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Wang C, Lan X, Zhu L, Wang Y, Gao X, Li J, Tian H, Liang Z, Xu W. Construction Strategy of Functionalized Liposomes and Multidimensional Application. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2309031. [PMID: 38258399 DOI: 10.1002/smll.202309031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/30/2023] [Indexed: 01/24/2024]
Abstract
Liposomes are widely used in the biological field due to their good biocompatibility and surface modification properties. With the development of biochemistry and material science, many liposome structures and their surface functional components have been modified and optimized one by one, pushing the liposome platform from traditional to functionalized and intelligent, which will better satisfy and expand the needs of scientific research. However, a main limiting factor effecting the efficiency of liposomes is the complicated environmental conditions in the living body. Currently, in order to overcome the above problem, functionalized liposomes have become a very promising strategy. In this paper, binding strategies of liposomes with four main functional elements, namely nucleic acids, antibodies, peptides, and stimuli-responsive motif have been summarized for the first time. In addition, based on the construction characteristics of functionalized liposomes, such as drug-carrying, targeting, long-circulating, and stimulus-responsive properties, a comprehensive overview of their features and respective research progress are presented. Finally, the paper critically presents the limitations of these functionalized liposomes in the current applications and also prospectively suggests the future development directions, aiming to accelerate realization of their industrialization.
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Affiliation(s)
- Chengyun Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Beijing, 100083, China
- College of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, 071000, China
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Xinyue Lan
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Yanhui Wang
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Xinru Gao
- College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Beijing, 100083, China
| | - Jie Li
- College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Hongtao Tian
- College of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Zhihong Liang
- College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Beijing, 100083, China
| | - Wentao Xu
- College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
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2
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Li P, Zhu C, Liu LS, Han CTJ, Chu HC, Li Z, Mao Z, Wang F, Lo PK. Ultra-stable threose nucleic acid-based biosensors for rapid and sensitive nucleic acid detection and in vivo imaging. Acta Biomater 2024; 177:472-485. [PMID: 38296012 DOI: 10.1016/j.actbio.2024.01.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 01/04/2024] [Accepted: 01/22/2024] [Indexed: 02/13/2024]
Abstract
The human genome's nucleotide sequence variation, such as single nucleotide mutations, can cause numerous genetic diseases. However, detecting nucleic acids accurately and rapidly in complex biological samples remains a major challenge. While natural deoxyribonucleic acid (DNA) has been used as biorecognition probes, it has limitations like poor specificity, reproducibility, nuclease-induced enzymatic degradation, and reduced bioactivity on solid surfaces. To address these issues, we introduce a stable and reliable biosensor called graphene oxide (GO)- threose nucleic acid (TNA). It comprises chemically modified TNA capture probes on GO for detecting and imaging target nucleic acids in vitro and in vivo, distinguishing single nucleobase mismatches, and monitoring dynamic changes in target microRNA (miRNA). By loading TNA capture probes onto the GO substrate, the GO-TNA sensing platform for nucleic acid detection demonstrates a significant 88-fold improvement in the detection limit compared to TNA probes alone. This platform offers a straightforward preparation method without the need for costly and labor-intensive isolation procedures or complex chemical reactions, enabling real-time analysis. The stable TNA-based GO sensing nanoplatform holds promise for disease diagnosis, enabling rapid and accurate detection and imaging of various disease-related nucleic acid molecules at the in vivo level. STATEMENT OF SIGNIFICANCE: The study's significance lies in the development of the GO-TNA biosensor, which addresses limitations in nucleic acid detection. By utilizing chemically modified nucleic acid analogues, the biosensor offers improved reliability and specificity, distinguishing single nucleobase mismatches and avoiding false signals. Additionally, its ability to detect and image target nucleic acids in vivo facilitates studying disease mechanisms. The simplified preparation process enhances practicality and accessibility, enabling real-time analysis. The biosensor's potential applications extend beyond healthcare, contributing to environmental analysis and food safety. Overall, this study's findings have substantial implications for disease diagnosis, biomedical research, and diverse applications, advancing nucleic acid detection and its impact on various fields.
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Affiliation(s)
- Pan Li
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, P. R. China
| | - Chiying Zhu
- Shenzhen Clinical Medical College, Guangzhou University of Chinese Medicine, 518116 Shenzhen, P. R. China
| | - Ling Sum Liu
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, Wood Lane, London W12 0BZ, United Kingdom
| | - Chang Tristan Juin Han
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, P. R. China
| | - Hoi Ching Chu
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, P. R. China
| | - Zhenhua Li
- The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), 523059 Dongguan, P. R. China
| | - Zhengwei Mao
- Department of Polymer Science and Engineering, Zhejiang University, 310027 Hangzhou, P. R. China.
| | - Fei Wang
- The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), 523059 Dongguan, P. R. China.
| | - Pik Kwan Lo
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, P. R. China; Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, 518057 Shenzhen, P. R. China.
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3
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Nie W, He K, Zhao Z, Luo X, Liu J. Luminescent Gold Nanoparticles with Discrete DNA Valences for Precisely Controlled Transport at the Subcellular Level. Angew Chem Int Ed Engl 2023; 62:e202314896. [PMID: 37929305 DOI: 10.1002/anie.202314896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/07/2023]
Abstract
Ultrasmall luminescent gold nanoparticles (AuNPs) with excellent capabilities to cross biological barriers offer great promise in designing intelligent model nanomedicines for investigating structure-property relationships at the subcellular level. However, the strict surface controllability of ultrasmall AuNPs is challenging because of their small size. Herein, we report a facile in situ method for precisely controlling DNA aptamer valences on the surface of luminescent AuNPs with emission in the second near-infrared window using a phosphorothioate-modified DNA aptamer, AS1411, as a template. The discrete DNA aptamer number of AS1411-functionalized AuNPs (AS1411-AuNPs, ≈1.8 nm) with emission at 1030 nm was controlled in one aptamer (V1), two aptamers (V2), and four aptamers (V4). It was then discovered that not only the tumor-targeting efficiencies but also the subcellular transport of AS1411-AuNPs were precisely dependent on valences. A slight increase in valence from V1 to V2 increased tumor-targeting efficiencies and resulted in higher nucleus accumulation, whereas a further increase in valence (e.g., V4) significantly increased tumor-targeting efficiencies and led to higher cytomembrane accumulation. These results provide a basis for the strict surface control of nanomedicines in the precise regulation of in vivo transport at the subcellular level and their translation into clinical practice in the future.
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Affiliation(s)
- Wenyan Nie
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Kui He
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Zhipeng Zhao
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Xiaoxi Luo
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Jinbin Liu
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, China
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Wang D, Li Y, Deng X, Torre M, Zhang Z, Li X, Zhang W, Cullion K, Kohane DS, Weldon CB. An aptamer-based depot system for sustained release of small molecule therapeutics. Nat Commun 2023; 14:2444. [PMID: 37117194 PMCID: PMC10147605 DOI: 10.1038/s41467-023-37002-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/24/2023] [Indexed: 04/30/2023] Open
Abstract
Delivery of hydrophilic small molecule therapeutics by traditional drug delivery systems is challenging. Herein, we have used the specific interaction between DNA aptamers and drugs to create simple and effective drug depot systems. The specific binding of a phosphorothioate-modified aptamer to drugs formed non-covalent aptamer/drug complexes, which created a sustained release system. We demonstrated the effectiveness of this system with small hydrophilic molecules, the site 1 sodium channel blockers tetrodotoxin and saxitoxin. The aptamer-based delivery system greatly prolonged the duration of local anesthesia and reduced systemic toxicity. The beneficial effects of the aptamers were restricted to the compounds they were specific to. These studies establish aptamers as a class of highly specific, modifiable drug delivery systems, and demonstrate potential usefulness in the management of postoperative pain.
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Affiliation(s)
- Dali Wang
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Yang Li
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Xiaoran Deng
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Matthew Torre
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Zipei Zhang
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Xiyu Li
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Wei Zhang
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kathleen Cullion
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Daniel S Kohane
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - Christopher B Weldon
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.
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5
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Chen Z, Luo H, Gubu A, Yu S, Zhang H, Dai H, Zhang Y, Zhang B, Ma Y, Lu A, Zhang G. Chemically modified aptamers for improving binding affinity to the target proteins via enhanced non-covalent bonding. Front Cell Dev Biol 2023; 11:1091809. [PMID: 36910146 PMCID: PMC9996316 DOI: 10.3389/fcell.2023.1091809] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
Nucleic acid aptamers are ssDNA or ssRNA fragments that specifically recognize targets. However, the pharmacodynamic properties of natural aptamers consisting of 4 naturally occurring nucleosides (A, G, C, T/U) are generally restricted for inferior binding affinity than the cognate antibodies. The development of high-affinity modification strategies has attracted extensive attention in aptamer applications. Chemically modified aptamers with stable three-dimensional shapes can tightly interact with the target proteins via enhanced non-covalent bonding, possibly resulting in hundreds of affinity enhancements. This review overviewed high-affinity modification strategies used in aptamers, including nucleobase modifications, fluorine modifications (2'-fluoro nucleic acid, 2'-fluoro arabino nucleic acid, 2',2'-difluoro nucleic acid), structural alteration modifications (locked nucleic acid, unlocked nucleic acid), phosphate modifications (phosphorothioates, phosphorodithioates), and extended alphabets. The review emphasized how these high-affinity modifications function in effect as the interactions with target proteins, thereby refining the pharmacodynamic properties of aptamers.
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Affiliation(s)
- Zefeng Chen
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Hang Luo
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Amu Gubu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Aptacure Therapeutics Limited, Kowloon, Hong Kong SAR, China
| | - Sifan Yu
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Huarui Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Hong Dai
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Yihao Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Baoting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Yuan Ma
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, Hong Kong SAR, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, Hong Kong SAR, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, Hong Kong SAR, China
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6
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Lee SH, Ng CX, Wong SR, Chong PP. MiRNAs Overexpression and Their Role in Breast Cancer: Implications for Cancer Therapeutics. Curr Drug Targets 2023; 24:484-508. [PMID: 36999414 DOI: 10.2174/1389450124666230329123409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/20/2022] [Accepted: 01/30/2023] [Indexed: 04/01/2023]
Abstract
MicroRNAs have a plethora of roles in various biological processes in the cells and most human cancers have been shown to be associated with dysregulation of the expression of miRNA genes. MiRNA biogenesis involves two alternative pathways, the canonical pathway which requires the successful cooperation of various proteins forming the miRNA-inducing silencing complex (miRISC), and the non-canonical pathway, such as the mirtrons, simtrons, or agotrons pathway, which bypasses and deviates from specific steps in the canonical pathway. Mature miRNAs are secreted from cells and circulated in the body bound to argonaute 2 (AGO2) and miRISC or transported in vesicles. These miRNAs may regulate their downstream target genes via positive or negative regulation through different molecular mechanisms. This review focuses on the role and mechanisms of miRNAs in different stages of breast cancer progression, including breast cancer stem cell formation, breast cancer initiation, invasion, and metastasis as well as angiogenesis. The design, chemical modifications, and therapeutic applications of synthetic anti-sense miRNA oligonucleotides and RNA mimics are also discussed in detail. The strategies for systemic delivery and local targeted delivery of the antisense miRNAs encompass the use of polymeric and liposomal nanoparticles, inorganic nanoparticles, extracellular vesicles, as well as viral vectors and viruslike particles (VLPs). Although several miRNAs have been identified as good candidates for the design of antisense and other synthetic modified oligonucleotides in targeting breast cancer, further efforts are still needed to study the most optimal delivery method in order to drive the research beyond preclinical studies.
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Affiliation(s)
- Sau Har Lee
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
- Centre for Drug Discovery and Molecular Pharmacology (CDDMP), Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Chu Xin Ng
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Sharon Rachel Wong
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Pei Pei Chong
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
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7
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Mráziková K, Kruse H, Mlýnský V, Auffinger P, Šponer J. Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions. J Chem Inf Model 2022; 62:6182-6200. [PMID: 36454943 DOI: 10.1021/acs.jcim.2c01064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Phosphate···π, also called anion···π, contacts occur between nucleobases and anionic phosphate oxygens (OP2) in r(GNRA) and r(UNNN) U-turn motifs (N = A,G,C,U; R = A,G). These contacts were investigated using state-of-the-art quantum-chemical methods (QM) to characterize their physicochemical properties and to serve as a reference to evaluate AMBER force field (AFF) performance. We found that phosphate···π interaction energies calculated with the AFF for dimethyl phosphate···nucleobase model systems are less stabilizing in comparison with double-hybrid DFT and that minimum contact distances are larger for all nucleobases. These distance stretches are also observed in large-scale AFF vs QM/MM computations and classical molecular dynamics (MD) simulations on several r(gcGNRAgc) tetraloop hairpins when compared to experimental data extracted from X-ray/cryo-EM structures (res. ≤ 2.5 Å) using the WebFR3D bioinformatic tool. MD simulations further revealed shifted OP2/nucleobase positions. We propose that discrepancies between the QM and AFF result from a combination of missing polarization in the AFF combined with too large AFF Lennard-Jones (LJ) radii of nucleobase carbon atoms in addition to an exaggerated short-range repulsion of the r-12 LJ repulsive term. We compared these results with earlier data gathered on lone pair···π contacts in CpG Z-steps occurring in r(UNCG) tetraloops. In both instances, charge transfer calculations do not support any significant n → π* donation effects. We also investigated thiophosphate···π contacts that showed reduced stabilizing interaction energies when compared to phosphate···π contacts. Thus, we challenge suggestions that the experimentally observed enhanced thermodynamic stability of phosphorothioated r(GNRA) tetraloops can be explained by larger London dispersion.
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Affiliation(s)
- Klaudia Mráziková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00Brno, Czech Republic
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65Brno, Czech Republic
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65Brno, Czech Republic
| | - Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg67084, France
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65Brno, Czech Republic
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8
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Hu Y, Wang Y, Singh J, Sun R, Xu L, Niu X, Huang K, Bai G, Liu G, Zuo X, Chen C, Qin PZ, Fang X. Phosphorothioate-Based Site-Specific Labeling of Large RNAs for Structural and Dynamic Studies. ACS Chem Biol 2022; 17:2448-2460. [PMID: 36069699 PMCID: PMC10186269 DOI: 10.1021/acschembio.2c00199] [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] [Indexed: 01/19/2023]
Abstract
Pulsed electron-electron double resonance (PELDOR) spectroscopy, X-ray scattering interferometry (XSI), and single-molecule Förster resonance energy transfer (smFRET) are molecular rulers that provide inter- or intramolecular pair-wise distance distributions in the nanometer range, thus being ideally suitable for structural and dynamic studies of biomolecules including RNAs. The prerequisite for such applications requires site-specific labeling of biomolecules with spin labels, gold nanoparticles, and fluorescent tags, respectively. Recently, site-specific labeling of large RNAs has been achieved by a combination of transcription of an expanded genetic alphabet containing A-T/G-C base pairs and NaM-TPT3 unnatural base pair (UBP) with post-transcriptional modifications at UBP bases by click chemistry or amine-NHS ester reactions. However, due to the bulky sizes of functional groups or labeling probes used, such strategies might cause structural perturbation and decrease the accuracy of distance measurements. Here, we synthesize an α-thiophosphorylated variant of rTPT3TP (rTPT3αS), which allows for post-transcriptional site-specific labeling of large RNAs at the internal α-phosphate backbone via maleimide-modified probes. Subsequent PELDOR, XSI, and smFRET measurements result in narrower distance distributions than labeling at the TPT3 base. The presented strategy provides a new route to empower the molecular rulers for structural and dynamic studies of large RNA and its complex.
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Affiliation(s)
- Yanping Hu
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yan Wang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jaideep Singh
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Ruirui Sun
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lilei Xu
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaolin Niu
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Keyun Huang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guangcan Bai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Guoquan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont Illinois 60439, United States
| | - Chunlai Chen
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Peter Z Qin
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
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9
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Flamme M, Hanlon S, Marzuoli I, Püntener K, Sladojevich F, Hollenstein M. Evaluation of 3'-phosphate as a transient protecting group for controlled enzymatic synthesis of DNA and XNA oligonucleotides. Commun Chem 2022; 5:68. [PMID: 36697944 PMCID: PMC9814670 DOI: 10.1038/s42004-022-00685-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/12/2022] [Indexed: 01/28/2023] Open
Abstract
Chemically modified oligonucleotides have advanced as important therapeutic tools as reflected by the recent advent of mRNA vaccines and the FDA-approval of various siRNA and antisense oligonucleotides. These sequences are typically accessed by solid-phase synthesis which despite numerous advantages is restricted to short sequences and displays a limited tolerance to functional groups. Controlled enzymatic synthesis is an emerging alternative synthetic methodology that circumvents the limitations of traditional solid-phase synthesis. So far, most approaches strived to improve controlled enzymatic synthesis of canonical DNA and no potential routes to access xenonucleic acids (XNAs) have been reported. In this context, we have investigated the possibility of using phosphate as a transient protecting group for controlled enzymatic synthesis of DNA and locked nucleic acid (LNA) oligonucleotides. Phosphate is ubiquitously employed in natural systems and we demonstrate that this group displays most characteristics required for controlled enzymatic synthesis. We have devised robust synthetic pathways leading to these challenging compounds and we have discovered a hitherto unknown phosphatase activity of various DNA polymerases. These findings open up directions for the design of protected DNA and XNA nucleoside triphosphates for controlled enzymatic synthesis of chemically modified nucleic acids.
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Affiliation(s)
- Marie Flamme
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université de Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724 Paris Cedex 15, Paris, France
| | - Steven Hanlon
- grid.417570.00000 0004 0374 1269Pharmaceutical Devision, Synthetic Molecules Technical Development, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Irene Marzuoli
- grid.417570.00000 0004 0374 1269Pharmaceutical Devision, Synthetic Molecules Technical Development, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Kurt Püntener
- grid.417570.00000 0004 0374 1269Pharmaceutical Devision, Synthetic Molecules Technical Development, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Filippo Sladojevich
- grid.417570.00000 0004 0374 1269Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Marcel Hollenstein
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université de Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724 Paris Cedex 15, Paris, France
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10
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Liu Y, Teng L, Yin B, Meng H, Yin X, Huan S, Song G, Zhang XB. Chemical Design of Activatable Photoacoustic Probes for Precise Biomedical Applications. Chem Rev 2022; 122:6850-6918. [PMID: 35234464 DOI: 10.1021/acs.chemrev.1c00875] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Photoacoustic (PA) imaging technology, a three-dimensional hybrid imaging modality that integrates the advantage of optical and acoustic imaging, has great application prospects in molecular imaging due to its high imaging depth and resolution. To endow PA imaging with the ability for real-time molecular visualization and precise biomedical diagnosis, numerous activatable molecular PA probes which can specifically alter their PA intensities upon reacting with the targets or biological events of interest have been developed. This review highlights the recent developments of activatable PA probes for precise biomedical applications including molecular detection of the biotargets and imaging of the biological events. First, the generation mechanism of PA signals will be given, followed by a brief introduction to contrast agents used for PA probe design. Then we will particularly summarize the general design principles for the alteration of PA signals and activatable strategies for developing precise PA probes. Furthermore, we will give a detailed discussion of activatable PA probes in molecular detection and biomedical imaging applications in living systems. At last, the current challenges and outlooks of future PA probes will be discussed. We hope that this review will stimulate new ideas to explore the potentials of activatable PA probes for precise biomedical applications in the future.
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Affiliation(s)
- Yongchao Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Lili Teng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Baoli Yin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Hongmin Meng
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou 450001, China
| | - Xia Yin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Shuangyan Huan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Guosheng Song
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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11
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Wang F, Li P, Chu HC, Lo PK. Nucleic Acids and Their Analogues for Biomedical Applications. BIOSENSORS 2022; 12:bios12020093. [PMID: 35200353 PMCID: PMC8869748 DOI: 10.3390/bios12020093] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 05/07/2023]
Abstract
Nucleic acids are emerging as powerful and functional biomaterials due to their molecular recognition ability, programmability, and ease of synthesis and chemical modification. Various types of nucleic acids have been used as gene regulation tools or therapeutic agents for the treatment of human diseases with genetic disorders. Nucleic acids can also be used to develop sensing platforms for detecting ions, small molecules, proteins, and cells. Their performance can be improved through integration with other organic or inorganic nanomaterials. To further enhance their biological properties, various chemically modified nucleic acid analogues can be generated by modifying their phosphodiester backbone, sugar moiety, nucleobase, or combined sites. Alternatively, using nucleic acids as building blocks for self-assembly of highly ordered nanostructures would enhance their biological stability and cellular uptake efficiency. In this review, we will focus on the development and biomedical applications of structural and functional natural nucleic acids, as well as the chemically modified nucleic acid analogues over the past ten years. The recent progress in the development of functional nanomaterials based on self-assembled DNA-based platforms for gene regulation, biosensing, drug delivery, and therapy will also be presented. We will then summarize with a discussion on the advanced development of nucleic acid research, highlight some of the challenges faced and propose suggestions for further improvement.
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Affiliation(s)
- Fei Wang
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Pan Li
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Hoi Ching Chu
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
- Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
- Correspondence:
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12
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Hunsicker-Wang LM, Vogt MJ, Hoogstraten CG, Cosper NJ, Davenport AM, Hendon CH, Scott RA, Britt RD, DeRose VJ. Spectroscopic characterization of Mn2+ and Cd2+ coordination to phosphorothioates in the conserved A9 metal site of the hammerhead ribozyme. J Inorg Biochem 2022; 230:111754. [DOI: 10.1016/j.jinorgbio.2022.111754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 11/25/2022]
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13
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Lu C, Zhou S, Gao F, Lin J, Liu J, Zheng J. DNA-Mediated Growth of Noble Metal Nanomaterials for Biosensing Applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116533] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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14
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Bakhshandeh B, Sorboni SG, Haghighi DM, Ahmadi F, Dehghani Z, Badiei A. New analytical methods using carbon-based nanomaterials for detection of Salmonella species as a major food poisoning organism in water and soil resources. CHEMOSPHERE 2022; 287:132243. [PMID: 34537453 DOI: 10.1016/j.chemosphere.2021.132243] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/21/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Abstract
Salmonella is one of the most prevalent causing agents of food- and water-borne illnesses, posing an ongoing public health threat. These food-poisoning bacteria contaminate the resources at different stages such as production, aggregation, processing, distribution, as well as marketing. According to the high incidence of salmonellosis, effective strategies for early-stage detection are required at the highest priority. Since traditional culture-dependent methods and polymerase chain reaction are labor-intensive and time-taking, identification of early and accurate detection of Salmonella in food and water samples can prevent significant health economic burden and lessen the costs. The immense potentiality of biosensors in diagnosis, such as simplicity in operation, the ability of multiplex analysis, high sensitivity, and specificity, have driven research in the evolution of nanotechnology, innovating newer biosensors. Carbon nanomaterials enhance the detection sensitivity of biosensors while obtaining low levels of detection limits due to their possibility to immobilize huge amounts of bioreceptor units at insignificant volume. Moreover, conjugation and functionalization of carbon nanomaterials with metallic nanoparticles or organic molecules enables surface functional groups. According to these remarkable properties, carbon nanomaterials are widely exploited in the development of novel biosensors. To be specific, carbon nanomaterials such as carbon nanotubes, graphene and fullerenes function as transducers in the analyte recognition process or surface immobilizers for biomolecules. Herein the potential application of carbon nanomaterials in the development of novel Salmonella biosensors platforms is reviewed comprehensively. In addition, the current problems and critical analyses of the future perspectives of Salmonella biosensors are discussed.
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Affiliation(s)
- Behnaz Bakhshandeh
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran; Department of Microbiology, Faculty of Biology, College of Science, University of Tehran, Tehran, Iran.
| | | | - Dorrin Mohtadi Haghighi
- Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Ahmadi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Zahra Dehghani
- Department of Cellular and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Alireza Badiei
- School of Chemistry, College of Science, University of Tehran, Tehran, Iran
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15
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Huang PJJ, Liu J. Sensing Metal Ions with Phosphorothioate-Modified DNAzymes. Methods Mol Biol 2022; 2439:277-289. [PMID: 35226327 DOI: 10.1007/978-1-0716-2047-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Phosphorothioate (PS) modification refers to replacing one of the nonbridging oxygen atoms in nucleic acids with sulfur. PS modifications can be easily introduced during solid-phase DNA synthesis. It has been extensively used in ribozyme and DNAzyme research to achieve a bioinorganic understanding of metal binding, bioanalytical applications of metal detection, and chemical biology of DNA modification. It allows for the access of new chemistry, not available to natural DNA. Since each PS modification is accompanied by the production of a chiral phosphorus center, a key technical challenge is to separate the two diastereomers called Rp and Sp. In this chapter, we describe our methods of HPLC-based separation followed by ligation to generate a long and fluorescently modified DNAzyme substrate. Subsequently, the use of the modified substrate for activity assay to understand metal binding and for metal ion detection is also described.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada.
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16
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Wang J, Ma JY, Wang DX, Liu B, Jing X, Chen DY, Tang AN, Kong DM. Oxidative Cleavage-Based Three-Dimensional DNA Biosensor for Ratiometric Detection of Hypochlorous Acid and Myeloperoxidase. Anal Chem 2021; 93:16231-16239. [PMID: 34818886 DOI: 10.1021/acs.analchem.1c04113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methods to detect and quantify disease biomarkers with high specificity and sensitivity in biological fluids play a key role in enabling clinical diagnosis, including point-of-care testing. Myeloperoxidase (MPO) is an emerging biomarker for the detection of inflammation, neurodegenerative diseases, and cardiovascular disease, where excess MPO can lead to oxidative damage to biomolecules in homeostatic systems. While numerous methods have been developed for MPO analysis, most techniques are challenging in clinical applications due to the lack of amplification methods, high cost, or other practical drawbacks. Enzyme-linked immunosorbent assays are currently used for the quantification of MPO in clinical practice, which is often limited by the availability of antibodies with high affinity and specificity and the significant nonspecific binding of antibodies to the analytical surface. In contrast, nucleic acid-based biosensors are of interest because of their simplicity, fast response time, low cost, high sensitivity, and low background signal, but detection targets are limited to nucleic acids and non-nucleic acid biomarkers are rare. Recent studies reveal that the modification of a genome in the form of phosphorothioate is specifically sensitive to the oxidative effects of the MPO/H2O2/Cl- system. We developed an oxidative cleavage-based three-dimensional DNA biosensor for rapid, ratiometric detection of HOCl and MPO in a "one-pot" method, which is simple, stable, sensitive, specific, and time-saving and does not require a complex reaction process, such as PCR and enzyme involvement. The constructed biosensor has also been successfully used for MPO detection in complex samples. This strategy is therefore of great value in disease diagnosis and biomedical research.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jia-Yi Ma
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Dong-Xia Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Bo Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xiao Jing
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Dan-Ye Chen
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
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17
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De Fazio AF, Misatziou D, Baker YR, Muskens OL, Brown T, Kanaras AG. Chemically modified nucleic acids and DNA intercalators as tools for nanoparticle assembly. Chem Soc Rev 2021; 50:13410-13440. [PMID: 34792047 PMCID: PMC8628606 DOI: 10.1039/d1cs00632k] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 12/26/2022]
Abstract
The self-assembly of inorganic nanoparticles to larger structures is of great research interest as it allows the fabrication of novel materials with collective properties correlated to the nanoparticles' individual characteristics. Recently developed methods for controlling nanoparticle organisation have enabled the fabrication of a range of new materials. Amongst these, the assembly of nanoparticles using DNA has attracted significant attention due to the highly selective recognition between complementary DNA strands, DNA nanostructure versatility, and ease of DNA chemical modification. In this review we discuss the application of various chemical DNA modifications and molecular intercalators as tools for the manipulation of DNA-nanoparticle structures. In detail, we discuss how DNA modifications and small molecule intercalators have been employed in the chemical and photochemical DNA ligation in nanostructures; DNA rotaxanes and catenanes associated with reconfigurable nanoparticle assemblies; and DNA backbone modifications including locked nucleic acids, peptide nucleic acids and borane nucleic acids, which affect the stability of nanostructures in complex environments. We conclude by highlighting the importance of maximising the synergy between the communities of DNA chemistry and nanoparticle self-assembly with the aim to enrich the library of tools available for the manipulation of nanostructures.
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Affiliation(s)
- Angela F De Fazio
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Doxi Misatziou
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Ysobel R Baker
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Otto L Muskens
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Antonios G Kanaras
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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18
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Hu Z, Yang J, Xu F, Sun G, Pan X, Xia M, Zhang S, Zhang X. Site-Specific Scissors Based on Myeloperoxidase for Phosphorothioate DNA. J Am Chem Soc 2021; 143:12361-12368. [PMID: 34324318 DOI: 10.1021/jacs.1c06370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tool box of site-specific cleavage for nucleic acid has been an increasingly attractive subject. Especially, the recent emergence of the orthogonally activatable DNA device is closely related to the site-specific scission. However, most of these cleavage strategies are based on exogenous assistance, such as laser irradiation. Endogenous strategies are highly desirable for the orthogonally regulatable DNA machine to explore the crucial intracellular biological process and cell signal network. Here, we found that the accurate site-specific cleavage reaction of phosphorothioate (PT) modified DNA by using myeloperoxidase (MPO). A scissors-like mechanism by which MPO breaks PT modification through chloride oxidation has been revealed. Furthermore, we have successfully applied the scissors to activate PT-modified hairpin-DNA machines to produce horseradish peroxidase (HRP)-mimicking DNAzyme or initiate hybridization chain reaction (HCR) amplification. Since MPO plays an important role in the pathway related to oxidative stress in cells, through the HCR amplification activated by this tool box, the oxidative stress in living cells has been robustly imaged. This work proposes an accurate and endogenous site-specific cleavage tool for the research of biostimuli and the construction of DNA molecular devices.
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Affiliation(s)
- Zhian Hu
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Jinlei Yang
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Fujian Xu
- School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, P. R. China
| | - Gongwei Sun
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Xingyu Pan
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Mengchan Xia
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
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19
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Towards the enzymatic synthesis of phosphorothioate containing LNA oligonucleotides. Bioorg Med Chem Lett 2021; 48:128242. [PMID: 34217829 DOI: 10.1016/j.bmcl.2021.128242] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 12/20/2022]
Abstract
Therapeutic oligonucleotides require the addition of multiple chemical modifications to the nucleosidic scaffold in order to improve their drug delivery efficiency, cell penetration capacity, biological stability, and pharmacokinetic properties. This chemical modification pattern is often accompanied by a synthetic burden and by limitations in sequence length. Here, we have synthesized a nucleoside triphosphate analog bearing two simultaneous modifications at the level of the sugar (LNA) and the backbone (thiophosphate) and have tested its compatibility with enzymatic DNA synthesis which could abrogate some of these synthetic limitations. While this novel analog is not as well tolerated by polymerases compared to the corresponding α-thio-dTTP or LNA-TTP, α -thio-LNA-TTP can readily be used for enzymatic synthesis on universal templates for the introduction of phosphorothioated LNA nucleotides.
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20
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Huang Z, Zhao Y, Liu B, Guan S, Liu J. Stronger Adsorption of Phosphorothioate DNA Oligonucleotides on Graphene Oxide by van der Waals Forces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:13708-13715. [PMID: 33161721 DOI: 10.1021/acs.langmuir.0c02761] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Finding DNA sequences that can adsorb strongly on nanomaterials is critical for bioconjugate and biointerface chemistry. In most previous work, unmodified DNA with a phosphodiester backbone (PO DNA) were screened or selected for adsorption on inorganic surfaces. In this work, the adsorption of phosphorothioate (PS)-modified DNA (PS DNA) on graphene oxide (GO) is studied. By use of fluorescently labeled oligonucleotides as probes, all the tested PS DNA strands are adsorbed more strongly on GO compared to the PO DNA of the same sequence. The adsorption mechanism is probed by washing the adsorbed DNA with proteins, surfactants, and urea. Molecular dynamics simulations show that van der Waals forces are responsible for the tighter adsorption of PS DNA. Polycytosine (poly-C) DNA, in general, has a high affinity for the GO surface, and PS poly-C DNA can adsorb even stronger, making it an ideal anchoring sequence on GO. With this knowledge, noncovalent functionalization of GO with a diblock DNA is demonstrated, where a PS poly-C block is used to anchor on the surface. This conjugate achieves better hybridization than the PO DNA of the same sequence for hybridization with the complementary DNA.
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Affiliation(s)
- Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Yu Zhao
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Shaokang Guan
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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