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Xian S, Chen Z, Huang W, Zhao L, Qiu Y, Hao P, Sun L, Yang Q, Song L, Kang L. One-step synthesis of a radioiodinated anti-microRNA-21 oligonucleotide for theranostics in prostate tumor xenografts. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.129519] [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]
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2
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Erel-Akbaba G, Akbaba H. Investigation of the potential therapeutic effect of cationic lipoplex mediated fibroblast growth factor-2 encoding plasmid DNA delivery on wound healing. ACTA ACUST UNITED AC 2021; 29:329-340. [PMID: 34491567 DOI: 10.1007/s40199-021-00410-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/04/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Developing an alternative and efficient therapy for wound healing has been an important research topic for pharmaceutical sciences. A straightforward but effective system for delivering fibroblast growth factor-2 (FGF-2) encoding plasmid DNA (pFGF-2) for wound healing therapy was aimed to develop in this study. METHODS In order to provide the delivery of pFGF-2, a delivery vector, namely, cationic lipid nanoparticle (cLN) was developed by the melt-emulsification process, complexed with pFGF-2 to form a lipoplex system and further characterized. The pFGF-2 binding and protecting ability of lipoplexes were evaluated. The cytotoxicity and transfection efficiency of the lipoplexes, FGF-2 expression levels, and in vitro wound healing ability have been investigated on the L929 fibroblast cell line. RESULTS The obtained lipoplex system has a particle size of 88.53 nm with a low PDI (0.185), and zeta potential values of 27.8 mV with a spherical shape. The ability of cLNs to bind pFGF-2 and protect against nucleases was demonstrated by gel retardation assay. Furthermore, the developed FGF-2 carrying lipoplexes system showed significant transfection and FGF-2 expression ability comparing naked plasmid. Finally, scratch assay revealed that the developed system is able to promote in vitro cell proliferation/migration in 48 h. CONCLUSION Promising results have been achieved with the use of lipoplexes carrying pFGF-2, and this approach could be considered as a potentially applicable concept for the future gene-based wound healing therapies.
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Affiliation(s)
- Gülşah Erel-Akbaba
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Izmir Katip Celebi University, 35620, Izmir, Turkey.
| | - Hasan Akbaba
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, 35100, Izmir, Turkey
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3
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Wu J, Wang S, Li X, Zhang Q, Yang J, Ma Y, Guan Z, Yang Z. Selective Anti-melanoma Effect of Phosphothioated Aptamer Encapsulated by Neutral Cytidinyl/Cationic Lipids. Front Cell Dev Biol 2021; 9:660233. [PMID: 34262898 PMCID: PMC8273494 DOI: 10.3389/fcell.2021.660233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 06/01/2021] [Indexed: 12/11/2022] Open
Abstract
BC15-31 is a DNA aptamer that targets heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), which plays a crucial role in the process of pre-RNA maturation and is also essential for the rapid proliferation of tumor cells. In this research, we modified BC15-31 with a phosphorothioate (PS) backbone, LNA, and 2-O-MOE to enhance its stability and target affinity. In addition, a neutral cytidinyl lipid (DNCA) and a cationic lipid (CLD) were mixed to encapsulate modified aptamers with the aim of improving their cell permeability with low toxicity. Under the DNCA/CLD package, aptamers are mainly distributed in the nucleus. A modified sequence WW-24 showed an excellent selective anti-melanoma (A375 cells, ∼25 nM, 80%) activity, targeted to both hnRNP A1 and hnRNP A2/B1 found by the BLI experiment, and induced more early and late apoptosis in vitro, which also showed stronger antitumor effect and longer accumulation time in vivo. These results provide a new strategy for further clinical applications.
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Affiliation(s)
- Jing Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Shuhe Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Xiang Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Qi Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Jie Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Yuan Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Zhu Guan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
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4
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Li L, Yang X, Li K, Zhang G, Ma Y, Cai B, Li S, Ding H, Deng J, Nan X, Sun J, Wu Y, Shao N, Zhang L, Yang Z. d-/l-Isothymidine incorporation in the core sequence of aptamer BC15 enhanced its binding affinity to the hnRNP A1 protein. Org Biomol Chem 2019; 16:7488-7497. [PMID: 30272759 DOI: 10.1039/c8ob01454j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) was reported to participate in the development of a variety of tumors. BC15 is a DNA aptamer targeting hnRNP A1. Firstly, through sequence truncation, we identified 31-mer sequence BC15-31 as the core sequence of BC15 with a strong binding affinity and high selectivity to the hnRNP A1 protein. Isothymidine (isoT) modification was then applied for the structural optimization of BC15-31, systematic modification and biological evaluation were carried out. Incorporation of isoT in the 1,3 sites at the 5'-end of BC15-31 can significantly enhance the protein affinity. Chemical modifications close to the 3'-end can greatly improve the stability of the aptamer. Furthermore, BC15-31 modified with isoT at both the 5'-end and 3'-end displayed an additive effect with enhanced bioactivity and stability at the same time. Our study strategy on BC15 provides a useful guideline for chemical modification and optimization of the aptamer for further clinical application.
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Affiliation(s)
- Liyu Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China.
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5
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Li K, Deng J, Jin H, Yang X, Fan X, Li L, Zhao Y, Guan Z, Wu Y, Zhang L, Yang Z. Chemical modification improves the stability of the DNA aptamer GBI-10 and its affinity towards tenascin-C. Org Biomol Chem 2018; 15:1174-1182. [PMID: 28084479 DOI: 10.1039/c6ob02577c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aptamers are useful tools in molecular imaging due to their numerous attractive properties, such as excellent affinity and selectivity to diverse types of target molecules and biocompatibility. We carried out structure-activity relationship studies with the tenascin-C (TN-C) binding aptamer GBI-10, which is a promising candidate in tumor imaging. To increase the tumor targeting ability and nuclease resistance under physiological conditions, systematic modifications of GBI-10 with single and multiple 2'-deoxyinosine (2'-dI) or d-/l-isonucleoside (d-/l-isoNA) were performed. Results indicated that sector 3 of the proposed secondary structure is the most important region for specific binding with TN-C. By correlating the affinity of eighty-four GBI-10 derivatives with their predicted secondary structure by Zuker Mfold, we first validated the preferred secondary structure at 37 °C. We found that d-/l-isoNA modified GBI-10 derivatives exhibited improved affinity to the target as well as plasma stability. Affinity measurement and confocal imaging analysis highlighted one potent compound: 4AL/26TL/32TL, which possessed a significantly increased targeting ability to tumor cells. These results revealed the types of modified nucleotides, and the position and number of substituents in GBI-10 that were critical to the TN-C binding ability. Stabilized TN-C-binding DNA aptamers were prepared and they could be further developed for tumor imaging. Our strategy to introduce 2'-dI and d-/l-isoNA modifications after the selection process is likely to be generally applicable to improve the in vivo stability of aptamers without compromising their binding ability.
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Affiliation(s)
- Kunfeng Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Jiali Deng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Xiantao Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Xinmeng Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Liyu Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Yi Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Zhu Guan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Yun Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
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6
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Ma Y, Liu S, Wang Y, Zhao Y, Huang Y, Zhong L, Guan Z, Zhang L, Yang Z. Isonucleotide incorporation into middle and terminal siRNA duplexes exhibits high gene silencing efficacy and nuclease resistance. Org Biomol Chem 2018; 15:5161-5170. [PMID: 28585968 DOI: 10.1039/c7ob01065f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this study, we introduced a pair of nucleotide enantiomers, d-/l-isonucleotides (d-/l-isoNA), to examine the interactions between siRNAs and their related proteins. The serum stability and gene-silencing activity of the modified siRNAs were systematically evaluated. Gene-silencing activity had a site-specific effect, and the incorporation of a single d-isoNA at the 8th position (counting from the 5'-terminus) in the antisense strand improved the gene-silencing activity by improving RISC loading and affecting the movement of the PIWI domain. d-isoNA incorporated at the terminus of siRNA including the 2nd position in the antisense strand and 3'-overhangs in the sense strand, especially the latter, enhanced nuclease resistance and prolonged the silencing retention time. In addition, l-isoNA incorporation into the middle of the sense strand enhanced activity. These results provide a chemical strategy for the modulation of siRNA gene-silencing activity and nuclease resistance.
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Affiliation(s)
- Yuan Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
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7
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Fan X, Sun L, Li K, Yang X, Cai B, Zhang Y, Zhu Y, Ma Y, Guan Z, Wu Y, Zhang L, Yang Z. The Bioactivity of D-/L-Isonucleoside- and 2'-Deoxyinosine-Incorporated Aptamer AS1411s Including DNA Replication/MicroRNA Expression. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 9:218-229. [PMID: 29246300 PMCID: PMC5651494 DOI: 10.1016/j.omtn.2017.09.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/28/2017] [Accepted: 09/28/2017] [Indexed: 12/20/2022]
Abstract
In this study, chemical modification of 2'-deoxyinosine (2'-dI) and D-/L-isothymidine (D-/L-isoT) was performed on AS1411. They could promote the nucleotide-protein interaction by changing the local conformation. Twenty modified sequences were obtained, FCL-I and FCL-II showed the most noticeable activity improvement. They stabilized the G-quadruplex, remained highly resistant to serum degradation and specificity for nucleolin, further inhibited tumor cell growth, exhibited a stronger ability to influence the different phases of the tumor cell cycle, induced S-phase arrest, promoted the inhibition of DNA replication, and suppressed the unwound function of a large T antigen as powerful as AS1411. The microarray analysis and TaqMan PCR results showed that FCL-II can upregulate the expression of four breast-cancer-related, lowly expressed miRNAs and downregulate the expression of three breast-cancer-related, highly expressed miRNAs (>2.5-fold). FCL-II resulted in enhanced treatment effects greater than AS1411 in animal experiments (p < 0.01). The computational results further proved that FCL-II exhibits more structural advantages than AS1411 for binding to the target protein nucleolin, indicating its great potential in antitumor therapy.
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Affiliation(s)
- Xinmeng Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Lidan Sun
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University Medical College, Yichang 443002, PR China
| | - Kunfeng Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Xiantao Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Baobin Cai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Yanfen Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Yuejie Zhu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Yuan Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Zhu Guan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Yun Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China.
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8
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Zhang LX, Li KF, Wang H, Gu MJ, Liu LS, Zheng ZZ, Han NY, Yang ZJ, Fan TY. Preparation and In Vitro Evaluation of a MRI Contrast Agent Based on Aptamer-Modified Gadolinium-Loaded Liposomes for Tumor Targeting. AAPS PharmSciTech 2017; 18:1564-1571. [PMID: 27604884 DOI: 10.1208/s12249-016-0600-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/24/2016] [Indexed: 11/30/2022] Open
Abstract
The aim of this study was to prepare aptamer-modified liposomes loaded with gadolinium (Gd) to enhance the effective diagnosis for tumor by MRI. A modified GBI-10 (GBI-10m) was used to prepare targeted liposomes (GmLs). Liposomes with GBI-10 aptamer (GLs) and without aptamer (non-targeted liposomes (NLs)) were also prepared as controls. The particle size and zeta potential of GmLs, GLs, and NLs were all assayed. A clinical 3.0 T MR scanner was employed to assess the imaging efficiency and measure the longitudinal relaxivity (r 1) of the above liposomes. Confocal laser scanning microscopy and flow cytometry were used to analyze and compare the targeting effects of GmLs, GLs, and NLs to MDA-MB-435s cells at 37°C. The particle size of the prepared liposomes was scattered at 100-200 nm, and their values of r 1 were ∼4 mM-1 s-1. The images of confocal laser scanning microscopy showed that GmLs in the cytoplasm were significantly more than GLs and both GmLs and GLs were more than NLs. The fluorescence intensity of GmLs was increased by about two times than that of GLs and three times than that of NLs by flow cytometry. Therefore, the GmLs in this initial study were suggested to be a potential MRI contrast agent at 37°C for diagnosing tumors with the protein of tenascin-C over-expressed.
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9
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Selvam C, Mutisya D, Prakash S, Ranganna K, Thilagavathi R. Therapeutic potential of chemically modified siRNA: Recent trends. Chem Biol Drug Des 2017; 90:665-678. [PMID: 28378934 DOI: 10.1111/cbdd.12993] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/26/2017] [Accepted: 03/27/2017] [Indexed: 12/17/2022]
Abstract
Small interfering RNAs (siRNAs) are one of the valuable tools to investigate the functions of genes and are also used for gene silencing. It has a wide scope in drug discovery through in vivo target validation. siRNA therapeutics are not optimal drug-like molecules due to poor bioavailability and immunogenic and off-target effects. To overcome the challenges associated with siRNA therapeutics, identification of appropriate chemical modifications that improves the stability, specificity and potency of siRNA is essential. This review focuses on the various chemical modifications and their implications in siRNA therapy.
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Affiliation(s)
- Chelliah Selvam
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX, USA
| | - Daniel Mutisya
- Department of Science and Mathematics, Albany State University, Albany, GA, USA
| | - Sandhya Prakash
- Department of Biotechnology, Faculty of Engineering, Karpagam University, Coimbatore, India
| | - Kasturi Ranganna
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX, USA
| | - Ramasamy Thilagavathi
- Department of Biotechnology, Faculty of Engineering, Karpagam University, Coimbatore, India
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10
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Fan X, Zhang Y, Liu X, He H, Ma Y, Sun J, Huang Y, Wang X, Wu Y, Zhang L, Yang Z. Biological Properties of a 3′,3″-Bis-Peptide-siRNA Conjugate in Vitro and in Vivo. Bioconjug Chem 2016; 27:1131-42. [DOI: 10.1021/acs.bioconjchem.6b00087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xinmeng Fan
- State Key
Laboratory of Natural
and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Yanfen Zhang
- State Key
Laboratory of Natural
and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Xinjie Liu
- State Key
Laboratory of Natural
and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Hongyan He
- State Key
Laboratory of Natural
and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Yuan Ma
- State Key
Laboratory of Natural
and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Jing Sun
- State Key
Laboratory of Natural
and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Ye Huang
- State Key
Laboratory of Natural
and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Xiaofeng Wang
- State Key
Laboratory of Natural
and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Yun Wu
- State Key
Laboratory of Natural
and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Lihe Zhang
- State Key
Laboratory of Natural
and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
| | - Zhenjun Yang
- State Key
Laboratory of Natural
and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China
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11
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Yang X, Xiao Z, Zhu J, Li Z, He J, Zhang L, Yang Z. Spatial conservation studies of nucleobases in 10–23 DNAzyme by 2′-positioned isonucleotides and enantiomers for increased activity. Org Biomol Chem 2016; 14:4032-8. [DOI: 10.1039/c6ob00390g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
d-/l-Isonucleotides were used to modify the catalytic core and recognition arms of 10–23 DNAzyme and prominently improved its bioactivity.
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Affiliation(s)
- Xiantao Yang
- State Key Laboratory of Natural and Biomimetic Drugs
- School of Pharmaceutical Sciences
- Peking University
- Beijing
- China
| | - Zhangping Xiao
- State Key Laboratory of Natural and Biomimetic Drugs
- School of Pharmaceutical Sciences
- Peking University
- Beijing
- China
| | - Junfei Zhu
- College of Life Sciences
- Guizhou University
- Guiyang 550025
- China
| | - Zhiwen Li
- College of Life Sciences
- Guizhou University
- Guiyang 550025
- China
| | - Junlin He
- Beijing Institute of Pharmacology and Toxicology
- Beijing 100850
- China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs
- School of Pharmaceutical Sciences
- Peking University
- Beijing
- China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs
- School of Pharmaceutical Sciences
- Peking University
- Beijing
- China
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12
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Toti K, Renders M, Groaz E, Herdewijn P, Van Calenbergh S. Nucleosides with Transposed Base or 4'-Hydroxymethyl Moieties and Their Corresponding Oligonucleotides. Chem Rev 2015; 115:13484-525. [PMID: 26655745 DOI: 10.1021/acs.chemrev.5b00545] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This review focuses on 4'-hydroxymethyl- or nucleobase-transposed nucleosides, nucleotides, and nucleoside phosphonates, their stereoisomers, and their close analogues. The biological activities of all known 4'-hydroxymethyl- or nucleobase-transposed nucleosides, nucleotides, and nucleoside phosphonates as potential antiviral or anticancer agents are compiled. The routes that have been taken for the chemical synthesis of such nucleoside derivatives are described, with special attention to the innovative strategies. The enzymatic synthesis, base-pairing properties, structure, and stability of oligonucleotides containing nucleobase- or 4'-hydroxymethyl-transposed nucleotides are discussed. The use of oligonucleotides containing nucleobase- or 4'-hydroxymethyl-transposed nucleotides as small oligonucleotide (e.g., human immunodeficiency virus integrase) inhibitors, in applications such as antisense therapy, silencing RNA (siRNA), or aptamer selections, is detailed.
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Affiliation(s)
- Kiran Toti
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University , Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Marleen Renders
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven , Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Elisabetta Groaz
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven , Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven , Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University , Ottergemsesteenweg 460, 9000 Ghent, Belgium
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13
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Cai B, Yang X, Sun L, Fan X, Li L, Jin H, Wu Y, Guan Z, Zhang L, Zhang L, Yang Z. Stability and bioactivity of thrombin binding aptamers modified with D-/L-isothymidine in the loop regions. Org Biomol Chem 2015; 12:8866-76. [PMID: 25264858 DOI: 10.1039/c4ob01525h] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thrombin binding aptamer (TBA) is a 15-mer single-strand DNA that was identified by SELEX screening technology. It adopts a chair-type antiparallel G-quadruplex and can specifically interact with thrombin, thus inhibiting blood coagulation. Isonucleoside (isoNA) is a type of nucleoside isomer in which the base is shifted to 2′-positions of the glycosyl group, endowed with the ability to modulate local conformation of nucleotides, and L-isoNA could alter the conformation more due to the inversion of glycosyl configuration. Incorporation of L-isothymidine (L-isoT) at T3, T9, T12 positions and D-isoT at the T7 position in TBA's loop regions promoted the formation of G-quadruplex, resulting in enhanced affinity with thrombin and an increased anticoagulant effect. Computer simulation indicated that TBA-12L showed the strongest binding with thrombin, which was consistent with experimental results. The bioactivity of double isoNA incorporated TBA with D-IsoT at T7 and L-IsoT at T12 was comparable to that of TBA-12L, suggesting that the T12 of TBA was very important in interaction with thrombin. Our study also suggested that TBA might interact with two thrombin molecules through the TT loops (T3T4, T12T13) and TGT loop, but the second bonding did not show additional biological effects.
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Affiliation(s)
- Baobin Cai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, PR China.
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14
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Huang Y, Tian M, Zhang Y, Sheng G, Chen Z, Ma Y, Chen Y, Peng Y, Zhao YL, Wang Y, Zhang L, Yang Z. d-Isonucleotide (isoNA) incorporation around cleavage site of passenger strand promotes the vibration of Ago2-PAZ domain and enhances in vitro potency of siRNA. Org Biomol Chem 2015; 13:10825-33. [DOI: 10.1039/c5ob01119a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Isonucleotide modification around the cleavage site of the passenger strand affects the in vitro potency of modified siRNAs by altering the motion pattern of the Ago2-PAZ domain.
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15
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Kamiya Y, Takai J, Ito H, Murayama K, Kashida H, Asanuma H. Enhancement of stability and activity of siRNA by terminal substitution with serinol nucleic acid (SNA). Chembiochem 2014; 15:2549-55. [PMID: 25233814 DOI: 10.1002/cbic.201402369] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Indexed: 12/21/2022]
Abstract
RNA interference (RNAi ), sequence-specific gene silencing triggered by double-stranded, small interfering RNA (siRNA), has become a facile and effective tool for biological research and holds potential for therapeutic applications. However, the application of siRNA is hindered by susceptibility to nucleases and off-target effects. In this study, we introduced artificial nucleotides, serinol nucleic acid (SNA), with an acyclic scaffold, at the termini of siRNA strands. Our aim was appropriately to accommodate the antisense strand in an RNA-induced silencing complex (RISC) by inhibiting sense-strand incorporation and thus improve resistance to nuclease-mediated degradation. Substitution of SNA into siRNA at both termini of the sense strand and at the 3' terminus of the antisense strand improved antisense strand selectivity remarkably in the formation of RISC, RNAi activity, and nuclease resistance.
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Affiliation(s)
- Yukiko Kamiya
- EcoTopia Science Institute and Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan)
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Wu L, Pei F, Zhang J, Wu J, Feng M, Wang Y, Jin H, Zhang L, Tang X. Synthesis of Site-Specifically Phosphate-Caged siRNAs and Evaluation of Their RNAi Activity and Stability. Chemistry 2014; 20:12114-22. [DOI: 10.1002/chem.201403430] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Indexed: 01/17/2023]
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Loss of silencing activity caused by 5′-terminal modification with d-/l-isonucleotide (isoNA) or locked nucleic acid (LNA) could not be restored by 5′-terminal phosphorylation. Sci China Chem 2013. [DOI: 10.1007/s11426-013-5032-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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