Urology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine. Changsha, Hunan, 410013, China
| | - Xiaoxiao Hu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Research Institute of Hunan University in Chongqing, Chongqing, 401120, China
- Shenzhen Research Institute, Hunan University, Shenzhen, 518000, China
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3
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Huang Y, Wu Q, Zhang J, Zhang Y, Cen S, Yang C, Song Y. Microfluidic Enrichment of Intact SARS-CoV-2 Viral Particles by Stoichiometric Balanced DNA Computation. ACS NANO 2023; 17:21973-21983. [PMID: 37901936 DOI: 10.1021/acsnano.3c08400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
Health diagnostic tools for community safety and environmental monitoring require selective and quantitatively accurate active viral load assessment. Herein, we report a microfluidic enrichment strategy to separate intact SARS-CoV-2 particles by AND logic gate with inputs of cholesterol oligonucleotides for the envelope and aptamers for the spike viral proteins. Considering the unequal quantity of endogenous spikes and lipid membranes on SARS-CoV-2, a dual-domain binding strategy, with two aptamers targeting different spike domains, was applied to balance the spike-envelope stoichiometric ratio. By balancing the stoichiometric with DNA computation and promoting microscale mass transfer of the herringbone chip, the developed strategy enabled high sensitivity detection of pseudotyped SARS-CoV-2 with a limit of detection as low as 37 active virions/μL while distinguishing it from inactive counterparts, other nontarget viruses, and free spike protein. Moreover, the captured viral particles can be released through DNase I treatment with up to 90% efficiency, which is fully compatible with virus culture and sequencing. Overall, the developed strategy not only identified SARS-CoV-2-infected patients (n = 14) with 100% identification from healthy donors (n = 8) but also provided a fresh perspective on the regulation of stoichiometric ratio to achieve a more biologically relevant DNA computation.
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Affiliation(s)
- Yihao Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Qiuyue Wu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Jialu Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Yuqian Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Shiyun Cen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
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4
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Shen H, Yang H. Binding of synthetic nanobodies to the SARS-CoV-2 receptor-binding domain: the importance of salt bridges. Phys Chem Chem Phys 2023; 25:24129-24142. [PMID: 37655617 DOI: 10.1039/d3cp02628k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
In this study, five different SARS-CoV-2 receptor-binding domain (RBD) models were created based on the crystal structures of RBD complexes with two synthetic nanobodies (Sb16 and Sb45). Microsecond all-atom MD simulations revealed that Sb16 and Sb45 substantially stabilized the flexible RBD loop (residues GLU471-SER494) due to the salt bridges and hydrogen bonding interactions between RBD and the synthetic nanobodies. However, the calculation of binding free energy displayed that Sb45 had a higher binding affinity to RBD than Sb16, in agreement with the experimental result. This is because Sb45 has stronger electrostatic attraction to RBD as compared to Sb16. In particular, the salt bridge GLU484-ARG33 in Sb45-RBD is stronger than the GLU484-LYS32 in Sb16-RBD. Furthermore, by comparing the binding affinity of Sb16 for two RBD mutants (E484K and K417N), we found that E484K mutation substantially reduced the binding affinity to Sb16, and K417N mutation had no significant effect, qualitatively in agreement with experimental studies. According to the binding free energy calculation, the strong electrostatic repulsion between LYS32 and LYS484 caused by E484K mutation destroys the salt bridge between LYS32 and GLU484 in the RBD wild type (WT). In contrast, the binding of the K417N mutant to Sb16 effectively maintains the salt bridge between LYS32 and GLU484. Therefore, our research suggests that the salt bridges between RBD and synthetic nanobodies are crucial for binding synthetic nanobodies to RBD, and a SARS-CoV-2 variant can escape neutralization from nanobodies by creating electrostatic repulsion between them.
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Affiliation(s)
- Hujun Shen
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Education University, Guiyang, 550018, China.
| | - Hengxiu Yang
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Education University, Guiyang, 550018, China.
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5
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Chen Y, Yang X, Liu J, Zhang D, He J, Tang L, Li J, Xiang Q. In vitro selection of a single-strand DNA aptamer targeting the receptor-binding domain of SARS-CoV-2 spike protein. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 42:105-118. [PMID: 35949145 DOI: 10.1080/15257770.2022.2109170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Nucleic acid aptamers are developed from a pool of random oligonucleotide libraries with an in vitro selection through systematic evolution of ligands via exponential enrichment (SELEX) process, which are capable of specific and high-affinity molecular binding against targets. The receptor-binding domain (RBD) of spike protein from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is involved in the early stages of viral infection, is a promising target for aptamer selection. Currently, there are no effective approaches to prevent virus from spreading. In this study, a new ssDNA aptamer RBD/S-A1 binding to the RBD of spike protein from SARS-CoV-2 with high affinity (Kd=1.74 ± 0.2 nM) and low cross-binding activity was selected and evaluated. Although aptamers targeting the RBD of spike protein from SARS-CoV-2 have been described in a handful of previous studies, the RBD/S-A1 aptamer identified in this work may be considered as a potential supplementation for the current diagnosis and research of coronavirus SARS-CoV-2.
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Affiliation(s)
- Yongjun Chen
- Department of Neurology, Nanhua Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Xuefeng Yang
- Department of Gastroenterology, Nanhua Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Jian Liu
- Department of Laboratory Medicine, Nanhua Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Dandan Zhang
- Department of Infectious Medicine, Nanhua Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Jun He
- Department of Laboratory Medicine, Nanhua Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Liang Tang
- Academics Working Station, Changsha Medical University, Changsha, China
| | - Jianming Li
- Department of Neurology, Nanhua Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China.,Academics Working Station, Changsha Medical University, Changsha, China
| | - Qin Xiang
- Department of Neurology, Nanhua Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China.,Academics Working Station, Changsha Medical University, Changsha, China
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6
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Geanes ES, LeMaster C, Fraley ER, Khanal S, McLennan R, Grundberg E, Selvarangan R, Bradley T. Cross-reactive antibodies elicited to conserved epitopes on SARS-CoV-2 spike protein after infection and vaccination. Sci Rep 2022; 12:6496. [PMID: 35444221 PMCID: PMC9019795 DOI: 10.1038/s41598-022-10230-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/05/2022] [Indexed: 12/13/2022] Open
Abstract
SARS-CoV-2 is a novel betacoronavirus that caused coronavirus disease 2019 and has resulted in millions of deaths worldwide. Novel coronavirus infections in humans have steadily become more common. Understanding antibody responses to SARS-CoV-2, and identifying conserved, cross-reactive epitopes among coronavirus strains could inform the design of vaccines and therapeutics with broad application. Here, we determined that individuals with previous SARS-CoV-2 infection or vaccinated with the Pfizer-BioNTech BNT162b2 vaccine produced antibody responses that cross-reacted with related betacoronaviruses. Moreover, we designed a peptide-conjugate vaccine with a conserved SARS-CoV-2 S2 spike epitope, immunized mice and determined cross-reactive antibody binding to SARS-CoV-2 and other related coronaviruses. This conserved spike epitope also shared sequence homology to proteins in commensal gut microbiota and could prime immune responses in humans. Thus, SARS-CoV-2 conserved epitopes elicit cross-reactive immune responses to both related coronaviruses and host bacteria that could serve as future targets for broad coronavirus therapeutics and vaccines.
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Affiliation(s)
- Eric S Geanes
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Cas LeMaster
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Elizabeth R Fraley
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Santosh Khanal
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Rebecca McLennan
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Kansas Medical Center, Kansas City, MO, USA.,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Rangaraj Selvarangan
- Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA.,Department of Pathology and Laboratory Medicine, Children's Mercy, Kansas City, MO, USA
| | - Todd Bradley
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA. .,Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA. .,Department of Pediatrics, University of Kansas Medical Center, Kansas City, MO, USA. .,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA.
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7
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Zhang Z, Li J, Gu J, Amini R, Stacey HD, Ang JC, White D, Filipe CDM, Mossman K, Miller MS, Salena BJ, Yamamura D, Sen P, Soleymani L, Brennan JD, Li Y. A Universal DNA Aptamer that Recognizes Spike Proteins of Diverse SARS‐CoV‐2 Variants of Concern. Chemistry 2022; 28:e202200078. [PMID: 35084794 PMCID: PMC9015322 DOI: 10.1002/chem.202200078] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Indexed: 12/15/2022]
Abstract
We report on a unique DNA aptamer, denoted MSA52, that displays universally high affinity for the spike proteins of wildtype SARS‐CoV‐2 as well as the Alpha, Beta, Gamma, Epsilon, Kappa, Delta and Omicron variants. Using an aptamer pool produced from round 13 of selection against the S1 domain of the wildtype spike protein, we carried out one‐round SELEX experiments using five different trimeric spike proteins from variants, followed by high‐throughput sequencing and sequence alignment analysis of aptamers that formed complexes with all proteins. A previously unidentified aptamer, MSA52, showed Kd values ranging from 2 to 10 nM for all variant spike proteins, and also bound similarly to variants not present in the reselection experiments. This aptamer also recognized pseudotyped lentiviruses (PL) expressing eight different spike proteins of SARS‐CoV‐2 with Kd values between 20 and 50 pM, and was integrated into a simple colorimetric assay for detection of multiple PL variants. This discovery provides evidence that aptamers can be generated with high affinity to multiple variants of a single protein, including emerging variants, making it well‐suited for molecular recognition of rapidly evolving targets such as those found in SARS‐CoV‐2.
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Affiliation(s)
- Zijie Zhang
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Jiuxing Li
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Hannah D. Stacey
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- McMaster Immunology Research Centre McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Jann C. Ang
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- McMaster Immunology Research Centre McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Dawn White
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Carlos D. M. Filipe
- Department of Chemical Engineering McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Karen Mossman
- Department of Medicine McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Matthew S. Miller
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- McMaster Immunology Research Centre McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Bruno J. Salena
- Department of Medicine McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Deborah Yamamura
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- Department of Pathology and Molecular Medicine McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Payel Sen
- School of Biomedical Engineering McMaster University 1280 Main Street West Hamilton, Ontario Canada L8S 4K1
| | - Leyla Soleymani
- School of Biomedical Engineering McMaster University 1280 Main Street West Hamilton, Ontario Canada L8S 4K1
| | - John D. Brennan
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- School of Biomedical Engineering McMaster University 1280 Main Street West Hamilton, Ontario Canada L8S 4K1
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8
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Zhang Z, Pandey R, Li J, Gu J, White D, Stacey HD, Ang JC, Steinberg C, Capretta A, Filipe CDM, Mossman K, Balion C, Miller MS, Salena BJ, Yamamura D, Soleymani L, Brennan JD, Li Y. High‐Affinity Dimeric Aptamers Enable the Rapid Electrochemical Detection of Wild‐Type and B.1.1.7 SARS‐CoV‐2 in Unprocessed Saliva. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110819] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Zijie Zhang
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | - Richa Pandey
- Department of Engineering Physics McMaster University Canada
| | - Jiuxing Li
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | - Dawn White
- Biointerfaces Institute McMaster University Canada
| | - Hannah D. Stacey
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University Canada
- McMaster Immunology Research Centre McMaster University Canada
| | - Jann C. Ang
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University Canada
- McMaster Immunology Research Centre McMaster University Canada
| | | | - Alfredo Capretta
- Biointerfaces Institute McMaster University Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University Canada
| | | | - Karen Mossman
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University Canada
- Department of Medicine McMaster University Canada
| | - Cynthia Balion
- Department of Pathology and Molecular Medicine McMaster University Canada
| | - Matthew S. Miller
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University Canada
- McMaster Immunology Research Centre McMaster University Canada
| | | | - Deborah Yamamura
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University Canada
- Department of Pathology and Molecular Medicine McMaster University Canada
| | - Leyla Soleymani
- Department of Engineering Physics McMaster University Canada
- School of Biomedical Engineering McMaster University 1280 Main Street West Hamilton Ontario L8S 4K1 Canada
| | | | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
- Biointerfaces Institute McMaster University Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University Canada
- School of Biomedical Engineering McMaster University 1280 Main Street West Hamilton Ontario L8S 4K1 Canada
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9
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Zhang Z, Pandey R, Li J, Gu J, White D, Stacey HD, Ang JC, Steinberg C, Capretta A, Filipe CDM, Mossman K, Balion C, Miller MS, Salena BJ, Yamamura D, Soleymani L, Brennan JD, Li Y. High-Affinity Dimeric Aptamers Enable the Rapid Electrochemical Detection of Wild-Type and B.1.1.7 SARS-CoV-2 in Unprocessed Saliva. Angew Chem Int Ed Engl 2021; 60:24266-24274. [PMID: 34464491 PMCID: PMC8596624 DOI: 10.1002/anie.202110819] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Indexed: 01/05/2023]
Abstract
We report a simple and rapid saliva-based SARS-CoV-2 antigen test that utilizes a newly developed dimeric DNA aptamer, denoted as DSA1N5, that specifically recognizes the spike proteins of the wildtype virus and its Alpha and Delta variants with dissociation constants of 120, 290 and 480 pM, respectively, and binds pseudotyped lentiviruses expressing the wildtype and alpha trimeric spike proteins with affinity constants of 2.1 pM and 2.3 pM, respectively. To develop a highly sensitive test, DSA1N5 was immobilized onto gold electrodes to produce an electrochemical impedance sensor, which was capable of detecting 1000 viral particles per mL in 1:1 diluted saliva in under 10 min without any further sample processing. Evaluation of 36 positive and 37 negative patient saliva samples produced a clinical sensitivity of 80.5 % and specificity of 100 % and the sensor could detect the wildtype virus as well as the Alpha and Delta variants in the patient samples, which is the first reported rapid test that can detect any emerging variant of SARS-CoV-2.
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Affiliation(s)
- Zijie Zhang
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
| | - Richa Pandey
- Department of Engineering PhysicsMcMaster UniversityCanada
| | - Jiuxing Li
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
| | - Dawn White
- Biointerfaces InstituteMcMaster UniversityCanada
| | - Hannah D. Stacey
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
- McMaster Immunology Research CentreMcMaster UniversityCanada
| | - Jann C. Ang
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
- McMaster Immunology Research CentreMcMaster UniversityCanada
| | | | - Alfredo Capretta
- Biointerfaces InstituteMcMaster UniversityCanada
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
| | | | - Karen Mossman
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
- Department of MedicineMcMaster UniversityCanada
| | - Cynthia Balion
- Department of Pathology and Molecular MedicineMcMaster UniversityCanada
| | - Matthew S. Miller
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
- McMaster Immunology Research CentreMcMaster UniversityCanada
| | | | - Deborah Yamamura
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
- Department of Pathology and Molecular MedicineMcMaster UniversityCanada
| | - Leyla Soleymani
- Department of Engineering PhysicsMcMaster UniversityCanada
- School of Biomedical EngineeringMcMaster University1280 Main Street WestHamiltonOntarioL8S 4K1Canada
| | | | - Yingfu Li
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
- Biointerfaces InstituteMcMaster UniversityCanada
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
- School of Biomedical EngineeringMcMaster University1280 Main Street WestHamiltonOntarioL8S 4K1Canada
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10
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Harini K, Srivastava A, Kulandaisamy A, Gromiha MM. ProNAB: database for binding affinities of protein-nucleic acid complexes and their mutants. Nucleic Acids Res 2021; 50:D1528-D1534. [PMID: 34606614 PMCID: PMC8728258 DOI: 10.1093/nar/gkab848] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 11/16/2022] Open
Abstract
Protein–nucleic acid interactions are involved in various biological processes such as gene expression, replication, transcription, translation and packaging. The binding affinities of protein–DNA and protein–RNA complexes are important for elucidating the mechanism of protein–nucleic acid recognition. Although experimental data on binding affinity are reported abundantly in the literature, no well-curated database is currently available for protein–nucleic acid binding affinity. We have developed a database, ProNAB, which contains more than 20 000 experimental data for the binding affinities of protein–DNA and protein–RNA complexes. Each entry provides comprehensive information on sequence and structural features of a protein, nucleic acid and its complex, experimental conditions, thermodynamic parameters such as dissociation constant (Kd), binding free energy (ΔG) and change in binding free energy upon mutation (ΔΔG), and literature information. ProNAB is cross-linked with GenBank, UniProt, PDB, ProThermDB, PROSITE, DisProt and Pubmed. It provides a user-friendly web interface with options for search, display, sorting, visualization, download and upload the data. ProNAB is freely available at https://web.iitm.ac.in/bioinfo2/pronab/ and it has potential applications such as understanding the factors influencing the affinity, development of prediction tools, binding affinity change upon mutation and design complexes with the desired affinity.
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Affiliation(s)
- Kannan Harini
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Ambuj Srivastava
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Arulsamy Kulandaisamy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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Xu Y, Jiang X, Zhou Y, Ma M, Wang M, Ying B. Systematic Evolution of Ligands by Exponential Enrichment Technologies and Aptamer-Based Applications: Recent Progress and Challenges in Precision Medicine of Infectious Diseases. Front Bioeng Biotechnol 2021; 9:704077. [PMID: 34447741 PMCID: PMC8383106 DOI: 10.3389/fbioe.2021.704077] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/26/2021] [Indexed: 02/05/2023] Open
Abstract
Infectious diseases are considered as a pressing challenge to global public health. Accurate and rapid diagnostics tools for early recognition of the pathogen, as well as individualized precision therapy are essential for controlling the spread of infectious diseases. Aptamers, which were screened by systematic evolution of ligands by exponential enrichment (SELEX), can bind to targets with high affinity and specificity so that have exciting potential in both diagnosis and treatment of infectious diseases. In this review, we provide a comprehensive overview of the latest development of SELEX technology and focus on the applications of aptamer-based technologies in infectious diseases, such as targeted drug-delivery, treatments and biosensors for diagnosing. The challenges and the future development in this field of clinical application will also be discussed.
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Affiliation(s)
- Yixin Xu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Xin Jiang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yanhong Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Ming Ma
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,The First People's Hospital of Shuangliu District, Chengdu/West China (Airport)Hospital Sichuan University, Chengdu, China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
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