1
|
Wen C, Wang G, Yang L, Chen T, Liu H, Gong W. Structural Basis for C2'-methoxy Recognition by DNA Polymerases and Function Improvement. J Mol Biol 2024; 436:168744. [PMID: 39147125 DOI: 10.1016/j.jmb.2024.168744] [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: 05/31/2024] [Revised: 07/26/2024] [Accepted: 08/08/2024] [Indexed: 08/17/2024]
Abstract
DNA modified with C2'-methoxy (C2'-OMe) greatly enhances its resistance to nucleases, which is beneficial for the half-life of aptamers and DNA nanomaterials. Although the unnatural DNA polymerases capable of incorporating C2'-OMe modified nucleoside monophosphates (C2'-OMe-NMPs) were engineered via directed evolution, the detailed molecular mechanism by which an evolved DNA polymerase recognizes C2'-OMe-NTPs remains poorly understood. Here, we present the crystal structures of the evolved Stoffel fragment of Taq DNA polymerase SFM4-3 processing the C2'-OMe-GTP in different states. Our results reveal the structural basis for recognition of C2'-methoxy by SFM4-3. Based on the analysis of other mutated residues in SFM4-3, a new Stoffel fragment variant with faster catalytic rate and stronger inhibitor-resistance was obtained. In addition, the capture of a novel pre-insertion co-existing with template 5'-overhang stacking conformation provides insight into the catalytic mechanism of Taq DNA polymerase.
Collapse
Affiliation(s)
- Chongzheng Wen
- Division of Biological Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, PR China
| | - Guangyuan Wang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Lin Yang
- Division of Biological Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, PR China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China.
| | - Haiping Liu
- Division of Biological Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, PR China.
| | - Weimin Gong
- Division of Biological Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, PR China.
| |
Collapse
|
2
|
Sun L, Xiang Y, Du Y, Wang Y, Ma J, Wang Y, Wang X, Wang G, Chen T. Template-independent synthesis and 3'-end labelling of 2'-modified oligonucleotides with terminal deoxynucleotidyl transferases. Nucleic Acids Res 2024; 52:10085-10101. [PMID: 39149896 PMCID: PMC11417362 DOI: 10.1093/nar/gkae691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/17/2024] Open
Abstract
Xenobiotic nucleic acids (XNAs) are artificial genetic polymers with altered structural moieties and useful features, such as enhanced biological and chemical stability. Enzymatic synthesis and efficient labelling of XNAs are crucial for their broader application. Terminal deoxynucleotidyl transferases (TdTs) have been exploited for the de novo synthesis and labelling of DNA and demonstrated the capability of recognizing various substrates. However, the activities of TdTs for the synthesis and labelling of commonly used XNAs with 2' modifications have not been systematically explored. In this work, we explored and demonstrated the varied activities of three TdTs (bovine TdT, MTdT-evo and murine TdT) for the template-independent incorporation of 2'-methoxy NTPs, 2'-fluoro NTPs and 2'-fluoroarabino NTPs into the 3' ends of single- and double-stranded DNAs and the extension of 2'-modified XNAs with (d)NTPs containing a natural or unnatural nucleobase. Taking advantages of these activities, we established a strategy for protecting single-stranded DNAs from exonuclease I degradation by TdT-synthesized 2'-modified XNA tails and methods for 3'-end labelling of 2'-modified XNAs by TdT-mediated synthesis of G-quadruplex-containing tails or incorporation of nucleotides with a functionalized nucleobase. A DNA-2'-fluoroarabino nucleic acid (FANA) chimeric hydrogel was also successfully constructed based on the extraordinary activity of MTdT-evo for template-independent FANA synthesis.
Collapse
Affiliation(s)
- Leping Sun
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
| | - Yuming Xiang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
| | - Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
| | - Yangming Wang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
| | - Jiezhao Ma
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
| | - Yaxin Wang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
| | - Xueting Wang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
| | - Guangyuan Wang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
| |
Collapse
|
3
|
Dong Y, Wang J, Chen L, Chen H, Dang S, Li F. Aptamer-based assembly systems for SARS-CoV-2 detection and therapeutics. Chem Soc Rev 2024; 53:6830-6859. [PMID: 38829187 DOI: 10.1039/d3cs00774j] [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: 06/05/2024]
Abstract
Nucleic acid aptamers are oligonucleotide chains with molecular recognition properties. Compared with antibodies, aptamers show advantages given that they are readily produced via chemical synthesis and elicit minimal immunogenicity in biomedicine applications. Notably, aptamer-encoded nucleic acid assemblies further improve the binding affinity of aptamers with the targets due to their multivalent synergistic interactions. Specially, aptamers can be engineered with special topological arrangements in nucleic acid assemblies, which demonstrate spatial and valence matching towards antigens on viruses, thus showing potential in the detection and therapeutic applications of viruses. This review presents the recent progress on the aptamers explored for SARS-CoV-2 detection and infection treatment, wherein applications of aptamer-based assembly systems are introduced in detail. Screening methods and chemical modification strategies for aptamers are comprehensively summarized, and the types of aptamers employed against different target domains of SARS-CoV-2 are illustrated. The evolution of aptamer-based assembly systems for the detection and neutralization of SARS-CoV-2, as well as the construction principle and characteristics of aptamer-based DNA assemblies are demonstrated. The typically representative works are presented to demonstrate how to assemble aptamers rationally and elaborately for specific applications in SARS-CoV-2 diagnosis and neutralization. Finally, we provide deep insights into the current challenges and future perspectives towards aptamer-based nucleic acid assemblies for virus detection and neutralization in nanomedicine.
Collapse
Affiliation(s)
- Yuhang Dong
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Jingping Wang
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Ling Chen
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Haonan Chen
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Shuangbo Dang
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Feng Li
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| |
Collapse
|
4
|
Hoshino H, Kasahara Y, Obika S. Polyamines promote xenobiotic nucleic acid synthesis by modified thermophilic polymerase mutants. RSC Chem Biol 2024; 5:467-472. [PMID: 38725908 PMCID: PMC11078213 DOI: 10.1039/d4cb00017j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/31/2024] [Indexed: 05/12/2024] Open
Abstract
The enzymatic synthesis of xenobiotic nucleic acids (XNA), which are artificially sugar-modified nucleic acids, is essential for the preparation of XNA libraries. XNA libraries are used in the in vitro selection of XNA aptamers and enzymes (XNAzymes). Efficient enzymatic synthesis of various XNAs can enable the screening of high-quality XNA aptamers and XNAzymes by expanding the diversity of XNA libraries and adding a variety of properties to XNA aptamers and XNAzymes. However, XNAs that form unstable duplexes with DNA, such as arabino nucleic acid (ANA), may dissociate during enzyme synthesis at temperatures suitable for thermophilic polymerases. Thus, such XNAs are not efficiently synthesised by the thermophilic polymerase mutants at the end of the sequence. This undesirable bias reduces the possibility of generating high-quality XNA aptamers and XNAzymes. Here, we demonstrate that polyamine-induced DNA/ANA duplex stabilisation promotes ANA synthesis that is catalysed by thermophilic polymerase mutants. Several polyamines, including spermine, spermidine, cadaverine, and putrescine promote ANA synthesis. The negative effect of polyamines on the fidelity of ANA synthesis was negligible. We also showed that polyamines promote the synthesis of other XNAs, including 2'-amino-RNA/2'-fluoro-RNA mixture and 2'-O-methyl-RNA. In addition, we found that polyamine promotes DNA synthesis from the 2'-O-methyl-RNA template. Polyamines, with the use of thermophilic polymerase mutants, may allow further development of XNA aptamers and XNAzymes by promoting the transcription and reverse transcription of XNAs.
Collapse
Affiliation(s)
- Hidekazu Hoshino
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) 7-6-8 Saito-Asagi Ibaraki 567-0085 Osaka Japan
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) 7-6-8 Saito-Asagi Ibaraki 567-0085 Osaka Japan
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6 Yamadaoka Suita 565-0871 Osaka Japan
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) 7-6-8 Saito-Asagi Ibaraki 567-0085 Osaka Japan
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6 Yamadaoka Suita 565-0871 Osaka Japan
| |
Collapse
|
5
|
Zhang Y, Li Y. Clinical Translation of Aptamers for COVID-19. J Med Chem 2023; 66:16568-16578. [PMID: 37880142 DOI: 10.1021/acs.jmedchem.3c01607] [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: 10/27/2023]
Abstract
The COVID-19 etiologic agent, SARS-CoV-2, continues to be one of the leading causes of death on a global scale. Although efficient methods for diagnosis and treatment of COVID-19 have been developed, new methods of battling SARS-CoV-2 variants and long COVID are still urgently needed. A number of aptamers have demonstrated tremendous potential to be developed into diagnostic and therapeutic agents for COVID-19. The translation of the aptamers for clinical uses, however, has been extremely slow. Overcoming the difficulties faced by aptamers would advance this technology toward clinical use for COVID-19 and other serious disorders.
Collapse
Affiliation(s)
- Yang Zhang
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China
| | - Yongen Li
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China
| |
Collapse
|
6
|
Ji C, Wei J, Zhang L, Hou X, Tan J, Yuan Q, Tan W. Aptamer-Protein Interactions: From Regulation to Biomolecular Detection. Chem Rev 2023; 123:12471-12506. [PMID: 37931070 DOI: 10.1021/acs.chemrev.3c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.
Collapse
Affiliation(s)
- Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xinru Hou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| |
Collapse
|
7
|
Ji D, Feng H, Liew SW, Kwok CK. Modified nucleic acid aptamers: development, characterization, and biological applications. Trends Biotechnol 2023; 41:1360-1384. [PMID: 37302912 DOI: 10.1016/j.tibtech.2023.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/30/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Abstract
Aptamers are single-stranded oligonucleotides that bind to their targets via specific structural interactions. To improve the properties and performance of aptamers, modified nucleotides are incorporated during or after a selection process such as systematic evolution of ligands by exponential enrichment (SELEX). We summarize the latest modified nucleotides and strategies used in modified (mod)-SELEX and post-SELEX to develop modified aptamers, highlight the methods used to characterize aptamer-target interactions, and present recent progress in modified aptamers that recognize different targets. We discuss the challenges and perspectives in further advancing the methodologies and toolsets to accelerate the discovery of modified aptamers, improve the throughput of aptamer-target characterization, and expand the functional diversity and complexity of modified aptamers.
Collapse
Affiliation(s)
- Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Hengxin Feng
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Shiau Wei Liew
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.
| |
Collapse
|
8
|
Qin Y, Ma X, Tao R, Du Y, Chen T. Synthesis, Reverse Transcription, Replication, and Inter-Transcription of 2'-Modified Nucleic Acids with Evolved Thermophilic Polymerases: Efforts toward Multidimensional Expansion of the Central Dogma. ACS Synth Biol 2023; 12:2616-2631. [PMID: 37646406 DOI: 10.1021/acssynbio.3c00213] [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: 09/01/2023]
Abstract
In the past decades, various xenobiotic nucleic acids (XNAs), including 2'-modified nucleic acids, have been developed as novel genetic materials and demonstrated great potential in synthetic biology and biotechnology. Enzymatic polymerization and replication of these artificial polymers are obviously the prerequisite to make full use of them, and DNA and RNA polymerases from different families have thus been extensively engineered for these purposes. However, the performance of engineered XNA polymerases is still far from satisfactory, especially in terms of the efficiency of synthesizing XNA with bigger lengths and the capability of directly replicating XNAs or transcribing one XNA to another. In this work, we tailored a mutant of Stoffel fragment of Taq DNA polymerase, SFM4-3, by engineering a key residue pair on the surfaces of fingers and thumb domains, and successfully obtained mutants with significantly enhanced efficiency for the synthesis of fully 2'-OMe-modified DNA with bigger lengths. Remarkably, we also found that these polymerase mutants are capable of synthesizing, reverse transcribing, and even replicating RNA and different fully 2'-modified XNAs, as well as transcribing one of these nucleic acids to another, with varied efficiencies. The application of these activities for producing DNA strands end-protected by XNA duplexes was then demonstrated. These results clearly suggest that the genetic information can be stored in and transmitted among DNA, RNA, and different 2'-modified XNAs with the assistance of polymerase mutants, and the central dogma of life can be expanded to higher dimensions via the development of XNAs together with engineering their polymerases.
Collapse
Affiliation(s)
- Yanjia Qin
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Xingyun Ma
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Rui Tao
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| |
Collapse
|
9
|
Thevendran R, Rogini S, Leighton G, Mutombwera A, Shigdar S, Tang TH, Citartan M. The Diagnostic Potential of RNA Aptamers against the NS1 Protein of Dengue Virus Serotype 2. BIOLOGY 2023; 12:biology12050722. [PMID: 37237536 DOI: 10.3390/biology12050722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/24/2023] [Accepted: 03/30/2023] [Indexed: 05/28/2023]
Abstract
Dengue infection, caused by the dengue virus, is a global threat which requires immediate attention and appropriate disease management. The current diagnosis of dengue infection is largely based on viral isolation, RT-PCR and serology-based detection, which are time-consuming and expensive, and require trained personnel. For early diagnosis of dengue, the direct detection of a dengue antigenic target is efficacious, and one such target is NS1. NS1-based detection is primarily antibody-centric and is beset by drawbacks pertaining to antibodies such as the high cost of synthesis and large batch-to-batch variation. Aptamers are potential surrogates of antibodies and are much cheaper, without exhibiting batch-to-batch variation. Given these advantages, we sought to isolate RNA aptamers against the NS1 protein of dengue virus serotype 2. A total of 11 cycles of SELEX were carried out, resulting in two potent aptamers, DENV-3 and DENV-6, with dissociation constant values estimated at 37.57 ± 10.34 nM and 41.40 ± 9.29 nM, respectively. These aptamers can be further miniaturized to TDENV-3 and TDENV-6a with an increased LOD upon their usage in direct ELASA. Moreover, these truncated aptamers are highly specific against the dengue NS1 while showing no cross-reactivity against the NS1 of the Zika virus, the E2 protein of the Chikungunya virus or the LipL32 protein of Leptospira, with target selectivity retained even in human serum. The usage of TDENV-3 as the capturing probe and TDENV-6a as the detection probe underpinned the development of an aptamer-based sandwich ELASA for the detection of dengue NS1. The sensitivity of the sandwich ELASA was further improved with the stabilization of the truncated aptamers and the repeated incubation strategy, which enabled a LOD of 2 nM when used with the target NS1 spiked in human serum diluted at 1:2000.
Collapse
Affiliation(s)
- Ramesh Thevendran
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), University Sains Malaysia, Bertam, Kepala Batas 13200, Malaysia
| | - Sivalingam Rogini
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), University Sains Malaysia, Bertam, Kepala Batas 13200, Malaysia
| | - Glenn Leighton
- Hutano Diagnostics Ltd. BioEscalator, Innovation Building, Old Road Campus, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Atherton Mutombwera
- Hutano Diagnostics Ltd. BioEscalator, Innovation Building, Old Road Campus, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Sarah Shigdar
- School of Medicine, Deakin University, Geelong, VIC 3217, Australia
- Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, VIC 3220, Australia
| | - Thean-Hock Tang
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), University Sains Malaysia, Bertam, Kepala Batas 13200, Malaysia
| | - Marimuthu Citartan
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), University Sains Malaysia, Bertam, Kepala Batas 13200, Malaysia
| |
Collapse
|
10
|
Jin B, Guo Z, Chen Z, Chen H, Li S, Deng Y, Jin L, Liu Y, Zhang Y, He N. Aptamers in cancer therapy: problems and new breakthroughs. J Mater Chem B 2023; 11:1609-1627. [PMID: 36744587 DOI: 10.1039/d2tb02579e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Aptamers, a class of oligonucleotides that can bind with molecular targets with high affinity and specificity, have been widely applied in research fields including biosensing, imaging, diagnosing, and therapy of diseases. However, compared with the rapid development in the research fields, the clinical application of aptamers is progressing at a much slower speed, especially in the therapy of cancer. Obstructions including nuclease degradation, renal clearance, a complex selection process, and potential side effects have inhibited the clinical transformation of aptamer-conjugated drugs. To overcome these problems, taking certain measures to improve the biocompatibility and stability of aptamer-conjugated drugs in vivo is necessary. In this review, the obstructions mentioned above are thoroughly discussed and the methods to overcome these problems are introduced in detail. Furthermore, landmark research works and the most recent studies on aptamer-conjugated drugs for cancer therapy are also listed as examples, and the future directions of research for aptamer clinical transformation are discussed.
Collapse
Affiliation(s)
- Baijiang Jin
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Zhukang Guo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Lian Jin
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Yuan Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Yuanying Zhang
- Department of Molecular Biology, Jiangsu Cancer Hospital, Nanjing 210009, P. R. China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China. .,Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| |
Collapse
|
11
|
CD44 and CD133 aptamer directed nanocarriers for cancer stem cells targeting. Eur Polym J 2023. [DOI: 10.1016/j.eurpolymj.2022.111770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
12
|
Wang G, Du Y, Ma X, Ye F, Qin Y, Wang Y, Xiang Y, Tao R, Chen T. Thermophilic Nucleic Acid Polymerases and Their Application in Xenobiology. Int J Mol Sci 2022; 23:ijms232314969. [PMID: 36499296 PMCID: PMC9738464 DOI: 10.3390/ijms232314969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/22/2022] [Accepted: 11/27/2022] [Indexed: 12/02/2022] Open
Abstract
Thermophilic nucleic acid polymerases, isolated from organisms that thrive in extremely hot environments, possess great DNA/RNA synthesis activities under high temperatures. These enzymes play indispensable roles in central life activities involved in DNA replication and repair, as well as RNA transcription, and have already been widely used in bioengineering, biotechnology, and biomedicine. Xeno nucleic acids (XNAs), which are analogs of DNA/RNA with unnatural moieties, have been developed as new carriers of genetic information in the past decades, which contributed to the fast development of a field called xenobiology. The broad application of these XNA molecules in the production of novel drugs, materials, and catalysts greatly relies on the capability of enzymatic synthesis, reverse transcription, and amplification of them, which have been partially achieved with natural or artificially tailored thermophilic nucleic acid polymerases. In this review, we first systematically summarize representative thermophilic and hyperthermophilic polymerases that have been extensively studied and utilized, followed by the introduction of methods and approaches in the engineering of these polymerases for the efficient synthesis, reverse transcription, and amplification of XNAs. The application of XNAs facilitated by these polymerases and their mutants is then discussed. In the end, a perspective for the future direction of further development and application of unnatural nucleic acid polymerases is provided.
Collapse
|
13
|
Sun L, Ma X, Zhang B, Qin Y, Ma J, Du Y, Chen T. From polymerase engineering to semi-synthetic life: artificial expansion of the central dogma. RSC Chem Biol 2022; 3:1173-1197. [PMID: 36320892 PMCID: PMC9533422 DOI: 10.1039/d2cb00116k] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/08/2022] [Indexed: 11/21/2022] Open
Abstract
Nucleic acids have been extensively modified in different moieties to expand the scope of genetic materials in the past few decades. While the development of unnatural base pairs (UBPs) has expanded the genetic information capacity of nucleic acids, the production of synthetic alternatives of DNA and RNA has increased the types of genetic information carriers and introduced novel properties and functionalities into nucleic acids. Moreover, the efforts of tailoring DNA polymerases (DNAPs) and RNA polymerases (RNAPs) to be efficient unnatural nucleic acid polymerases have enabled broad application of these unnatural nucleic acids, ranging from production of stable aptamers to evolution of novel catalysts. The introduction of unnatural nucleic acids into living organisms has also started expanding the central dogma in vivo. In this article, we first summarize the development of unnatural nucleic acids with modifications or alterations in different moieties. The strategies for engineering DNAPs and RNAPs are then extensively reviewed, followed by summarization of predominant polymerase mutants with good activities for synthesizing, reverse transcribing, or even amplifying unnatural nucleic acids. Some recent application examples of unnatural nucleic acids with their polymerases are then introduced. At the end, the approaches of introducing UBPs and synthetic genetic polymers into living organisms for the creation of semi-synthetic organisms are reviewed and discussed.
Collapse
Affiliation(s)
- Leping Sun
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Xingyun Ma
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Binliang Zhang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Yanjia Qin
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Jiezhao Ma
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| |
Collapse
|
14
|
Hervey JRD, Freund N, Houlihan G, Dhaliwal G, Holliger P, Taylor AI. Efficient synthesis and replication of diverse sequence libraries composed of biostable nucleic acid analogues. RSC Chem Biol 2022; 3:1209-1215. [PMID: 36320888 PMCID: PMC9533476 DOI: 10.1039/d2cb00035k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/15/2022] [Indexed: 11/10/2022] Open
Abstract
Functional nucleic acids can be evolved in vitro using cycles of selection and amplification, starting from diverse-sequence libraries, which are typically restricted to natural or partially-modified polymer chemistries. Here, we describe the efficient DNA-templated synthesis and reverse transcription of libraries entirely composed of serum nuclease resistant alternative nucleic acid chemistries validated in nucleic acid therapeutics; locked nucleic acid (LNA), 2'-O-methyl-RNA (2'OMe-RNA), or mixtures of the two. We evaluate yield and diversity of synthesised libraries and measure the aggregate error rate of a selection cycle. We find that in addition to pure 2'-O-methyl-RNA and LNA, several 2'OMe-RNA/LNA blends seem suitable and promising for discovery of biostable functional nucleic acids for biomedical applications.
Collapse
Affiliation(s)
- John R D Hervey
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge Cambridge CB2 0AW UK
| | - Niklas Freund
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Gillian Houlihan
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Gurpreet Dhaliwal
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge Cambridge CB2 0AW UK
| | - Philipp Holliger
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Alexander I Taylor
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge Cambridge CB2 0AW UK
| |
Collapse
|
15
|
Alhaj-Suliman SO, Wafa EI, Salem AK. Engineering nanosystems to overcome barriers to cancer diagnosis and treatment. Adv Drug Deliv Rev 2022; 189:114482. [PMID: 35944587 DOI: 10.1016/j.addr.2022.114482] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 01/24/2023]
Abstract
Over the past two decades, multidisciplinary investigations into the development of nanoparticles for medical applications have continually increased. However, nanoparticles are still subject to biological barriers and biodistribution challenges, which limit their overall clinical potential. This has motivated the implementation of innovational modifications to a range of nanoparticle formulations designed for cancer imaging and/or cancer treatment to overcome specific barriers and shift the accumulation of payloads toward the diseased tissues. In recent years, novel technological and chemical approaches have been employed to modify or functionalize the surface of nanoparticles or manipulate the characteristics of nanoparticles. Combining these approaches with the identification of critical biomarkers provides new strategies for enhancing nanoparticle specificity for both cancer diagnostic and therapeutic applications. This review discusses the most recent advances in the design and engineering of nanoparticles as well as future directions for developing the next generation of nanomedicines.
Collapse
Affiliation(s)
- Suhaila O Alhaj-Suliman
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA 52242, United States
| | - Emad I Wafa
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA 52242, United States
| | - Aliasger K Salem
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA 52242, United States; Holden Comprehensive Cancer Center, University of Iowa Hospitals & Clinics, Iowa City, IA 52242, United States.
| |
Collapse
|
16
|
Tu T, Huan S, Ke G, Zhang X. Functional Xeno Nucleic Acids for Biomedical Application. Chem Res Chin Univ 2022. [DOI: 10.1007/s40242-021-2186-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
17
|
Tu T, Huan S, Ke G, Zhang X. Functional Xeno Nucleic Acids for Biomedical Application. Chem Res Chin Univ 2022:1-7. [PMID: 35814030 PMCID: PMC9253239 DOI: 10.1007/s40242-022-2186-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/26/2022] [Indexed: 11/26/2022]
Abstract
Functional nucleic acids(FNAs) refer to a type of oligonucleotides with functions over the traditional genetic roles of nucleic acids, which have been widely applied in screening, sensing and imaging fields. However, the potential application of FNAs in biomedical field is still restricted by the unsatisfactory stability, biocompatibility, biodistribution and immunity of natural nucleic acids(DNA/RNA). Xeno nucleic acids(XNAs) are a kind of nucleic acid analogues with chemically modified sugar groups that possess improved biological properties, including improved biological stability, increased binding affinity, reduced immune responses, and enhanced cell penetration or tissue specificity. In the last two decades, scientists have made great progress in the research of functional xeno nucleic acids, which makes it an emerging attractive biomedical application material. In this review, we summarized the design of functional xeno nucleic acids and their applications in the biomedical field.
Collapse
Affiliation(s)
- Tingting Tu
- 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
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Xiaobing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| |
Collapse
|
18
|
Yuhan J, Zhu L, Zhu L, Huang K, He X, Xu W. Cell-specific aptamers as potential drugs in therapeutic applications: A review of current progress. J Control Release 2022; 346:405-420. [PMID: 35489545 DOI: 10.1016/j.jconrel.2022.04.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/23/2022] [Accepted: 04/24/2022] [Indexed: 12/23/2022]
Abstract
Cell-specific aptamers are a promising emerging player in the field of disease therapy. This paper reviews the multidimensional research progress made in terms of their classification, modification, and application. Based on the target location of cell-specific aptamers, it is defined and classified cell-specific aptamers into three groups including aptamers for cell surface markers, aptamers for intracellular components, and aptamers for extracellular components. Moreover, the modification methods of aptamers to achieve improved stability and affinity are concluded. In addition, recent advances in the application of cell-specific aptamers are discussed, mainly focusing on the increasing research attraction of cell state improving helpers and cell recruitment mediators in the improvement of cellular microenvironments to achieve successful disease therapy. This review also highlights 11 types of clinical aptamer drugs. Finally, the challenges and future directions of potential clinical applications are presented. In summary, we believe that cell-specific aptamers are promising drugs in disease therapy.
Collapse
Affiliation(s)
- Jieyu Yuhan
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Liye Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Kunlun Huang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiaoyun He
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China.
| |
Collapse
|
19
|
Aliouat H, Peng Y, Waseem Z, Wang S, Zhou W. Pure DNA scaffolded drug delivery systems for cancer therapy. Biomaterials 2022; 285:121532. [DOI: 10.1016/j.biomaterials.2022.121532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/04/2022] [Accepted: 04/15/2022] [Indexed: 02/07/2023]
|
20
|
Pal S, Chandra G, Patel S, Singh S. Fluorinated Nucleosides: Synthesis, Modulation in Conformation and Therapeutic Application. CHEM REC 2022; 22:e202100335. [PMID: 35253973 DOI: 10.1002/tcr.202100335] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/22/2022] [Indexed: 12/17/2022]
Abstract
Over the last twenty years, fluorination on nucleoside has established itself as the most promising tool to use to get biologically active compounds that could sustain the clinical trial by affecting the pharmacodynamics and pharmacokinetic properties. Due to fluorine's inherent unique properties and its judicious introduction into the molecule, makes the corresponding nucleoside metabolically very stable, lipophilic, and opens a new site of intermolecular binding. Fluorination on various nucleosides has been extensively studied as a result, a series of fluorinated nucleosides come up for different therapeutic uses which are either approved by the FDA or under the advanced stage of the clinical trial. Here in this review, we are summarizing the latest development in the chemistry of fluorination on nucleoside that led to varieties of new analogs like carbocyclic, acyclic, and conformationally biased nucleoside and their biological properties, the influence of fluorine on conformation, oligonucleotide stability, and their use in therapeutics.
Collapse
Affiliation(s)
- Shantanu Pal
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar Argul, Odisha, India, 752050
| | - Girish Chandra
- Department of Chemistry, School of Physical and Chemical Sciences, Central University of South Bihar, SH-7, Gaya Panchanpur Road, Gaya, Bihar, India, 824236
| | - Samridhi Patel
- Department of Chemistry, School of Physical and Chemical Sciences, Central University of South Bihar, SH-7, Gaya Panchanpur Road, Gaya, Bihar, India, 824236
| | - Sakshi Singh
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar Argul, Odisha, India, 752050
| |
Collapse
|
21
|
Wang F, Li P, Chu HC, Lo PK. Nucleic Acids and Their Analogues for Biomedical Applications. BIOSENSORS 2022; 12:93. [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] [Grants] [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.
Collapse
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
| |
Collapse
|
22
|
Qi S, Duan N, Khan IM, Dong X, Zhang Y, Wu S, Wang Z. Strategies to manipulate the performance of aptamers in SELEX, post-SELEX and microenvironment. Biotechnol Adv 2022; 55:107902. [DOI: 10.1016/j.biotechadv.2021.107902] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/21/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023]
|
23
|
Christensen TA, Lee KY, Gottlieb SZP, Carrier MB, Leconte AM. Mutant polymerases capable of 2′ fluoro-modified nucleic acid synthesis and amplification with improved accuracy. RSC Chem Biol 2022; 3:1044-1051. [PMID: 35975008 PMCID: PMC9347352 DOI: 10.1039/d2cb00064d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/16/2022] [Indexed: 11/21/2022] Open
Abstract
Nonnatural nucleic acids (xeno nucleic acids, XNA) can possess several useful properties such as expanded reactivity and nuclease resistance, which can enhance the utility of DNA as a biotechnological tool. Native DNA polymerases are unable to synthesize XNA, so, in recent years mutant XNA polymerases have been engineered with sufficient activity for use in processes such as PCR. While substantial improvements have been made, accuracy still needs to be increased by orders of magnitude to approach natural error rates and make XNA polymerases useful for applications that require high fidelity. Here, we systematically evaluate leading Taq DNA polymerase mutants for their fidelity during synthesis of 2′F XNA. To further improve their accuracy, we add mutations that have been shown to increase the fidelity of wild-type Taq polymerases, to some of the best current XNA polymerases (SFM4–3, SFM4–6, and SFP1). The resulting polymerases show significant improvements in synthesis accuracy. In addition to generating more accurate XNA polymerases, this study also informs future polymerase engineering efforts by demonstrating that mutations that improve the accuracy of DNA synthesis may also have utility in improving the accuracy of XNA synthesis. Polymerases that have been evolved to synthesize 2′F XNA are often inaccurate. Here, we show that you can improve the accuracy of 2′F XNA polymerase synthesis by adding mutations previously found to improve the accuracy of natural DNA synthesis.![]()
Collapse
Affiliation(s)
- Trevor A. Christensen
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, USA
| | - Kristi Y. Lee
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, USA
| | - Simone Z. P. Gottlieb
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, USA
| | - Mikayla B. Carrier
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, USA
| | - Aaron M. Leconte
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, USA
| |
Collapse
|
24
|
|
25
|
Song P, Zhang R, He C, Chen T. Transcription, Reverse Transcription, and Amplification of Backbone-Modified Nucleic Acids with Laboratory-Evolved Thermophilic DNA Polymerases. Curr Protoc 2021; 1:e188. [PMID: 34232574 DOI: 10.1002/cpz1.188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Backbone-modified nucleic acids are usually more stable enzymatically than their natural counterparts, enabling their broad application as potential diagnostic or therapeutic agents. Moreover, the development of nucleic acids with unnatural backbones has expanded the pool of genetic information carriers and paved the way toward synthetic xenobiology. However, synthesizing these molecules remains very challenging due to the requirement for harsh reaction conditions and the low coupling efficiency during their traditional solid-phase synthesis. Although enzymatic synthesis provides an attractive alternative that also allows the replication and artificial evolution of these molecules, it is crucially dependent on the availability of polymerases capable of synthesizing these backbone-modified nucleotides. Previously, a series of thermostable polymerases that can efficiently synthesize or even amplify backbone-modified DNA or RNA have been evolved through a polymerase evolution method based on phage display. Herein we summarize protocols to use these evolved polymerase mutants to transcribe, reverse transcribe, and PCR amplify backbone-modified nucleic acids. We also outline the polymerase chain transcription method, developed later for the rapid production of RNA or backbone-modified RNA with one of these evolved polymerases, SFM4-3. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Transcription/synthesis of modified DNA/RNA from DNA templates with evolved polymerases SFM4-3 or SFM4-6 Basic Protocol 2: Reverse transcription of modified DNA/RNA with evolved polymerase SFM4-9 Basic Protocol 3: PCR amplification of modified DNA with evolved polymerase SFM4-3 Basic Protocol 4: Polymerase chain transcription for the production of RNA/modified RNA oligonucleotides with evolved polymerase SFM4-3.
Collapse
Affiliation(s)
- Ping Song
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P. R. China
| | - Rujie Zhang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P. R. China
| | - Chuanping He
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P. R. China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P. R. China
| |
Collapse
|
26
|
Matsunaga KI, Kimoto M, Lim VW, Tan HP, Wong YQ, Sun W, Vasoo S, Leo YS, Hirao I. High-affinity five/six-letter DNA aptamers with superior specificity enabling the detection of dengue NS1 protein variants beyond the serotype identification. Nucleic Acids Res 2021; 49:11407-11424. [PMID: 34169309 PMCID: PMC8599795 DOI: 10.1093/nar/gkab515] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/24/2021] [Accepted: 06/04/2021] [Indexed: 12/25/2022] Open
Abstract
Genetic alphabet expansion of DNA by introducing unnatural bases (UBs), as a fifth letter, dramatically augments the affinities of DNA aptamers that bind to target proteins. To determine whether UB-containing DNA (UB-DNA) aptamers obtained by affinity selection could spontaneously achieve high specificity, we have generated a series of UB-DNA aptamers (KD: 27-182 pM) targeting each of four dengue non-structural protein 1 (DEN-NS1) serotypes. The specificity of each aptamer is remarkably high, and the aptamers can recognize the subtle variants of DEN-NS1 with at least 96.9% amino acid sequence identity, beyond the capability of serotype identification (69-80% sequence identities). Our UB-DNA aptamers specifically identified two major variants of dengue serotype 1 with 10-amino acid differences in the DEN-NS1 protein (352 aa) in Singaporeans' clinical samples. These results suggest that the high-affinity UB-DNA aptamers generated by affinity selection also acquire high target specificity. Intriguingly, one of the aptamers contained two different UBs as fifth and sixth letters, which are essential for the tight binding to the target. These two types of unnatural bases with distinct physicochemical properties profoundly expand the potential of DNA aptamers. Detection methods incorporating the UB-DNA aptamers will facilitate precise diagnoses of viral infections and other diseases.
Collapse
Affiliation(s)
- Ken-Ichiro Matsunaga
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - Michiko Kimoto
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - Vanessa Weixun Lim
- National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore 308442, Singapore
| | - Hui Pen Tan
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - Yu Qian Wong
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - William Sun
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Shawn Vasoo
- National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore 308442, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore 308433, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Dr., Experimental Medicine Building, Singapore 636921, Singapore
| | - Yee Sin Leo
- National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore 308442, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore 308433, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Dr., Experimental Medicine Building, Singapore 636921, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, #10-01, Singapore 117549, Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| |
Collapse
|
27
|
Redman RL, Krauss IJ. Directed Evolution of 2'-Fluoro-Modified, RNA-Supported Carbohydrate Clusters That Bind Tightly to HIV Antibody 2G12. J Am Chem Soc 2021; 143:8565-8571. [PMID: 34096703 DOI: 10.1021/jacs.1c03194] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Carbohydrate binding proteins (CBPs) are attractive targets in medicine and biology. Multivalency, with several glycans binding to several binding pockets in the CBP, is important for high-affinity interactions. Herein, we describe a novel platform for design of multivalent carbohydrate cluster ligands by directed evolution, in which serum-stable 2'-fluoro modified RNA (F-RNA) backbones evolve to present the glycan in optimal clusters. We have validated this method by the selection of oligomannose (Man9) glycan clusters from a sequence pool of ∼1013 that bind to broadly neutralizing HIV antibody 2G12 with 13 to 36 nM affinities.
Collapse
Affiliation(s)
- Richard L Redman
- Department of Chemistry, Brandeis University, 415 South Street MS 015, Waltham, Massachusetts 02454, United States
| | - Isaac J Krauss
- Department of Chemistry, Brandeis University, 415 South Street MS 015, Waltham, Massachusetts 02454, United States
| |
Collapse
|
28
|
Yang C, Wu KB, Deng Y, Yuan J, Niu J. Geared Toward Applications: A Perspective on Functional Sequence-Controlled Polymers. ACS Macro Lett 2021; 10:243-257. [PMID: 34336395 PMCID: PMC8320758 DOI: 10.1021/acsmacrolett.0c00855] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sequence-controlled polymers are an emerging class of synthetic polymers with a regulated sequence of monomers. In the past decade, tremendous progress has been made in the synthesis of polymers with the sophisticated sequence control approaching the level manifested in biopolymers. In contrast, the exploration of novel functions that can be achieved by controlling synthetic polymer sequences represents an emerging focus in polymer science. This Viewpoint will survey recent advances in the functional applications of sequence-controlled polymers and provide a perspective on the challenges and outlook for pursuing future applications of this fascinating class of macromolecules.
Collapse
Affiliation(s)
- Cangjie Yang
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Kevin B. Wu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Yu Deng
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Jingsong Yuan
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Jia Niu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| |
Collapse
|
29
|
Rangel AE, Hariri AA, Eisenstein M, Soh HT. Engineering Aptamer Switches for Multifunctional Stimulus-Responsive Nanosystems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2003704. [PMID: 33165999 DOI: 10.1002/adma.202003704] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/19/2020] [Indexed: 05/15/2023]
Abstract
Although RNA and DNA are best known for their capacity to encode biological information, it has become increasingly clear over the past few decades that these biomolecules are also capable of performing other complex functions, such as molecular recognition (e.g., aptamers) and catalysis (e.g., ribozymes). Building on these foundations, researchers have begun to exploit the predictable base-pairing properties of RNA and DNA in order to utilize nucleic acids as functional materials that can undergo a molecular "switching" process, performing complex functions such as signaling or controlled payload release in response to external stimuli including light, pH, ligand-binding and other microenvironmental cues. Although this field is still in its infancy, these efforts offer exciting potential for the development of biologically based "smart materials". Herein, ongoing progress in the use of nucleic acids as an externally controllable switching material is reviewed. The diverse range of mechanisms that can trigger a stimulus response, and strategies for engineering those functionalities into nucleic acid materials are explored. Finally, recent progress is discussed in incorporating aptamer switches into more complex synthetic nucleic acid-based nanostructures and functionalized smart materials.
Collapse
Affiliation(s)
- Alexandra E Rangel
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Amani A Hariri
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Michael Eisenstein
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - H Tom Soh
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| |
Collapse
|
30
|
Thompson AS, Barrett SE, Weiden AG, Venkatesh A, Seto MKC, Gottlieb SZP, Leconte AM. Accurate and Efficient One-Pot Reverse Transcription and Amplification of 2'-Fluoro-Modified Nucleic Acids by Commercial DNA Polymerases. Biochemistry 2020; 59:2833-2841. [PMID: 32659079 DOI: 10.1021/acs.biochem.0c00494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
DNA is a foundational tool in biotechnology and synthetic biology but is limited by sensitivity to DNA-modifying enzymes. Recently, researchers have identified DNA polymerases that can enzymatically synthesize long oligonucleotides of modified DNA (M-DNA) that are resistant to DNA-modifying enzymes. Most applications require M-DNA to be reverse transcribed, typically using a RNA reverse transcriptase, back into natural DNA for sequence analysis or further manipulation. Here, we tested commercially available DNA-dependent DNA polymerases for their ability to reverse transcribe and amplify M-DNA in a one-pot reaction. Three of the six polymerases chosen (Phusion, Q5, and Deep Vent) could reverse transcribe and amplify synthetic 2'F M-DNA in a single reaction with <5 × 10-3 error per base pair. We further used Q5 DNA polymerase to reverse transcribe and amplify M-DNA synthesized by two candidate M-DNA polymerases (SFP1 and SFM4-6), allowing for quantification of the frequency, types, and locations of errors made during M-DNA synthesis. From these studies, we identify SFP1 as one of the most accurate M-DNA polymerases identified to date. Collectively, these studies establish a simple, robust method for the conversion of 2'F M-DNA to DNA in <1 h using commercially available materials, significantly improving the ease of use of M-DNA.
Collapse
Affiliation(s)
- Arianna S Thompson
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Susanna E Barrett
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Aurora G Weiden
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Ananya Venkatesh
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Madison K C Seto
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Simone Z P Gottlieb
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Aaron M Leconte
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| |
Collapse
|
31
|
Abstract
DNA polymerases play a central role in biology by transferring genetic information from one generation to the next during cell division. Harnessing the power of these enzymes in the laboratory has fueled an increase in biomedical applications that involve the synthesis, amplification, and sequencing of DNA. However, the high substrate specificity exhibited by most naturally occurring DNA polymerases often precludes their use in practical applications that require modified substrates. Moving beyond natural genetic polymers requires sophisticated enzyme-engineering technologies that can be used to direct the evolution of engineered polymerases that function with tailor-made activities. Such efforts are expected to uniquely drive emerging applications in synthetic biology by enabling the synthesis, replication, and evolution of synthetic genetic polymers with new physicochemical properties.
Collapse
|
32
|
ZHAO LP, YANG G, ZHANG XM, QU F. Development of Aptamer Screening against Proteins and Its Applications. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60012-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
33
|
Li Q, Chen J, Trajkovski M, Zhou Y, Fan C, Lu K, Tang P, Su X, Plavec J, Xi Z, Zhou C. 4′-Fluorinated RNA: Synthesis, Structure, and Applications as a Sensitive 19F NMR Probe of RNA Structure and Function. J Am Chem Soc 2020; 142:4739-4748. [DOI: 10.1021/jacs.9b13207] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Qiang Li
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jialiang Chen
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Ljubljana, EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Yifei Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Chaochao Fan
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Kuan Lu
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Pingping Tang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xuncheng Su
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Ljubljana, EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| |
Collapse
|
34
|
Shao Q, Chen T, Sheng K, Liu Z, Zhang Z, Romesberg FE. Selection of Aptamers with Large Hydrophobic 2'-Substituents. J Am Chem Soc 2020; 142:2125-2128. [PMID: 31961667 DOI: 10.1021/jacs.9b10538] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Previously, we evolved a DNA polymerase, SFM4-3, for the recognition of substrates modified at their 2' positions with a fluoro, O-methyl, or azido substituent. Here we use SFM4-3 to synthesize 2'-azido-modified DNA; we then use the azido group to attach different, large hydrophobic groups via click chemistry. We show that SFM4-3 recognizes the modified templates under standard conditions, producing natural DNA and thereby allowing amplification. To demonstrate the utility of this remarkable property, we use SFM4-3 to select aptamers with large hydrophobic 2' substituents that bind human neutrophil elastase or the blood coagulation protein factor IXa. The results indicate that SFM4-3 should facilitate the discovery of aptamers that adopt novel and perhaps more protein-like folds with hydrophobic cores that in turn allow them to access novel activities.
Collapse
Affiliation(s)
- Qian Shao
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Tingjian Chen
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Kai Sheng
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Zhixia Liu
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Zhuochen Zhang
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Floyd E Romesberg
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| |
Collapse
|
35
|
Song J, Zheng Y, Huang M, Wu L, Wang W, Zhu Z, Song Y, Yang C. A Sequential Multidimensional Analysis Algorithm for Aptamer Identification based on Structure Analysis and Machine Learning. Anal Chem 2020; 92:3307-3314. [PMID: 31876151 DOI: 10.1021/acs.analchem.9b05203] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Molecular recognition ligands are of great significance in many fields, but our ability to develop new recognition molecules remains to be expanded. Here, we developed a Sequential Multidimensional Analysis algoRiThm for aptamer discovery (SMART-Aptamer) from high-throughput sequencing (HTS) data of SELEX libraries based on multilevel structure analysis and unsupervised machine learning to discover nucleic acid recognition ligands with high accuracy and efficiency. We validated SMART-Aptamer with three sets of HTS data from screening pools against hESCs, EpCAM, and CSV. High affinity aptamers for all three targets were successfully obtained, and the results revealed that SMART-Aptamer is able to pick out high affinity aptamers with low false positive and negative rates. With the advantages of accuracy, efficiency, and robustness, SMART-Aptamer represents a paradigm-shift strategy for the discovery of binding ligands for a variety of biomedical applications.
Collapse
Affiliation(s)
- Jia Song
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Yuan Zheng
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Mengjiao Huang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , 361005 , People's Republic of China
| | - Lingling Wu
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Wei Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Zhi Zhu
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , 361005 , People's Republic of China
| | - Yanling Song
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China.,State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , 361005 , People's Republic of China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China.,State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , 361005 , People's Republic of China
| |
Collapse
|
36
|
Odeh F, Nsairat H, Alshaer W, Ismail MA, Esawi E, Qaqish B, Bawab AA, Ismail SI. Aptamers Chemistry: Chemical Modifications and Conjugation Strategies. Molecules 2019; 25:E3. [PMID: 31861277 PMCID: PMC6982925 DOI: 10.3390/molecules25010003] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/14/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022] Open
Abstract
Soon after they were first described in 1990, aptamers were largely recognized as a new class of biological ligands that can rival antibodies in various analytical, diagnostic, and therapeutic applications. Aptamers are short single-stranded RNA or DNA oligonucleotides capable of folding into complex 3D structures, enabling them to bind to a large variety of targets ranging from small ions to an entire organism. Their high binding specificity and affinity make them comparable to antibodies, but they are superior regarding a longer shelf life, simple production and chemical modification, in addition to low toxicity and immunogenicity. In the past three decades, aptamers have been used in a plethora of therapeutics and drug delivery systems that involve innovative delivery mechanisms and carrying various types of drug cargos. However, the successful translation of aptamer research from bench to bedside has been challenged by several limitations that slow down the realization of promising aptamer applications as therapeutics at the clinical level. The main limitations include the susceptibility to degradation by nucleases, fast renal clearance, low thermal stability, and the limited functional group diversity. The solution to overcome such limitations lies in the chemistry of aptamers. The current review will focus on the recent arts of aptamer chemistry that have been evolved to refine the pharmacological properties of aptamers. Moreover, this review will analyze the advantages and disadvantages of such chemical modifications and how they impact the pharmacological properties of aptamers. Finally, this review will summarize the conjugation strategies of aptamers to nanocarriers for developing targeted drug delivery systems.
Collapse
Affiliation(s)
- Fadwa Odeh
- Faculty of Science, The University of Jordan, Amman 11942, Jordan; (F.O.); (H.N.); (A.A.B.)
- Hamdi Mango Center for Scientific Research, The University of Jordan, Amman 11942, Jordan
| | - Hamdi Nsairat
- Faculty of Science, The University of Jordan, Amman 11942, Jordan; (F.O.); (H.N.); (A.A.B.)
| | - Walhan Alshaer
- Cell Therapy Center, The University of Jordan, Amman 11942, Jordan
| | - Mohammad A. Ismail
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
| | - Ezaldeen Esawi
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
| | - Baraa Qaqish
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
| | - Abeer Al Bawab
- Faculty of Science, The University of Jordan, Amman 11942, Jordan; (F.O.); (H.N.); (A.A.B.)
- Hamdi Mango Center for Scientific Research, The University of Jordan, Amman 11942, Jordan
| | - Said I. Ismail
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
- Qatar Genome Project, Qatar Foundation, Doha 5825, Qatar
| |
Collapse
|
37
|
Kimoto M, Shermane Lim YW, Hirao I. Molecular affinity rulers: systematic evaluation of DNA aptamers for their applicabilities in ELISA. Nucleic Acids Res 2019; 47:8362-8374. [PMID: 31392985 PMCID: PMC6895277 DOI: 10.1093/nar/gkz688] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/09/2019] [Accepted: 07/30/2019] [Indexed: 12/15/2022] Open
Abstract
Many nucleic acid aptamers that bind to target molecules have been reported as antibody alternatives. However, while the affinities of aptamers vary widely, little is known about the relationship between the affinities and their applicabilities for practical use. Here, we developed molecular affinity rulers: a series of DNA aptamers with different affinities that bind to the same area of target molecules, to measure the aptamer and its device applicabilities. For the ruler preparation, we used high-affinity DNA aptamers containing a hydrophobic unnatural base (Ds) as the fifth base. By replacing Ds bases with A bases in Ds-DNA aptamers targeting VEGF165 and interferon-γ, we prepared two sets of DNA aptamers with dissociation constants (KD) ranging from 10−12 to 10−8 M. Using these molecular affinity rulers, we evaluated the sensitivity of DNA aptamers in ELISA (enzyme-linked immunosorbent assay), which showed the clear relationship between aptamer affinities and their detection sensitivities. In sandwich-type ELISA using combinations of aptamers and antibodies, aptamers with KD values lower than ∼10−9 M were required for sufficient sensitivities (limit of detection (LOD) < 10 pM) and signal intensities, but optimizations improved the lower-affinity aptamers’ applicabilities. These aptamer affinity rulers could be useful for evaluating and improving aptamer applicabilities.
Collapse
Affiliation(s)
- Michiko Kimoto
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - Yun Wei Shermane Lim
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore.,NUS High School of Mathematics and Science, 20 Clementi Avenue 1, Singapore 129957, Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| |
Collapse
|
38
|
Abstract
To increase the scope of natural biosystem, nucleic acids have been intensively modified. One direction includes the development of a synthetic alternative to the native DNA and RNA, denoted Xenobiotic nucleic acids (XNAs) that are able to store and transfer genetic information either by base-modification or backbone-modification. Another line of research aims to develop alternative third base pair additional to natural A:T and G:C. These unnatural base pairs (UBPs) can store increased information content encoded in three base pairs. This review outlines the recent progress made towards XNA and UBP applications as new components of the genomic DNA as well as biostable aptamers. New achievements in the replacement of a bacterial genome by unnatural non-canonical nucleotides are also described.
Collapse
Affiliation(s)
- Elena Eremeeva
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, 3000 Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, 3000 Leuven, Belgium.
| |
Collapse
|
39
|
Huang M, Song J, Huang P, Chen X, Wang W, Zhu Z, Song Y, Yang C. Molecular Crowding Evolution for Enabling Discovery of Enthalpy-Driven Aptamers for Robust Biomedical Applications. Anal Chem 2019; 91:10879-10886. [PMID: 31347355 DOI: 10.1021/acs.analchem.9b02697] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An enthalpy-driven ligand is an ideal probe for practical applications because of the formation of abundant specific bonds between the ligand and target, compared to an entropy-driven ligand with a similar Gibbs free energy change. However, there has been a lack of direct discovery strategy for identifying enthalpy-driven ligands. In this work, a molecular crowding SELEX (systematic evolution of ligands by exponential enrichment) strategy for discovering enthalpy-driven aptamers was developed to improve the affinity and selectivity of aptamers in complex samples. Three aptamer sequences were successfully evolved against a tumor biomarker protein, and all proved to be enthalpy-driven by thermodynamics analysis, establishing the feasibility of molecular crowding SELEX for effective discovery of enthalpy-driven aptamers. Further comparison of aptamers evolved from conventional SELEX in buffer and molecular crowding SELEX (SYL-H2C) revealed much higher affinity of SYL-H2C. With its improved thermodynamic properties, the enthalpy-driven SYL-H2C aptamer was able to detect circulating tumor cells in real cancer patient blood samples with excellent detection accuracy (10/10). The proposed molecular crowding screening strategy offers a promising direction for discovering robust binding probes for a great variety of biomedical applications.
Collapse
Affiliation(s)
- Mengjiao Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Jia Song
- Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
| | - Peifeng Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Xiaofeng Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Wei Wang
- Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China.,Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China.,Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
| |
Collapse
|
40
|
Rangel AE, Chen Z, Ayele TM, Heemstra JM. In vitro selection of an XNA aptamer capable of small-molecule recognition. Nucleic Acids Res 2019; 46:8057-8068. [PMID: 30085205 PMCID: PMC6144807 DOI: 10.1093/nar/gky667] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/16/2018] [Indexed: 01/06/2023] Open
Abstract
Despite advances in XNA evolution, the binding capabilities of artificial genetic polymers are currently limited to protein targets. Here, we describe the expansion of in vitro evolution techniques to enable selection of threose nucleic acid (TNA) aptamers to ochratoxin A (OTA). This research establishes the first example of an XNA aptamer of any kind to be evolved having affinity to a small-molecule target. Selection experiments against OTA yielded aptamers having affinities in the mid nanomolar range; with the best binders possessing KD values comparable to or better than those of the best previously reported DNA aptamer to OTA. Importantly, the TNA can be incubated in 50% human blood serum for seven days and retain binding to OTA with only a minor change in affinity, while the DNA aptamer is completely degraded and loses all capacity to bind the target. This not only establishes the remarkable biostability of the TNA aptamer, but also its high level of selectivity, as it is capable of binding OTA in a large background of competing biomolecules. Together, this research demonstrates that refining methods for in vitro evolution of XNA can enable the selection of aptamers to a broad range of increasingly challenging target molecules.
Collapse
Affiliation(s)
- Alexandra E Rangel
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA
| | - Zhe Chen
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Jennifer M Heemstra
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA.,Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| |
Collapse
|
41
|
Li Y, Lee JS. Recent developments in affinity-based selection of aptamers for binding disease-related protein targets. CHEMICAL PAPERS 2019. [DOI: 10.1007/s11696-019-00842-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
42
|
Taylor AI, Houlihan G, Holliger P. Beyond DNA and RNA: The Expanding Toolbox of Synthetic Genetics. Cold Spring Harb Perspect Biol 2019; 11:11/6/a032490. [PMID: 31160351 DOI: 10.1101/cshperspect.a032490] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The remarkable physicochemical properties of the natural nucleic acids, DNA and RNA, define modern biology at the molecular level and are widely believed to have been central to life's origins. However, their ability to form repositories of information as well as functional structures such as ligands (aptamers) and catalysts (ribozymes/DNAzymes) is not unique. A range of nonnatural alternatives, collectively termed xeno nucleic acids (XNAs), are also capable of supporting genetic information storage and propagation as well as evolution. This gives rise to a new field of "synthetic genetics," which seeks to expand the nucleic acid chemical toolbox for applications in both biotechnology and molecular medicine. In this review, we outline XNA polymerase and reverse transcriptase engineering as a key enabling technology and summarize the application of "synthetic genetics" to the development of aptamers, enzymes, and nanostructures.
Collapse
Affiliation(s)
- Alexander I Taylor
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Gillian Houlihan
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Philipp Holliger
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| |
Collapse
|
43
|
Boussebayle A, Groher F, Suess B. RNA-based Capture-SELEX for the selection of small molecule-binding aptamers. Methods 2019; 161:10-15. [PMID: 30953759 DOI: 10.1016/j.ymeth.2019.04.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 11/16/2022] Open
Abstract
Despite their wide applicability, the selection of small molecule-binding RNA aptamers with both high affinity binding and specificity is still challenging. Aptamers that excel at both binding and structure switching are particularly rare and difficult to find. Here, we present the protocol of a Capture-SELEX that specifically allows the in vitro selection of small-molecule binding aptamers, which are essential building blocks for the design process of synthetic riboswitches and biosensors. Moreover, we provide a comparative overview of our proposed methodology versus alternative in vitro selection protocols with a special focus on the design of the pool. Finally, we have included detailed notes to point out useful tips and pitfalls for future application.
Collapse
Affiliation(s)
- Adrien Boussebayle
- Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Florian Groher
- Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.
| |
Collapse
|
44
|
Blanco C, Janzen E, Pressman A, Saha R, Chen IA. Molecular Fitness Landscapes from High-Coverage Sequence Profiling. Annu Rev Biophys 2019; 48:1-18. [PMID: 30601678 DOI: 10.1146/annurev-biophys-052118-115333] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The function of fitness (or molecular activity) in the space of all possible sequences is known as the fitness landscape. Evolution is a random walk on the fitness landscape, with a bias toward climbing hills. Mapping the topography of real fitness landscapes is fundamental to understanding evolution, but previous efforts were hampered by the difficulty of obtaining large, quantitative data sets. The accessibility of high-throughput sequencing (HTS) has transformed this study, enabling large-scale enumeration of fitness for many mutants and even complete sequence spaces in some cases. We review the progress of high-throughput studies in mapping molecular fitness landscapes, both in vitro and in vivo, as well as opportunities for future research. Such studies are rapidly growing in number. HTS is expected to have a profound effect on the understanding of real molecular fitness landscapes.
Collapse
Affiliation(s)
- Celia Blanco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA; , , , ,
| | - Evan Janzen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA; , , , , .,Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106, USA
| | - Abe Pressman
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA; , , , , .,Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Ranajay Saha
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA; , , , ,
| | - Irene A Chen
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106, USA
| |
Collapse
|
45
|
Non canonical genetic material. Curr Opin Biotechnol 2018; 57:25-33. [PMID: 30554069 DOI: 10.1016/j.copbio.2018.12.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 11/13/2018] [Accepted: 12/03/2018] [Indexed: 01/20/2023]
Abstract
To increase the scope of natural biosystem, nucleic acids have been intensively modified. One direction includes the development of a synthetic alternative to the native DNA and RNA, denoted Xenobiotic nucleic acids (XNAs) that are able to store and transfer genetic information either by base-modification or backbone-modification. Another line of research aims to develop alternative third base pair additional to natural A:T and G:C. These unnatural base pairs (UBPs) can store increased information content encoded in three base pairs. This review outlines the recent progress made towards XNA and UBP applications as new components of the genomic DNA as well as biostable aptamers. New achievements in the replacement of a bacterial genome by unnatural non-canonical nucleotides are also described.
Collapse
|
46
|
Röthlisberger P, Hollenstein M. Aptamer chemistry. Adv Drug Deliv Rev 2018; 134:3-21. [PMID: 29626546 DOI: 10.1016/j.addr.2018.04.007] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 12/12/2022]
Abstract
Aptamers are single-stranded DNA or RNA molecules capable of tightly binding to specific targets. These functional nucleic acids are obtained by an in vitro Darwinian evolution method coined SELEX (Systematic Evolution of Ligands by EXponential enrichment). Compared to their proteinaceous counterparts, aptamers offer a number of advantages including a low immunogenicity, a relative ease of large-scale synthesis at affordable costs with little or no batch-to-batch variation, physical stability, and facile chemical modification. These alluring properties have propelled aptamers into the forefront of numerous practical applications such as the development of therapeutic and diagnostic agents as well as the construction of biosensing platforms. However, commercial success of aptamers still proceeds at a weak pace. The main factors responsible for this delay are the susceptibility of aptamers to degradation by nucleases, their rapid renal filtration, suboptimal thermal stability, and the lack of functional group diversity. Here, we describe the different chemical methods available to mitigate these shortcomings. Particularly, we describe the chemical post-SELEX processing of aptamers to include functional groups as well as the inclusion of modified nucleoside triphosphates into the SELEX protocol. These methods will be illustrated with successful examples of chemically modified aptamers used as drug delivery systems, in therapeutic applications, and as biosensing devices.
Collapse
|
47
|
Taylor AI, Holliger P. Selecting Fully-Modified XNA Aptamers Using Synthetic Genetics. ACTA ACUST UNITED AC 2018; 10:e44. [PMID: 29927117 DOI: 10.1002/cpch.44] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This unit describes the application of "synthetic genetics," i.e., the replication of xeno nucleic acids (XNAs), artificial analogs of DNA and RNA bearing alternative backbone or sugar congeners, to the directed evolution of synthetic oligonucleotide ligands (XNA aptamers) specific for target proteins or nucleic acid motifs, using a cross-chemistry selective exponential enrichment (X-SELEX) approach. Protocols are described for synthesis of diverse-sequence XNA repertoires (typically 1014 molecules) using DNA templates, isolation and panning for functional XNA sequences using targets immobilized on solid phase or gel shift induced by target binding in solution, and XNA reverse transcription to allow cDNA amplification or sequencing. The method may be generally applied to select fully-modified XNA aptamers specific for a wide range of target molecules. © 2018 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Alexander I Taylor
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Philipp Holliger
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| |
Collapse
|
48
|
Röthlisberger P, Levi-Acobas F, Sarac I, Marlière P, Herdewijn P, Hollenstein M. On the enzymatic incorporation of an imidazole nucleotide into DNA. Org Biomol Chem 2018; 15:4449-4455. [PMID: 28485736 DOI: 10.1039/c7ob00858a] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The expansion of the genetic alphabet with an additional, artificial base pair is of high relevance for numerous applications in synthetic biology. The enzymatic construction of metal base pairs is an alluring strategy that would ensure orthogonality to canonical nucleic acids. So far, very little is known on the enzymatic fabrication of metal base pairs. Here, we report on the synthesis and the enzymatic incorporation of an imidazole nucleotide into DNA. The imidazole nucleotide dIm is known to form highly stable dIm-Ag+-dIm artificial base pairs that cause minimal structural perturbation of DNA duplexes and was considered to be an ideal candidate for the enzymatic construction of metal base pairs. We demonstrate that dImTP is incorporated with high efficiency and selectivity opposite a templating dIm nucleotide by the Kf exo-. The presence of Mn2+, and to a smaller extent Ag+, enhances the efficiency of this polymerization reaction, however, without being strictly required. In addition, multiple incorporation events could be observed, albeit with modest efficiency. We demonstrate that the dIm-Mn+-dIm cannot be constructed by DNA polymerases and suggest that parameters other than stability of a metal base pair and its impact on the structure of DNA duplexes govern the enzymatic formation of artificial metal base pairs.
Collapse
Affiliation(s)
- Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.
| | | | | | | | | | | |
Collapse
|
49
|
Guo F, Li Q, Zhou C. Synthesis and biological applications of fluoro-modified nucleic acids. Org Biomol Chem 2018; 15:9552-9565. [PMID: 29086791 DOI: 10.1039/c7ob02094e] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Owing to the unique physical properties of a fluorine atom, incorporating fluoro-modifications into nucleic acids offers striking biophysical and biochemical features, and thus significantly extends the breadth and depth of biological applications of nucleic acids. In this review, fluoro-modified nucleic acids that have been synthesized through either solid phase synthesis or the enzymatic approach are briefly summarised, followed by a section describing their biomedical applications in nucleic acid-based therapeutics, 18F PET imaging and mechanistic studies of DNA modifying enzymes. In the last part, the utility of 19F NMR and MRI for probing the structure, dynamics and molecular interactions of fluorinated nucleic acids is reviewed.
Collapse
Affiliation(s)
- Fengmin Guo
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China.
| | | | | |
Collapse
|
50
|
Moriou C, Da Silva AD, Vianelli Prado MJ, Denhez C, Plashkevych O, Chattopadhyaya J, Guillaume D, Clivio P. C2′-F Stereoconfiguration As a Puckering Switch for Base Stacking at the Dinucleotide Level. J Org Chem 2018; 83:2473-2478. [DOI: 10.1021/acs.joc.7b03186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Céline Moriou
- Institut de Chimie des Substances Naturelles, CNRS, Gif-sur-Yvette 91198 Cedex, France
| | - Adilson D. Da Silva
- Departamento
de Quimica, ICE, Universidade Federal de Juiz de Fora, 36036-900 Juiz de Fora, Minas Gerais, Brazil
| | - Marcos Joel Vianelli Prado
- Departamento
de Quimica, ICE, Universidade Federal de Juiz de Fora, 36036-900 Juiz de Fora, Minas Gerais, Brazil
| | - Clément Denhez
- Université
de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, Reims 51096 Cedex, France
- Université
de Reims Champagne Ardenne, Multiscale Molecular Modelling Platform, UFR Sciences Exactes et Naturelles, Reims F-51687 Cedex 2, France
| | - Oleksandr Plashkevych
- Institute of Cell & Molecular Biology, Program of Chemical Biology, Box 581, Biomedical Center, University of Uppsala, S-75123 Uppsala, Sweden
| | - Jyoti Chattopadhyaya
- Institute of Cell & Molecular Biology, Program of Chemical Biology, Box 581, Biomedical Center, University of Uppsala, S-75123 Uppsala, Sweden
| | - Dominique Guillaume
- Université
de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, Reims 51096 Cedex, France
| | - Pascale Clivio
- Université
de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, Reims 51096 Cedex, France
| |
Collapse
|