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Zhang Y, Gaetano CM, Williams KR, Bassell GJ, Mihailescu MR. FMRP interacts with G-quadruplex structures in the 3'-UTR of its dendritic target Shank1 mRNA. RNA Biol 2015; 11:1364-74. [PMID: 25692235 DOI: 10.1080/15476286.2014.996464] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Fragile X syndrome (FXS), the most common cause of inherited intellectual disability, is caused by the loss of expression of the fragile X mental retardation protein (FMRP). FMRP, which regulates the transport and translation of specific mRNAs, uses its RGG box domain to bind mRNA targets that form G-quadruplex structures. One of the FMRP in vivo targets, Shank1 mRNA, encodes the master scaffold proteins of the postsynaptic density (PSD) which regulate the size and shape of dendritic spines because of their capacity to interact with many different PSD components. Due to their effect on spine morphology, altered translational regulation of Shank1 transcripts may contribute to the FXS pathology. We hypothesized that the FMRP interactions with Shank1 mRNA are mediated by the recognition of the G quadruplex structure, which has not been previously demonstrated. In this study we used biophysical techniques to analyze the Shank1 mRNA 3'-UTR and its interactions with FMRP and its phosphorylated mimic FMRP S500D. We found that the Shank1 mRNA 3 ' -UTR adopts two very stable intramolecular G-quadruplexes which are bound specifically and with high affinity by FMRP both in vitro and in vivo. These results suggest a role of G-quadruplex RNA motif as a structural element in the common mechanism of FMRP regulation of its dendritic mRNA targets.
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Affiliation(s)
- Yang Zhang
- a Graduate School of Pharmaceutical Sciences; Mylan School of Pharmacy ; Duquesne University ; Pittsburgh , PA USA
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102
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Jiang F, Liu B, Lu J, Li F, Li D, Liang C, Dang L, Liu J, He B, Badshah SA, Lu C, He X, Guo B, Zhang XB, Tan W, Lu A, Zhang G. Progress and Challenges in Developing Aptamer-Functionalized Targeted Drug Delivery Systems. Int J Mol Sci 2015; 16:23784-822. [PMID: 26473828 PMCID: PMC4632726 DOI: 10.3390/ijms161023784] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 09/16/2015] [Accepted: 09/21/2015] [Indexed: 02/06/2023] Open
Abstract
Aptamers, which can be screened via systematic evolution of ligands by exponential enrichment (SELEX), are superior ligands for molecular recognition due to their high selectivity and affinity. The interest in the use of aptamers as ligands for targeted drug delivery has been increasing due to their unique advantages. Based on their different compositions and preparation methods, aptamer-functionalized targeted drug delivery systems can be divided into two main categories: aptamer-small molecule conjugated systems and aptamer-nanomaterial conjugated systems. In this review, we not only summarize recent progress in aptamer selection and the application of aptamers in these targeted drug delivery systems but also discuss the advantages, challenges and new perspectives associated with these delivery systems.
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Affiliation(s)
- Feng Jiang
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Hong Kong Baptist University Branch of State Key Laboratory of Chemo/Biosensing and Chemometrics of Hunan University, Hong Kong, China.
| | - Biao Liu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Hong Kong Baptist University Branch of State Key Laboratory of Chemo/Biosensing and Chemometrics of Hunan University, Hong Kong, China.
| | - Jun Lu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Hong Kong Baptist University Branch of State Key Laboratory of Chemo/Biosensing and Chemometrics of Hunan University, Hong Kong, China.
| | - Fangfei Li
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Hong Kong Baptist University Branch of State Key Laboratory of Chemo/Biosensing and Chemometrics of Hunan University, Hong Kong, China.
| | - Defang Li
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Hong Kong Baptist University Branch of State Key Laboratory of Chemo/Biosensing and Chemometrics of Hunan University, Hong Kong, China.
| | - Chao Liang
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Hong Kong Baptist University Branch of State Key Laboratory of Chemo/Biosensing and Chemometrics of Hunan University, Hong Kong, China.
| | - Lei Dang
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Hong Kong Baptist University Branch of State Key Laboratory of Chemo/Biosensing and Chemometrics of Hunan University, Hong Kong, China.
| | - Jin Liu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Hong Kong Baptist University Branch of State Key Laboratory of Chemo/Biosensing and Chemometrics of Hunan University, Hong Kong, China.
| | - Bing He
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Hong Kong Baptist University Branch of State Key Laboratory of Chemo/Biosensing and Chemometrics of Hunan University, Hong Kong, China.
| | - Shaikh Atik Badshah
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Hong Kong Baptist University Branch of State Key Laboratory of Chemo/Biosensing and Chemometrics of Hunan University, Hong Kong, China.
| | - Cheng Lu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Hong Kong Baptist University Branch of State Key Laboratory of Chemo/Biosensing and Chemometrics of Hunan University, Hong Kong, China.
| | - Xiaojuan He
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Hong Kong Baptist University Branch of State Key Laboratory of Chemo/Biosensing and Chemometrics of Hunan University, Hong Kong, China.
| | - Baosheng Guo
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Hong Kong Baptist University Branch of State Key Laboratory of Chemo/Biosensing and Chemometrics of Hunan University, Hong Kong, China.
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410000, China.
- College of Biology, Hunan University, Changsha 410000, China.
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410000, China.
- College of Biology, Hunan University, Changsha 410000, China.
| | - Aiping Lu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Hong Kong Baptist University Branch of State Key Laboratory of Chemo/Biosensing and Chemometrics of Hunan University, Hong Kong, China.
| | - Ge Zhang
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
- Hong Kong Baptist University Branch of State Key Laboratory of Chemo/Biosensing and Chemometrics of Hunan University, Hong Kong, China.
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103
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Investigating actinomycin D binding to G-quadruplex, i-motif and double-stranded DNA in 27-nt segment of c-MYC gene promoter. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2015; 58:1188-93. [PMID: 26478420 DOI: 10.1016/j.msec.2015.09.072] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 09/13/2015] [Accepted: 09/18/2015] [Indexed: 01/03/2023]
Abstract
c-MYC DNA is an attractive target for drug design, especially for cancer chemotherapy. Around 90% of c-MYC transcription is controlled by NHE III1, whose 27-nt purine-rich strand has the ability to form G-quadruplex structure. In this investigation, interaction of ActD with 27-nt G-rich strand (G/c-MYC) and its equimolar mixture with the complementary sequence, (GC/c-MYC) as well as related C-rich oligonucleotide (C/c-MYC) was evaluated. Molecular dynamic simulations showed that phenoxazine and lactone rings of ActD come close to the outer G-tetrad nucleotides indicating that ActD binds through end-stacking to the quadruplex DNA. RMSD and RMSF revealed that fluctuation of the quadruplex DNA increases upon interaction with the drug. The results of spectrophotometry and spectrofluorometry indicated that ActD most probably binds to the c-MYC quadruplex and duplex DNA via end-stacking and intercalation, respectively and polarity of ActD environment decreases due to the interaction. It was also found that binding of ActD to the GC-rich DNA is stronger than the two other forms of DNA. Circular dichroism results showed that the type of the three forms of DNA structures doesn't change, but their compactness alters due to their interaction with ActD. Finally, it can be concluded that ActD binds differently to double stranded DNA, quadruplex DNA and i-motif.
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104
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Scuotto M, Rivieccio E, Varone A, Corda D, Bucci M, Vellecco V, Cirino G, Virgilio A, Esposito V, Galeone A, Borbone N, Varra M, Mayol L. Site specific replacements of a single loop nucleoside with a dibenzyl linker may switch the activity of TBA from anticoagulant to antiproliferative. Nucleic Acids Res 2015; 43:7702-16. [PMID: 26250112 PMCID: PMC4652776 DOI: 10.1093/nar/gkv789] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 07/23/2015] [Indexed: 12/20/2022] Open
Abstract
Many antiproliferative G-quadruplexes (G4s) arise from the folding of GT-rich strands. Among these, the Thrombin Binding Aptamer (TBA), as a rare example, adopts a monomolecular well-defined G4 structure. Nevertheless, the potential anticancer properties of TBA are severely hampered by its anticoagulant action and, consequently, no related studies have appeared so far in the literature. We wish to report here that suitable chemical modifications in the TBA sequence can preserve its antiproliferative over anticoagulant activity. Particularly, we replaced one residue of the TT or TGT loops with a dibenzyl linker to develop seven new quadruplex-forming TBA based sequences (TBA-bs), which were studied for their structural (CD, CD melting, 1D NMR) and biological (fibrinogen, PT and MTT assays) properties. The three-dimensional structures of the TBA-bs modified at T13 (TBA-bs13) or T12 (TBA-bs12), the former endowed with selective antiproliferative activity, and the latter acting as potently as TBA in both coagulation and MTT assays, were further studied by 2D NMR restrained molecular mechanics. The comparative structural analyses indicated that neither the stability, nor the topology of the G4s, but the different localization of the two benzene rings of the linker was responsible for the loss of the antithrombin activity for TBA-bs13.
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Affiliation(s)
- Maria Scuotto
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Elisa Rivieccio
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Alessia Varone
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Daniela Corda
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Mariarosaria Bucci
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Valentina Vellecco
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Giuseppe Cirino
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Antonella Virgilio
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Veronica Esposito
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Aldo Galeone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Michela Varra
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Luciano Mayol
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
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105
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Hu J, Zhao Z, Liu Q, Ye M, Hu B, Wang J, Tan W. Study of the Function of G-Rich Aptamers Selected for Lung Adenocarcinoma. Chem Asian J 2015; 10:1519-25. [PMID: 25864879 PMCID: PMC4966285 DOI: 10.1002/asia.201500187] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Indexed: 11/08/2022]
Abstract
Guanine (G)-rich oligonucleotides have attracted considerable interest as therapeutic agents. Two G-rich aptamers were selected against epidermal growth factor receptor (EGFR)-transfected A549 cells, and their G-rich domains (S13 and S50) were identified to account for the binding of parental aptamers. Circular dichroism (CD) spectra showed that S13 and S50 bound to their targets by forming parallel quadruplexes. Their binding, internalization, and antiproliferation activity in cancer and noncancer cells were investigated by flow cytometry and 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay, and compared with those of nucleolin-binding AS1411 and thrombin-binding aptamer. The two truncated aptamers (S13 and S50) have good binding and internalization in cancer cells and noncancer cells; however, only S50, similar to AS1411, shows potent antiproliferation against cancer cells. Our data suggest that tumor-selective antiproliferation of G-rich oligonucleotides does not directly depend on the binding of the G-rich aptamer to cells.
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Affiliation(s)
- Jun Hu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, and Collaborative Research Center of Molecular, Engineering for Theranostics, Hunan University, Changsha, 410082, P.R. China
- Hunan Tumor Hospital, Changsha, 410013, P.R. China
| | - Zilong Zhao
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, and Collaborative Research Center of Molecular, Engineering for Theranostics, Hunan University, Changsha, 410082, P.R. China
- Center for Research at Bio/Nano Interface, Department of Chemistry and, Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute, and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, and Collaborative Research Center of Molecular, Engineering for Theranostics, Hunan University, Changsha, 410082, P.R. China
| | - Mao Ye
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, and Collaborative Research Center of Molecular, Engineering for Theranostics, Hunan University, Changsha, 410082, P.R. China
| | - Bingqiang Hu
- Hunan Tumor Hospital, Changsha, 410013, P.R. China
| | - Jing Wang
- Hunan Tumor Hospital, Changsha, 410013, P.R. China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, and Collaborative Research Center of Molecular, Engineering for Theranostics, Hunan University, Changsha, 410082, P.R. China.
- Center for Research at Bio/Nano Interface, Department of Chemistry and, Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute, and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA.
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106
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Kim IS, Seo YJ. TT Dimerization and Its Effect on Human Telomere G-Quadruplex Formation. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- In Sun Kim
- Department of Chemistry; Chonbuk National University; Jeonju 561-756 South Korea
| | - Young Jun Seo
- Department of Chemistry; Chonbuk National University; Jeonju 561-756 South Korea
- Department of Bioactive Material Sciences; Chonbuk National University; Jeonju 561-756 South Korea
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107
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Kim BG, Evans HM, Dubins DN, Chalikian TV. Effects of Salt on the Stability of a G-Quadruplex from the Human c-MYC Promoter. Biochemistry 2015; 54:3420-30. [DOI: 10.1021/acs.biochem.5b00097] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Byul G. Kim
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Heather M. Evans
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - David N. Dubins
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Tigran V. Chalikian
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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108
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Williams JD, Fleetwood S, Berroyer A, Kim N, Larson ED. Sites of instability in the human TCF3 (E2A) gene adopt G-quadruplex DNA structures in vitro. Front Genet 2015; 6:177. [PMID: 26029241 PMCID: PMC4426816 DOI: 10.3389/fgene.2015.00177] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 04/25/2015] [Indexed: 01/23/2023] Open
Abstract
The formation of highly stable four-stranded DNA, called G-quadruplex (G4), promotes site-specific genome instability. G4 DNA structures fold from repetitive guanine sequences, and increasing experimental evidence connects G4 sequence motifs with specific gene rearrangements. The human transcription factor 3 (TCF3) gene (also termed E2A) is subject to genetic instability associated with severe disease, most notably a common translocation event t(1;19) associated with acute lymphoblastic leukemia. The sites of instability in TCF3 are not randomly distributed, but focused to certain sequences. We asked if G4 DNA formation could explain why TCF3 is prone to recombination and mutagenesis. Here we demonstrate that sequences surrounding the major t(1;19) break site and a region associated with copy number variations both contain G4 sequence motifs. The motifs identified readily adopt G4 DNA structures that are stable enough to interfere with DNA synthesis in physiological salt conditions in vitro. When introduced into the yeast genome, TCF3 G4 motifs promoted gross chromosomal rearrangements in a transcription-dependent manner. Our results provide a molecular rationale for the site-specific instability of human TCF3, suggesting that G4 DNA structures contribute to oncogenic DNA breaks and recombination.
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Affiliation(s)
| | - Sara Fleetwood
- School of Biological Sciences, Illinois State University Normal, IL, USA
| | - Alexandra Berroyer
- School of Biological Sciences, Illinois State University Normal, IL, USA
| | - Nayun Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston Houston, TX, USA
| | - Erik D Larson
- School of Biological Sciences, Illinois State University Normal, IL, USA
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109
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Housaindokht MR, Verdian-Doghaei A. Biophysical probing of the binding properties of a Cu(II) complex with G-quadruplex DNA: an experimental and computational study. LUMINESCENCE 2015; 31:22-9. [DOI: 10.1002/bio.2916] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 02/08/2015] [Accepted: 03/08/2015] [Indexed: 11/10/2022]
Affiliation(s)
| | - Asma Verdian-Doghaei
- Biophysical Chemistry Laboratory, Department of Chemistry; Ferdowsi University of Mashhad; Mashhad Iran
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110
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Zhou Z, Li D, Zhang L, Wang E, Dong S. G-quadruplex DNA/protoporphyrin IX-based synergistic platform for targeted photodynamic cancer therapy. Talanta 2015; 134:298-304. [PMID: 25618671 DOI: 10.1016/j.talanta.2014.11.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 11/14/2014] [Accepted: 11/19/2014] [Indexed: 01/17/2023]
Abstract
Photodynamic therapy (PDT) is an emerging technique to induce cancer cell death. However, the tumor specificity, cellular uptake and biodistribution of many photosensitizers urgently need to be improved. In this regard, we show here that the integrated nanoassemblies based on G-quadruplex DNAs (GQDs)/protoporphyrin IX (PPIX) can serve as a synergistic platform for targeted high-performance PDT. In the nanoassemblies, GQDs function as carriers of sensitiser PPIX and confers the system cancer cell targeting ability. After nucleolin-mediated efficient binding and cellular uptake of GQDs/PPIX assemblies, the strong red fluorescence of GQDs/PPIX complex provides a powerful tool for biological imaging. Moreover, the reactive oxygen species (ROS) generated by GQDs/PPIX under light illumination can effectively kill cancer cells. The present approach is simply composed by DNA and photosensitizers, thereby avoiding any complicated and time-consuming covalent modification or chemical labeling procedure.
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Affiliation(s)
- Zhixue Zhou
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Dan Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Libing Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China.
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111
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Qin M, Chen Z, Luo Q, Wen Y, Zhang N, Jiang H, Yang H. Two-quartet G-quadruplexes formed by DNA sequences containing four contiguous GG runs. J Phys Chem B 2015; 119:3706-13. [PMID: 25689673 DOI: 10.1021/jp512914t] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The DNA sequence containing four contiguous GG runs (G2NxG2NyG2NzG2, G2 sequence) has the potential to form a two-quartet G-quadruplex. However, the prevalence, structure, and function of G2 sequences have not been well-studied. Here, bioinformatics analysis reveals the abundance of G2 sequences in the human genome and their enrichment in promoter regions. The density of G2 sequences in the genome and promoters is much higher than that of the G3 sequence (G3NxG3NyG3NzG3). Experiments show that the conformations and thermal stabilities of the two-quartet G-quadruplexes of G2 sequences are highly sensitive to the length and composition of the loops. Among the two-quartet G-quadruplexes, the parallel G-quadruplex with a loop length of 1 and the antiparallel G-quadruplex with a loop length of 3 show high thermal stabilities. Additionally, the stable parallel G-quadruplexes are stacked into intermolecular higher-order structures. This work determines the prevalence of G2 sequences in the human genome and demonstrates that the G-quadruplex structures for certain loop lengths and compositions may be stable in vivo. Thus, more attention should be paid to the structure and function of the two-quartet G-quadruplex.
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Affiliation(s)
- Mingyan Qin
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China
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112
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Xu L, Chen X, Wu J, Wang J, Ji L, Chao H. Dinuclear Ruthenium(II) Complexes That Induce and Stabilise G-Quadruplex DNA. Chemistry 2015; 21:4008-20. [DOI: 10.1002/chem.201405991] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Indexed: 11/08/2022]
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113
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Wang X, Sun X, He H, Yang H, Lao J, Song Y, Xia Y, Xu H, Zhang X, Huang F. A two-component active targeting theranostic agent based on graphene quantum dots. J Mater Chem B 2015; 3:3583-3590. [DOI: 10.1039/c5tb00211g] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Selective tumour cell imaging and synergistic anti-cancer therapeutics are achieved by using the conjugate of AS1411 and graphene quantum dots.
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Affiliation(s)
- Xiaojuan Wang
- State Key Laboratory of Heavy Oil Processing
- China University of Petroleum (East China)
- Qingdao 266555
- China
- Centre for Bioengineering and Biotechnology
| | - Xing Sun
- Centre for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao 266555
- China
| | - Hua He
- State Key Laboratory of Heavy Oil Processing
- China University of Petroleum (East China)
- Qingdao 266555
- China
- Centre for Bioengineering and Biotechnology
| | - Hao Yang
- Centre for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao 266555
- China
| | - Jun Lao
- Centre for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao 266555
- China
| | - Yanzhuo Song
- Centre for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao 266555
- China
| | - Yongqing Xia
- State Key Laboratory of Heavy Oil Processing
- China University of Petroleum (East China)
- Qingdao 266555
- China
- Centre for Bioengineering and Biotechnology
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing
- China University of Petroleum (East China)
- Qingdao 266555
- China
- Centre for Bioengineering and Biotechnology
| | - Xiaodong Zhang
- Institute of Radiation Medicine and Tianjin Key Laboratory of Molecular Nuclear Medicine
- Chinese Academy of Medical Sciences and Peking Union Medical College
- Tianjin 300192
- China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing
- China University of Petroleum (East China)
- Qingdao 266555
- China
- Centre for Bioengineering and Biotechnology
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114
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Xu L, Shen X, Hong S, Wang J, Zhang Y, Wang H, Zhang J, Pei R. Turn-on and label-free fluorescence detection of lead ions based on target-induced G-quadruplex formation. Chem Commun (Camb) 2015; 51:8165-8. [DOI: 10.1039/c5cc01590a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Using a guanine-rich sequence (AGRO100) and N-methyl mesoporphyrin IX (NMM), a turn-on and label-free fluorescent Pb2+ sensor with high sensitivity and low background fluorescence was presented as a representative of five turn-on sensing systems.
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Affiliation(s)
- Lijun Xu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
| | - Xiaoqiang Shen
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
| | - Shanni Hong
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
| | - Jine Wang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
| | - Yuanyuan Zhang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
| | - Hongyan Wang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
| | - Jianye Zhang
- School of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
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115
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Perschbacher K, Smestad JA, Peters JP, Standiford MM, Denic A, Wootla B, Warrington AE, Rodriguez M, Maher LJ. Quantitative PCR analysis of DNA aptamer pharmacokinetics in mice. Nucleic Acid Ther 2014; 25:11-9. [PMID: 25536292 PMCID: PMC4296750 DOI: 10.1089/nat.2014.0515] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
DNA aptamer oligonucleotides and their protein conjugates show promise as therapeutics in animal models of diseases such as multiple sclerosis. These molecules are large and highly charged, raising questions about their biodistribution and pharmacokinetics in mammals. Here we exploit the power of quantitative polymerase chain reaction to accurately quantitate the tissue distribution of 40-nucleotide DNA aptamers and their streptavidin conjugates after intraperitoneal injection in mice. We show remarkably rapid distribution to peripheral tissues including the central nervous system. Modeling of tissue distribution data reveals the importance of DNA aptamer sequence, 3′ modification, and protein conjugation in enhancing tissue exposure. These data help to interpret the previously observed effectiveness of aptamer conjugates, as opposed to free aptamers, in stimulating central nervous system remyelination in a mouse model of multiple sclerosis.
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Affiliation(s)
- Katherine Perschbacher
- 1 Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine , Rochester, Minnesota
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116
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Hagiwara K, Fujita H, Kasahara Y, Irisawa Y, Obika S, Kuwahara M. In vitro selection of DNA-based aptamers that exhibit RNA-like conformations using a chimeric oligonucleotide library that contains two different xeno-nucleic acids. MOLECULAR BIOSYSTEMS 2014; 11:71-6. [PMID: 25325213 DOI: 10.1039/c4mb00436a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We successfully generated chimeric DNA aptamers that contained six nucleoside analogs of 2'-O,4'-C-methylene bridged/locked nucleic acid (2',4'-BNA/LNA) in the primer region and multiple guanosine analogs of 2'-deoxy-2'-fluoro-ribonucleic acid (FNA) in the non-primer region using capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX). Active species enrichment became saturated only after five selection rounds, and we obtained DNA-based xeno-nucleic acid (XNA) aptamers that had high binding affinities for the target human thrombin, with dissociation constant (Kd) values of ≥10 nanomolar. Based on sequence and circular dichroism (CD) analyses, these XNA aptamers exhibited RNA-like conformations, which could cause DNA-based strands to adopt structurally diverse conformations.
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Affiliation(s)
- Kenta Hagiwara
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan.
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117
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Zhao X, Liu B, Yan J, Yuan Y, An L, Guan Y. Structure variations of TBA G-quadruplex induced by 2'-O-methyl nucleotide in K+ and Ca2+ environments. Acta Biochim Biophys Sin (Shanghai) 2014; 46:837-50. [PMID: 25246433 DOI: 10.1093/abbs/gmu077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Thrombin binding aptamer (TBA), a 15-mer oligonucleotide of d(GGTTGGTGTGGTTGG) sequence, folds into a chair-type antiparallel G-quadruplex in the K(+) environment, and each of two G-tetrads is characterized by a syn-anti-syn-anti glycosidic conformation arrangement. To explore its folding topology and structural stability, 2'-O-methyl nucleotide (OMe) with the C3'-endo sugar pucker conformation and anti glycosidic angle was used to selectively substitute for the guanine residues of G-tetrads of TBA, and these substituted TBAs were characterized using a circular dichroism spectrum, thermally differential spectrum, ultraviolet stability analysis, electrophoresis mobility shift assay, and thermodynamic analysis in K(+) and Ca(2+) environments. Results showed that single substitutions for syn-dG residues destabilized the G-quadruplex structure, while single substitutions for anti-dG residues could preserve the G-quadruplex in the K(+) environment. When one or two G-tetrads were modified with OMe, TBA became unstructured. In contrast, in Ca(2+) environment, the native TBA appeared to be unstructured. When two G-tetrads were substituted with OMe, TBA seemed to become a more stable parallel G-4 structure. Further thermodynamic data suggested that OMe-substitutions were an enthalpy-driven event. The results in this study enrich our understanding about the effects of nucleotide derivatives on the G-quadruplex structure stability in different ionic environments, which will help to design G-quadruplex for biological and medical applications.
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Affiliation(s)
- Xiaoyang Zhao
- Key Laboratory of Medical Cell Biology, Ministry of Education, Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110001, China Department of Chemistry, Shenyang Medical College, Shenyang 110034, China
| | - Bo Liu
- Key Laboratory of Medical Cell Biology, Ministry of Education, Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110001, China
| | - Jing Yan
- Key Laboratory of Medical Cell Biology, Ministry of Education, Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110001, China
| | - Ying Yuan
- Key Laboratory of Medical Cell Biology, Ministry of Education, Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110001, China
| | - Liwen An
- Key Laboratory of Medical Cell Biology, Ministry of Education, Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110001, China
| | - Yifu Guan
- Key Laboratory of Medical Cell Biology, Ministry of Education, Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110001, China
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118
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Ku SH, Kim K, Choi K, Kim SH, Kwon IC. Tumor-targeting multifunctional nanoparticles for siRNA delivery: recent advances in cancer therapy. Adv Healthc Mater 2014; 3:1182-93. [PMID: 24577795 DOI: 10.1002/adhm.201300607] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/20/2014] [Indexed: 11/06/2022]
Abstract
RNA interference (RNAi) is a naturally occurring regulatory process that controls posttranscriptional gene expression. Small interfering RNA (siRNA), a common form of RNAi-based therapeutics, offers new opportunities for cancer therapy via silencing specific genes, which are associated to cancer progress. However, clinical applications of RNAi-based therapy are still limited due to the easy degradation of siRNA during body circulation and the difficulty in the delivery of siRNA to desired tissues and cells. Thus, there have been many efforts to develop efficient siRNA delivery systems, which protect siRNA from serum nucleases and deliver siRNA to the intracellular region of target cells. Here, the recent advances in siRNA nanocarriers, which possess tumor-targeting ability are reviewed; various nanoparticle systems and their antitumor effects are summarized. The development of multifunctional nanocarriers for theranostics or combinatorial therapy is also discussed.
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Affiliation(s)
- Sook Hee Ku
- Center for Theragnosis, Biomedical Research Institute; Korea Institute of Science and Technology (KIST); Seoul 136-791 Republic of Korea
| | - Kwangmeyung Kim
- Center for Theragnosis, Biomedical Research Institute; Korea Institute of Science and Technology (KIST); Seoul 136-791 Republic of Korea
| | - Kuiwon Choi
- Center for Theragnosis, Biomedical Research Institute; Korea Institute of Science and Technology (KIST); Seoul 136-791 Republic of Korea
| | - Sun Hwa Kim
- Center for Theragnosis, Biomedical Research Institute; Korea Institute of Science and Technology (KIST); Seoul 136-791 Republic of Korea
| | - Ick Chan Kwon
- Center for Theragnosis, Biomedical Research Institute; Korea Institute of Science and Technology (KIST); Seoul 136-791 Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology; Korea University; Seoul 136-701 Republic of Korea
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119
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Lu XH, Shi S, Yao JL, Gao X, Huang HL, Yao TM. Two structurally analogous ruthenium complexes as naked-eye and reversible molecular "light switch" for G-quadruplex DNA. J Inorg Biochem 2014; 140:64-71. [PMID: 25063909 DOI: 10.1016/j.jinorgbio.2014.07.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 07/07/2014] [Accepted: 07/07/2014] [Indexed: 11/30/2022]
Abstract
A pair of symmetrical furyl based ruthenium(II) complexes ([Ru(phen)2dpq-df](2+) (1) and [Ru(bpy)2dpq-df](2+) (2) (phen=1,10-phenanthroline, bpy=2,2'-bipyridine, dpq-df=dipyrido (3,2-a:2',3'-c) quinoxaline-difuran) have been prepared and characterized. The binding properties of both complexes toward G-quadruplex DNA have been investigated by fluorescence spectroscopy, UV-Vis spectroscopy, circular dichroism (CD), fluorescence resonance energy transfer (FRET) melting assays and molecular docking studies. The experimental results indicated that both Ru-complexes exhibited a remarkable "light switch" effect in the presence of hybrid G-quadruplex DNA. Interestingly, the "light switch" can be repeated off and on through the successive addition of Cu(2+) ions and EDTA, and all these behaviors can be observed even by the naked eyes. Moreover, FRET melting assay revealed that both complexes could be potential stabilizers for G-quadruplex architectures. The computational studies not only confirmed that the two complex molecules bound to one G-quadruplex DNA molecule, but also explained the "light switch" effect.
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Affiliation(s)
- Xiao-Hui Lu
- Department of Chemistry, Tongji University, Shanghai 200092, PR China
| | - Shuo Shi
- Department of Chemistry, Tongji University, Shanghai 200092, PR China.
| | - Jun-Liang Yao
- Department of Chemistry, Tongji University, Shanghai 200092, PR China
| | - Xing Gao
- Department of Chemistry, Tongji University, Shanghai 200092, PR China
| | - Hai-Liang Huang
- Department of Chemistry, Tongji University, Shanghai 200092, PR China
| | - Tian-Ming Yao
- Department of Chemistry, Tongji University, Shanghai 200092, PR China.
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120
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Englund EA, Gupta P, Micklitsch CM, Onyshchenko MI, Remeeva E, Neumann RD, Panyutin IG, Appella DH. PPG peptide nucleic acids that promote DNA guanine quadruplexes. Chembiochem 2014; 15:1887-90. [PMID: 25044379 DOI: 10.1002/cbic.201402224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Indexed: 12/11/2022]
Abstract
Recent studies have shown that guanine-rich (G-rich) sequences with the potential to form quadruplexes might play a role in normal transcription as well as overexpression of oncogenes. Chemical tools that allow examination of the specific roles of G-quadruplex formation in vivo, and their association with gene regulation will be essential to understanding the functions of these quadruplexes and might lead to beneficial therapies. Properly designed peptide nucleic acids (PNAs) can invade G-rich DNA duplexes and induce the formation of a G-quadruplex in the free DNA strand. Replacing guanines in the PNA sequence with pyrazolo[3,4-d]pyrimidine guanine (PPG) nucleobases eliminates G-quadruplex formation with PNA and promotes invasion of the target DNA.
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Affiliation(s)
- Ethan A Englund
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, DHHS, 8 Center Drive, Bethesda, MD 20892 (USA)
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121
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Rodrigues Pontinha AD, Chiorcea-Paquim AM, Eritja R, Oliveira-Brett AM. Quadruplex nanostructures of d(TGGGGT): influence of sodium and potassium ions. Anal Chem 2014; 86:5851-7. [PMID: 24794539 DOI: 10.1021/ac500624z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Tetrahymena telomeric repeat sequence d(TG4T) contains only guanine (G) and thymine (T) bases and has medical and nanotechnological applications because of its ability to self-assemble into stiff tetra-molecular parallel-stranded G-quadruplexes. The hexadeoxynucleotide d(TG4T) was studied using atomic force microscopy (AFM) on the highly oriented pyrolytic graphite surface and differential pulse (DP) voltammetry at a glassy carbon electrode. The d(TG4T) single-strands self-assembled into G-quadruplex structures, very fast in K(+) ions solution and slowly in Na(+) ions containing solution. The G-quadruplex structures were detected in AFM by the adsorption of small spherical aggregates and by DP voltammetry by the G oxidation peak decrease and G-quartets oxidation peak occurrence, in a time and K(+) ions concentration dependent manner. In the presence of Na(+) ions, the d(TG4T) single-strands also slowly self-assembled into higher-order nanostructures, detected by AFM as short nanowires and nanostructured films that were never observed in K(+) ions containing solution.
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122
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Hudson JS, Ding L, Le V, Lewis E, Graves D. Recognition and binding of human telomeric G-quadruplex DNA by unfolding protein 1. Biochemistry 2014; 53:3347-56. [PMID: 24831962 PMCID: PMC4038342 DOI: 10.1021/bi500351u] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
![]()
The specific recognition by proteins
of G-quadruplex structures
provides evidence of a functional role for in vivo G-quadruplex structures. As previously reported, the ribonucleoprotein,
hnRNP Al, and it is proteolytic derivative, unwinding protein 1 (UP1),
bind to and destabilize G-quadruplex structures formed by the human
telomeric repeat d(TTAGGG)n. UP1 has been
proposed to be involved in the recruitment of telomerase to telomeres
for chain extension. In this study, a detailed thermodynamic characterization
of the binding of UP1 to a human telomeric repeat sequence, the d[AGGG(TTAGGG)3] G-quadruplex, is presented and reveals key insights into
the UP1-induced unfolding of the G-quadruplex structure. The UP1–G-quadruplex
interactions are shown to be enthalpically driven, exhibiting large
negative enthalpy changes for the formation of both the Na+ and K+ G-quadruplex–UP1 complexes (ΔH values of −43 and −19 kcal/mol, respectively).
These data reveal three distinct enthalpic contributions from the
interactions of UP1 with the Na+ form of G-quadruplex DNA.
The initial interaction is characterized by a binding affinity of
8.5 × 108 M–1 (strand), 200 times
stronger than the binding of UP1 to a single-stranded DNA with a comparable
but non-quadruplex-forming sequence [4.1 × 106 M–1 (strand)]. Circular dichroism spectroscopy reveals
the Na+ form of the G-quadruplex to be completely unfolded
by UP1 at a binding ratio of 2:1 (UP1:G-quadruplex DNA). The data
presented here demonstrate that the favorable energetics of the initial
binding event are closely coupled with and drive the unfolding of
the G-quadruplex structure.
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Affiliation(s)
- Jason S Hudson
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
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123
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Liu B, Li D. Structural transformation induced by locked nucleic acid or 2'-O-methyl nucleic acid site-specific modifications on thrombin binding aptamer. Chem Cent J 2014; 8:19. [PMID: 24642032 PMCID: PMC4000052 DOI: 10.1186/1752-153x-8-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 03/13/2014] [Indexed: 11/25/2022] Open
Abstract
Background Locked nucleic acid (LNA) and 2'–O-methyl nucleic acid (OMeNA) are two of the most extensively studied nucleotide derivatives in the last decades. However, how they affect DNA quadruplex structures remains largely unknown. To explore their possible biological affinities for quadruplexes, we investigated how LNA- or OMeNA-substitutions affect G-quadruplex structure formation using a thrombin binding aptamer (TBA), the most studied extracorporal G-quadruplex-forming DNA sequence, which is frequently modified to increase its analytical performance. Results The experimental results showed that when two or more nucleotides were substituted with LNA or OMeNA, the anti-parallel TBA structure was transformed into an unstructured random conformation in a 50 mM K+ environment; OMeNA appeared to have greater power to induce this transformation. However, the native TBA was unstructured in a 50 mM Ca2+ environment, whereas four or more LNA- or OMeNA- substitutions could convert this unstructured TBA into a parallel quadruplex structure. PAGE mobility measurements suggested that these TBAs might be a dimeric form. Conclusion LNA or 2'-OMeNA site-specific modifications induced G-quadruplex structural transformation of TBA, which enriched our understanding of the intrinsic G-quadrupex forming property and affinity of LNA and OMeNA modifications. This study demonstrates possible applications in the regulation of gene expression (i.e. manual intervention of gene therapy), genetic analyses, molecular diagnosis and the construction of nano-scale biostructures.
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Affiliation(s)
- Bo Liu
- Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang 110001, China.
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124
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Liu L, Shao Y, Peng J, Huang C, Liu H, Zhang L. Molecular Rotor-Based Fluorescent Probe for Selective Recognition of Hybrid G-Quadruplex and as a K+ Sensor. Anal Chem 2014; 86:1622-31. [DOI: 10.1021/ac403326m] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lingling Liu
- Institute of Physical
Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Yong Shao
- Institute of Physical
Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Jian Peng
- Institute of Physical
Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Chaobiao Huang
- Department
of Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People’s Republic of China
| | - Hua Liu
- Institute of Physical
Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Lihua Zhang
- Institute of Physical
Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
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125
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Blice-Baum AC, Mihailescu MR. Biophysical characterization of G-quadruplex forming FMR1 mRNA and of its interactions with different fragile X mental retardation protein isoforms. RNA (NEW YORK, N.Y.) 2014; 20:103-114. [PMID: 24249225 PMCID: PMC3866639 DOI: 10.1261/rna.041442.113] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/14/2013] [Indexed: 06/02/2023]
Abstract
Fragile X syndrome, the most common form of inherited mental impairment in humans, is caused by the absence of the fragile X mental retardation protein (FMRP) due to a CGG trinucleotide repeat expansion in the 5'-untranslated region (UTR) and subsequent translational silencing of the fragile x mental retardation-1 (FMR1) gene. FMRP, which is proposed to be involved in the translational regulation of specific neuronal messenger RNA (mRNA) targets, contains an arginine-glycine-glycine (RGG) box RNA binding domain that has been shown to bind with high affinity to G-quadruplex forming mRNA structures. FMRP undergoes alternative splicing, and the binding of FMRP to a proposed G-quadruplex structure in the coding region of its mRNA (named FBS) has been proposed to affect the mRNA splicing events at exon 15. In this study, we used biophysical methods to directly demonstrate the folding of FMR1 FBS into a secondary structure that contains two specific G-quadruplexes and analyze its interactions with several FMRP isoforms. Our results show that minor splice isoforms, ISO2 and ISO3, created by the usage of the second and third acceptor sites at exon 15, bind with higher affinity to FBS than FMRP ISO1, which is created by the usage of the first acceptor site. FMRP ISO2 and ISO3 cannot undergo phosphorylation, an FMRP post-translational modification shown to modulate the protein translation regulation. Thus, their expression has to be tightly regulated, and this might be accomplished by a feedback mechanism involving the FMRP interactions with the G-quadruplex structures formed within FMR1 mRNA.
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126
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Long X, Stone MD. Kinetic partitioning modulates human telomere DNA G-quadruplex structural polymorphism. PLoS One 2013; 8:e83420. [PMID: 24367594 PMCID: PMC3867459 DOI: 10.1371/journal.pone.0083420] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 11/03/2013] [Indexed: 11/23/2022] Open
Abstract
Telomeres are specialized chromatin structures found at the end of chromosomes and are crucial to the maintenance of eukaryotic genome stability. Human telomere DNA is comprised of the repeating sequence (T2AG3)n, which is predominantly double-stranded but terminates with a 3’ single-stranded tail. The guanine-rich tail can fold into secondary structures known as a G-quadruplexes (GQs) that may exist as a polymorphic mixture of anti-parallel, parallel, and several hybrid topological isomers. Using single-molecule Förster resonance energy transfer (smFRET), we have reconstructed distributions of telomere DNA GQ conformations generated by an in situ refolding protocol commonly employed in single-molecule studies of GQ structure, or using a slow cooling DNA annealing protocol typically used in the preparation of GQ samples for ensemble biophysical analyses. We find the choice of GQ folding protocol has a marked impact on the observed distributions of DNA conformations under otherwise identical buffer conditions. A detailed analysis of the kinetics of GQ folding over timescales ranging from minutes to hours revealed the distribution of GQ structures generated by in situ refolding gradually equilibrates to resemble the distribution generated by the slow cooling DNA annealing protocol. Interestingly, conditions of low ionic strength, which promote transient GQ unfolding, permit the fraction of folded DNA molecules to partition into a distribution that more closely approximates the thermodynamic folding equilibrium. Our results are consistent with a model in which kinetic partitioning occurs during in situ folding at room temperature in the presence of K+ ions, producing a long-lived non-equilibrium distribution of GQ structures in which the parallel conformation predominates on the timescale of minutes. These results suggest that telomere DNA GQ folding kinetics, and not just thermodynamic stability, likely contributes to the physiological ensemble GQ structures.
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Affiliation(s)
- Xi Long
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Michael D. Stone
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
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127
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Balinsky CA, Schmeisser H, Ganesan S, Singh K, Pierson TC, Zoon KC. Nucleolin interacts with the dengue virus capsid protein and plays a role in formation of infectious virus particles. J Virol 2013; 87:13094-106. [PMID: 24027323 PMCID: PMC3838225 DOI: 10.1128/jvi.00704-13] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 09/03/2013] [Indexed: 01/24/2023] Open
Abstract
Dengue virus (DENV) is a mosquito-transmitted flavivirus that can cause severe disease in humans and is considered a reemerging pathogen of significant importance to public health. The DENV capsid (C) protein functions as a structural component of the infectious virion; however, it may have additional functions in the virus replicative cycle. Here, we show that the DENV C protein interacts and colocalizes with the multifunctional host protein nucleolin (NCL). Furthermore, we demonstrate that this interaction can be disrupted by the addition of an NCL binding aptamer (AS1411). Knockdown of NCL with small interfering RNA (siRNA) or treatment of cells with AS1411 results in a significant reduction of viral titers after DENV infection. Western blotting and quantitative RT-PCR (qRT-PCR) analysis revealed no differences in viral RNA or protein levels at early time points postinfection, suggesting a role for NCL in viral morphogenesis. We support this hypothesis by showing that treatment with AS1411 alters the migration characteristics of the viral capsid, as visualized by native electrophoresis. Here, we identify a critical interaction between DENV C protein and NCL that represents a potential new target for the development of antiviral therapeutics.
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Affiliation(s)
- Corey A. Balinsky
- Cytokine Biology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Hana Schmeisser
- Cytokine Biology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sundar Ganesan
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kavita Singh
- Structural Biology Unit, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Theodore C. Pierson
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kathryn C. Zoon
- Cytokine Biology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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128
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Yuan Q, Wu Y, Wang J, Lu D, Zhao Z, Liu T, Zhang X, Tan W. Targeted Bioimaging and Photodynamic Therapy Nanoplatform Using an Aptamer-Guided G-Quadruplex DNA Carrier and Near-Infrared Light. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305707] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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129
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Yuan Q, Wu Y, Wang J, Lu D, Zhao Z, Liu T, Zhang X, Tan W. Targeted bioimaging and photodynamic therapy nanoplatform using an aptamer-guided G-quadruplex DNA carrier and near-infrared light. Angew Chem Int Ed Engl 2013; 52:13965-9. [PMID: 24281972 DOI: 10.1002/anie.201305707] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/05/2013] [Indexed: 12/25/2022]
Affiliation(s)
- Quan Yuan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082 (China); Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072 (China)
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130
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Xing H, Tang L, Yang X, Hwang K, Wang W, Yin Q, Wong NY, Dobrucki LW, Yasui N, Katzenellenbogen JA, Helferich WG, Cheng J, Lu Y. Selective Delivery of an Anticancer Drug with Aptamer-Functionalized Liposomes to Breast Cancer Cells in Vitro and in Vivo.. J Mater Chem B 2013; 1:5288-5297. [PMID: 24159374 PMCID: PMC3800741 DOI: 10.1039/c3tb20412j] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Selective targeting of cancer cells is a critical step in cancer diagnosis and therapy. To address this need, DNA aptamers have attracted significant attention as possible targeting ligands. However, while their use in targeting cancer cells in vitro has been reported, their effectiveness has rarely been established in vivo. Here we report the development of a liposomal drug delivery system for targeted anticancer chemotherapy. Liposomes were prepared containing doxorubicin as a payload, and functionalized with AS1411, a DNA aptamer with strong binding affinity for nucleolin. AS1411 aptamer-functionalized liposomes increased cellular internalization and cytotoxicity to MCF-7 breast cancer cells as compared to non-targeting liposomes. Furthermore, targeted liposomal doxorubicin improved antitumor efficacy against xenograft MCF-7 breast tumors in athymic nude mice, attributable to their enhanced tumor tissue penetration. This study suggests that AS1411 aptamer-functionalized liposomes can recognize nucleolin overexpressed on MCF-7 cell surface, and therefore enable drug delivery with high specificity and selectivity.
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Affiliation(s)
- Hang Xing
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. Tel: +1-217-333-2619
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. Tel: +1-217-244-5023
| | - Li Tang
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. Tel: +1-217-244-3924
| | - Xujuan Yang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. Tel: +1-217-244-5414
| | - Kevin Hwang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. Tel: +1-217-333-2619
| | - Wendan Wang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. Tel: +1-217-244-5414
| | - Qian Yin
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. Tel: +1-217-244-3924
| | - Ngo Yin Wong
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. Tel: +1-217-244-3924
| | - Lawrence W. Dobrucki
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. Tel: +1-217-244-5023
| | - Norio Yasui
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. Tel: +1-217-333-2619
| | - John A. Katzenellenbogen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. Tel: +1-217-333-2619
| | - William G. Helferich
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. Tel: +1-217-244-5414
| | - Jianjun Cheng
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. Tel: +1-217-244-3924
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. Tel: +1-217-333-2619
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. Tel: +1-217-244-3924
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. Tel: +1-217-244-5023
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131
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Sirois CM, Jin T, Miller AL, Bertheloot D, Nakamura H, Horvath GL, Mian A, Jiang J, Schrum J, Bossaller L, Pelka K, Garbi N, Brewah Y, Tian J, Chang C, Chowdhury PS, Sims GP, Kolbeck R, Coyle AJ, Humbles AA, Xiao TS, Latz E. RAGE is a nucleic acid receptor that promotes inflammatory responses to DNA. ACTA ACUST UNITED AC 2013; 210:2447-63. [PMID: 24081950 PMCID: PMC3804942 DOI: 10.1084/jem.20120201] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Receptor for advanced glycation end-products (RAGE) detects nucleic acids and promotes DNA uptake into endosomes, which in turn lowers the immune recognition threshold for TLR9 activation. Recognition of DNA and RNA molecules derived from pathogens or self-antigen is one way the mammalian immune system senses infection and tissue damage. Activation of immune signaling receptors by nucleic acids is controlled by limiting the access of DNA and RNA to intracellular receptors, but the mechanisms by which endosome-resident receptors encounter nucleic acids from the extracellular space are largely undefined. In this study, we show that the receptor for advanced glycation end-products (RAGE) promoted DNA uptake into endosomes and lowered the immune recognition threshold for the activation of Toll-like receptor 9, the principal DNA-recognizing transmembrane signaling receptor. Structural analysis of RAGE–DNA complexes indicated that DNA interacted with dimers of the outermost RAGE extracellular domains, and could induce formation of higher-order receptor complexes. Furthermore, mice deficient in RAGE were unable to mount a typical inflammatory response to DNA in the lung, indicating that RAGE is important for the detection of nucleic acids in vivo.
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Affiliation(s)
- Cherilyn M Sirois
- Department of Medicine, Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA 01605
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132
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Tlučková K, Marušič M, Tóthová P, Bauer L, Šket P, Plavec J, Viglasky V. Human Papillomavirus G-Quadruplexes. Biochemistry 2013; 52:7207-16. [DOI: 10.1021/bi400897g] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Katarína Tlučková
- Department
of Biochemistry, Institute of Chemistry, Faculty of Sciences, P. J. Safarik University, 04001 Kosice, Slovakia
| | - Maja Marušič
- Slovenian
NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Petra Tóthová
- Department
of Biochemistry, Institute of Chemistry, Faculty of Sciences, P. J. Safarik University, 04001 Kosice, Slovakia
| | - Lubos Bauer
- Department
of Biochemistry, Institute of Chemistry, Faculty of Sciences, P. J. Safarik University, 04001 Kosice, Slovakia
| | - Primož Šket
- Slovenian
NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN-FIST Center of Excellence, SI-1000 Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian
NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN-FIST Center of Excellence, SI-1000 Ljubljana, Slovenia
- Faculty
of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Viktor Viglasky
- Department
of Biochemistry, Institute of Chemistry, Faculty of Sciences, P. J. Safarik University, 04001 Kosice, Slovakia
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133
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Wu K, Liu S, Luo Q, Hu W, Li X, Wang F, Zheng R, Cui J, Sadler PJ, Xiang J, Shi Q, Xiong S. Thymines in Single-Stranded Oligonucleotides and G-Quadruplex DNA Are Competitive with Guanines for Binding to an Organoruthenium Anticancer Complex. Inorg Chem 2013; 52:11332-42. [DOI: 10.1021/ic401606v] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Kui Wu
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- CAS Key Laboratory of Analytical
Chemistry for Living Biosystems, Beijing Centre for Mass Spectrometry, Beijing 100190, P. R. China
| | - Suyan Liu
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- CAS Key Laboratory of Analytical
Chemistry for Living Biosystems, Beijing Centre for Mass Spectrometry, Beijing 100190, P. R. China
| | - Qun Luo
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- CAS Key Laboratory of Analytical
Chemistry for Living Biosystems, Beijing Centre for Mass Spectrometry, Beijing 100190, P. R. China
| | - Wenbing Hu
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- CAS Key Laboratory of Analytical
Chemistry for Living Biosystems, Beijing Centre for Mass Spectrometry, Beijing 100190, P. R. China
| | - Xianchan Li
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- CAS Key Laboratory of Analytical
Chemistry for Living Biosystems, Beijing Centre for Mass Spectrometry, Beijing 100190, P. R. China
| | - Fuyi Wang
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- CAS Key Laboratory of Analytical
Chemistry for Living Biosystems, Beijing Centre for Mass Spectrometry, Beijing 100190, P. R. China
| | - Renhui Zheng
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing 100190, P. R. China
| | - Jie Cui
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Peter J. Sadler
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4
7AL, United Kingdom
| | - Junfeng Xiang
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Qiang Shi
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing 100190, P. R. China
| | - Shaoxiang Xiong
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- CAS Key Laboratory of Analytical
Chemistry for Living Biosystems, Beijing Centre for Mass Spectrometry, Beijing 100190, P. R. China
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134
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Chen X, Wu JH, Lai YW, Zhao R, Chao H, Ji LN. Targeting telomeric G-quadruplexes with the ruthenium(II) complexes [Ru(bpy)(2)(ptpn)](2+) and [Ru(phen)(2)(ptpn)](2+). Dalton Trans 2013; 42:4386-97. [PMID: 23400220 DOI: 10.1039/c3dt32921f] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two ruthenium(II) polypyridyl complexes, [Ru(bpy)(2)(ptpn)](2+) (1) (bpy = 2,2'-bipyridine, ptpn = 3-(1,10-phenanthroline-2-yl)-as-triazino[5,6-f]1,10-phenanthroline) and [Ru(phen)(2)(ptpn)](2+) (2) (phen = 1,10-phenanthroline), were synthesized and characterized. Crystal structure analysis shows that complex 1 has a large planar aromatic area and possesses the potential to fit the geometric structure of G-quadruplex. The interaction of the G-quadruplex DNA with Ru(ii) complexes was explored by means of circular dichroism (CD), fluorescence resonance energy transfer (FRET) melting assay, competitive FRET assay and polymerase chain reaction (PCR) stop assay. The results indicated that complexes 1 and 2 both have the ability to promote the formation and stabilization of the human telomeric d[(TTAGGG)(n)] (HTG22) quadruplex and exhibit high G-quadruplex DNA selectivity over duplex DNA. The telomere repeat amplification protocol (TRAP) assay and long-term proliferation experiments further demonstrate that the Ru(II) complexes are potent telomerase inhibitors and HeLa cell proliferation inhibitors.
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Affiliation(s)
- Xiang Chen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, State Key Laboratory of Optoelectronic Materials and Technologies, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, PR China
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135
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Al-Furoukh N, Goffart S, Szibor M, Wanrooij S, Braun T. Binding to G-quadruplex RNA activates the mitochondrial GTPase NOA1. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:2933-2942. [PMID: 23933583 DOI: 10.1016/j.bbamcr.2013.07.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/26/2013] [Accepted: 07/29/2013] [Indexed: 11/19/2022]
Abstract
NOA1 is an evolutionary conserved, nuclear encoded GTPase essential for mitochondrial function and cellular survival. The function of NOA1 for assembly of mitochondrial ribosomes and regulation of OXPHOS activity depends on its GTPase activity, but so far no ligands have been identified that regulate the GTPase activity of NOA1. To identify nucleic acids that bind to the RNA-binding domain of NOA1 we employed SELEX (Systemic Evolution of Ligands by EXponential Enrichment) using recombinant mouse wildtype NOA1 and the GTPase mutant NOA1-K353R. We found that NOA1 binds specifically to oligonucleotides that fold into guanine tetrads (G-quadruplexes). Binding of G-quadruplex oligonucleotides stimulated the GTPase activity of NOA1 suggesting a regulatory link between G-quadruplex containing RNAs, NOA1 function and assembly of mitochondrial ribosomes.
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Affiliation(s)
- Natalie Al-Furoukh
- Max-Planck-Institute for Heart and Lung Research, Ludwigstrasse 43, 61231 Bad Nauheim, Germany.
| | - Steffi Goffart
- Max-Planck-Institute for Heart and Lung Research, Ludwigstrasse 43, 61231 Bad Nauheim, Germany; University of Eastern Finland, Department of Biology, Yliopistokatu 7, 80101 Joensuu, Finland.
| | - Marten Szibor
- Max-Planck-Institute for Heart and Lung Research, Ludwigstrasse 43, 61231 Bad Nauheim, Germany.
| | - Sjoerd Wanrooij
- University of Gothenburg, Department of Medical Biochemistry and Cell Biology, Box 440, SE-40530, Göteborg, Sweden; Burgers Lab, Department of Biochemistry and Biophysics, Washington University, Campus Box 8231, 4566 Scott Avenue, MO 63110, St. Louis, USA.
| | - Thomas Braun
- Max-Planck-Institute for Heart and Lung Research, Ludwigstrasse 43, 61231 Bad Nauheim, Germany.
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136
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The design and structure-functional properties of DNA-based immunomodulatory sequences. Methods Mol Biol 2013; 986:41-56. [PMID: 23436404 DOI: 10.1007/978-1-62703-311-4_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
DNA-based immunomodulatory sequences (DIMS) are promising compounds for the treatment of different diseases, including inflammation and cancer. They act through the interaction with TLR9, a member of the Toll-like receptor family whose essential role in innate immunity was recently recognised by being awarded the Nobel Prize 2011. Combining the data obtained from in vitro and in vivo models with circular dichroism spectroscopy approach, we could show that formation of certain tertiary structures by DIMS can be connected to their specific physiologic effects such as activation of immune cells, induction of interferons and delay of the disease progression. Moreover the ability of selected DIMS compounds to form certain tertiary structures must be regarded as important for biological activities as is the presence of functional primary structure motifs such as unmethylated deoxyribodinucleotide CpG. These findings are useful when considering the design of DNA-based immunomodulators.
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137
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Kuo TC, Lee PC, Tsai CW, Chen WY. Salt bridge exchange binding mechanism between streptavidin and its DNA aptamer--thermodynamics and spectroscopic evidences. J Mol Recognit 2013; 26:149-59. [PMID: 23345105 DOI: 10.1002/jmr.2260] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 11/05/2012] [Accepted: 12/04/2012] [Indexed: 12/19/2022]
Abstract
Protein-nucleic acids binding driven by electrostatic interactions typically are characterized by the release of counter ions, and the salt-inhibited binding association constant (K(a)) and the magnitude of exothermic binding enthalpy (ΔH). Here, we report a non-classical thermodynamics of streptavidin (SA)-aptamer binding in NaCl (140-350 mM) solutions near room temperatures (23-27 °C). By using isothermal titration calorimetry (ITC) and circular dichroism (CD)/fluorescence spectroscopy, we found that the binding was enthalpy driven with a large entropy cost (ΔH -20.58 kcal mol(-1), TΔS -10.99 kcal mol(-1), and K(a) 1.08 × 10(7) M(-1) at 140 mM NaCl 25 °C). With the raise of salt concentrations, the ΔH became more exothermic, yet the K(a) was almost unchanged (ΔH -26.29 kcal mol(-1) and K(a) 1.50 × 10(7) M(-1) at 350 mM NaCl 25 °C). The data suggest that no counter Na(+) was released in the binding. Spectroscopy data suggest that the binding, with a stoichiometry of 2, was accompanied with substantial conformational changes on SA, and the changes were insensitive to the variation of salt concentrations. To account for the non-classical results, we propose a salt bridge exchange model. The intramolecular binding-site salt bridge(s) of the free SA and the charged phosphate group of aptamers re-organize to form the binding complex by forming a new intermolecular salt bridge(s). The salt bridge exchange binding process requires minimum amount of counter ions releasing but dehydration of the contacting surface of SA and the aptamer. The energy required for dehydration is reduced in the case of binding solution with higher salt concentration and account for the higher binding exothermic mainly.
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Affiliation(s)
- Tai-Chih Kuo
- Department of Biochemistry, Taipei Medical University, Taipei, 11031, Taiwan
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138
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Molecular basis of recognition of quadruplexes human telomere and c-myc promoter by the putative anticancer agent sanguinarine. Biochim Biophys Acta Gen Subj 2013; 1830:4189-201. [DOI: 10.1016/j.bbagen.2013.03.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/19/2013] [Accepted: 03/26/2013] [Indexed: 01/24/2023]
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139
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Wang X, Wang L, Wan M, Wu X, Yu Y, Wang L. Fully phosphorothioate-modified CpG ODN with PolyG motif inhibits the adhesion of B16 melanoma cells in vitro and tumorigenesis in vivo. Nucleic Acid Ther 2013; 23:253-63. [PMID: 23848522 PMCID: PMC3723239 DOI: 10.1089/nat.2013.0419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Accepted: 05/30/2013] [Indexed: 01/20/2023] Open
Abstract
Adhesion to the extracellular matrix and endothelial lining of blood vessels is critical for tumor cells to grow at original or metastatic sites. Inhibition of tumor cell adhesion can be an antitumor strategy. Guanosine-rich (G-rich) oligodeoxynucleotides (ODNs) can inhibit the adhesion of certain tumor cells. However, no data exist on how inclusion of the CpG motif in the G-rich sequence influences tumor cell adhesion and subsequent tumorigenesis. In this study, in vitro and in vivo assays were used to evaluate how a panel of ODN-containing contiguous guanosines and the CpG motif influenced adhesion of B16 melanoma cells. The results showed that a self-designed ODN, named BW001, containing the polyG motif and a full phosphorothioate modification backbone could inhibit B16 melanoma cell adhesion on a culture plate or on a plate coated with various substances. In vivo data revealed that B16 melanoma cells co-administered with BW001 and intraperitoneally injected into mice formed fewer tumor colonies in peritoneal cavities. This effect was related to the polyG motif and the full phosphorothioate modification backbone and enhanced by the existence of the CpG motif. Additional in vivo data showed that survival of tumor-bearing mice in the BW001 group was significantly prolonged, subcutaneous melanoma developed much more slowly, and lung dissemination colonies formed much less often than in mice inoculated with B16 melanoma cells only. The effect was CpG motif-dependent. These results suggest that BW001 may exert an integrated antitumor effect.
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Affiliation(s)
- Xueju Wang
- Department of Molecular Biology, Norman Bethune College of Medicine, Jilin University, Changchun, China
- Department of Pathology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Liying Wang
- Department of Molecular Biology, Norman Bethune College of Medicine, Jilin University, Changchun, China
- Department of Pathology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Min Wan
- Department of Molecular Biology, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Xiuli Wu
- Department of Molecular Biology, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Yongli Yu
- Department of Immunology, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Liping Wang
- Department of Pathology, China-Japan Union Hospital of Jilin University, Changchun, China
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140
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Pandey S, Agarwala P, Maiti S. Effect of loops and G-quartets on the stability of RNA G-quadruplexes. J Phys Chem B 2013; 117:6896-905. [PMID: 23683360 DOI: 10.1021/jp401739m] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The loop length, loop composition, salt concentration, and number of G-quartets are major determinants of G-quadruplex stability. We examined the effect of each of these factors on the thermal stability and folding topology of a library of RNA quadruplexes. The thermal stability of G2 and G3 RNA quadruplexes was investigated upon varying the loop length (from 1-1-1 to 15-15-15) and salt concentration (from 1 to 100 mM KCl), while the effect of loop composition was explored using 18 naturally occurring potential RNA quadruplexes predicted in untranslated regions (UTRs). We found loop length and quadruplex stability to be inversely related for G2 RNA quadruplexes and G3 RNA quadruplexes with shorter loops. However, melting temperature saturates for G3 RNA quadruplexes with longer loops. RNA G-quadruplexes with longer loops (G3 15-15-15) displayed Tm values significantly higher than the physiological temperature. This study thus highlights the need to modify the consensus motif presently used by quadruplex prediction tools. An increase in the loop size from 7 bases to 15 bases in the consensus motif will add to its predictive value for the discovery of potential RNA quadruplexes across transcriptomes.
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Affiliation(s)
- Satyaprakash Pandey
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110007, India
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141
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Chiorcea-Paquim AM, Santos PV, Eritja R, Oliveira-Brett AM. Self-assembled G-quadruplex nanostructures: AFM and voltammetric characterization. Phys Chem Chem Phys 2013; 15:9117-24. [PMID: 23644414 DOI: 10.1039/c3cp50866h] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
G-rich oligodeoxynucleotides (ODNs) have great medical and nanotechnological potential, because they can self-assemble into G-quadruplexes and higher-order nanostructures. The folding properties of d(G)10, d(TG9) and d(TG8T) ODNs were studied using atomic force microscopy (AFM) and voltammetry at carbon electrodes. Single-stranded ODNs, in Na(+) containing solutions and for short incubation times, were detected using AFM as network films and polymeric structures and using voltammetry by the occurrence of only the guanine oxidation peak. G-quadruplexes, in Na(+) containing solutions and long incubation times, or in K(+) containing solutions, were detected using AFM as spherical aggregates and using voltammetry by the decrease of the guanine oxidation peak and the occurrence of the G-quartet oxidation peak. Concerning the self-assembling into higher-order nanostructures, d(G)10 was the only sequence forming G-nanowires observed using AFM, d(TG9) formed short G-based super-structures that adsorbed as rod-like shape aggregates, and d(TG8T) formed no nanostructures, due to the presence of thymine residues at both 5' and 3' ends.
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Affiliation(s)
- Ana-Maria Chiorcea-Paquim
- Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade de Coimbra, Coimbra, Portugal
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142
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Chang T, Qi C, Meng J, Zhang N, Bing T, Yang X, Cao Z, Shangguan D. General cell-binding activity of intramolecular G-quadruplexes with parallel structure. PLoS One 2013; 8:e62348. [PMID: 23638046 PMCID: PMC3637168 DOI: 10.1371/journal.pone.0062348] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/20/2013] [Indexed: 01/19/2023] Open
Abstract
G-quadruplexes (G4s) are four-stranded nucleic acid structures adopted by some repetitive guanine-rich sequences. Putative G-quadruplex-forming sequences (PQSs) are highly prevalent in human genome. Recently some G4s have been reported to have cancer-selective antiproliferative activity. A G4 DNA, AS1411, is currently in phase II clinical trials as an anticancer agent, which is reported to bind tumor cells by targeting surface nucleolin. AS1411 also has been extensively investigated as a target-recognition element for cancer cell specific drug delivery or cancer cell imaging. Here we show that, in addition to AS1411, intramolecular G4s with parallel structure (including PQSs in genes) have general binding activity to many cell lines with different affinity. The binding of these G4s compete with each other, and their targets are certain cellular surface proteins. The tested G4s exhibit enhanced cellular uptake than non-G4 sequences. This uptake may be through the endosome/lysosome pathway, but it is independent of cellular binding of the G4s. The tested G4s also show selective antiproliferative activity that is independent of their cellular binding. Our findings provide new insight into the molecular recognition of G4s by cells; offer new clues for understanding the functions of G4s in vivo, and may extend the potential applications of G4s.
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Affiliation(s)
- Tianjun Chang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Cui Qi
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Jie Meng
- National Center for Nanoscience and Technology, Beijing, China
| | - Nan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Tao Bing
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Xianda Yang
- National Center for Nanoscience and Technology, Beijing, China
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zehui Cao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
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143
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Zhang H, Chen C, Hou L, Jin N, Shi J, Wang Z, Liu Y, Feng Q, Zhang Z. Targeting and hyperthermia of doxorubicin by the delivery of single-walled carbon nanotubes to EC-109 cells. J Drug Target 2013; 21:312-319. [DOI: 10.3109/1061186x.2012.749880] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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144
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Zhou W, Suntharalingam K, Brand NJ, Barton PJR, Vilar R, Ying L. Possible regulatory roles of promoter g-quadruplexes in cardiac function-related genes - human TnIc as a model. PLoS One 2013; 8:e53137. [PMID: 23326389 PMCID: PMC3541360 DOI: 10.1371/journal.pone.0053137] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 11/23/2012] [Indexed: 12/15/2022] Open
Abstract
G-quadruplexes (G4s) are four-stranded DNA secondary structures, which are involved in a diverse range of biological processes. Although the anti-cancer potential of G4s in oncogene promoters has been thoroughly investigated, the functions of promoter G4s in non-cancer-related genes are not well understood. We have explored the possible regulatory roles of promoter G4s in cardiac function-related genes using both computational and a wide range of experimental approaches. According to our bioinformatics results, it was found that potential G4-forming sequences are particularly enriched in the transcription regulatory regions (TRRs) of cardiac function-related genes. Subsequently, the promoter of human cardiac troponin I (TnIc) was chosen as a model, and G4s found in this region were subjected to biophysical characterisations. The chromosome 19 specific minisatellite G4 sequence (MNSG4) and near transcription start site (TSS) G4 sequence (−80 G4) adopt anti-parallel and parallel structures respectively in 100 mM KCl, with stabilities comparable to those of oncogene G4s. It was also found that TnIc G4s act cooperatively as enhancers in gene expression regulation in HEK293 cells, when stabilised by a synthetic G4-binding ligand. This study provides the first evidence of the biological significance of promoter G4s in cardiac function-related genes. The feasibility of using a single ligand to target multiple G4s in a particular gene has also been discussed.
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Affiliation(s)
- Wenhua Zhou
- Molecular Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | | | - Nigel J. Brand
- Harefield Heart Science Centre, National Heart and Lung Institute, Imperial College London, Middlesex, United Kingdom
| | - Paul J. R. Barton
- Harefield Heart Science Centre, National Heart and Lung Institute, Imperial College London, Middlesex, United Kingdom
- NIHR Cardiovascular Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, United Kingdom
| | - Ramon Vilar
- Department of Chemistry, Imperial College London, London, United Kingdom
| | - Liming Ying
- Molecular Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
- * E-mail:
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145
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Li J, Wang W, Sun D, Chen J, Zhang PH, Zhang JR, Min Q, Zhu JJ. Aptamer-functionalized silver nanoclusters-mediated cell type-specific siRNA delivery and tracking. Chem Sci 2013. [DOI: 10.1039/c3sc51538a] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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146
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Yao JL, Gao X, Sun W, Shi S, Yao TM. [Ru(bpy)2dppz-idzo]2+: a colorimetric molecular “light switch” and powerful stabilizer for G-quadruplex DNA. Dalton Trans 2013; 42:5661-72. [DOI: 10.1039/c3dt32640c] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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147
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Zhou J, Murayama K, Amrane S, Rosu F, Kashida H, Bourdoncle A, Asanuma H, Mergny JL. A “sugar-deficient” G-quadruplex: incorporation of aTNA in G4 structures. Chem Sci 2013. [DOI: 10.1039/c3sc50474c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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148
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Le HT, Miller MC, Buscaglia R, Dean WL, Holt PA, Chaires JB, Trent JO. Not all G-quadruplexes are created equally: an investigation of the structural polymorphism of the c-Myc G-quadruplex-forming sequence and its interaction with the porphyrin TMPyP4. Org Biomol Chem 2012; 10:9393-404. [PMID: 23108607 PMCID: PMC3501587 DOI: 10.1039/c2ob26504d] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
G-quadruplexes, DNA tertiary structures highly localized to functionally important sites within the human genome, have emerged as important new drug targets. The putative G-quadruplex-forming sequence (Pu27) in the NHE-III(1) promoter region of the c-Myc gene is of particular interest as stabilization of this G-quadruplex with TMPyP4 has been shown to repress c-Myc transcription. In this study, we examine the Pu27 G-quadruplex-forming sequence and its interaction with TMPyP4. We report that the Pu27 sequence exists as a heterogeneous mixture of monomeric and higher-order G-quadruplex species in vitro and that this mixture can be partially resolved by size exclusion chromatography (SEC) separation. Within this ensemble of configurations, the equilibrium can be altered by modifying the buffer composition, annealing procedure, and dialysis protocol thereby affecting the distribution of G-quadruplex species formed. TMPyP4 was found to bind preferentially to higher-order G-quadruplex species suggesting the possibility of stabilization of the junctions of the c-Myc G-quadruplex multimers by porphyrin end-stacking. We also examined four modified c-Myc sequences that have been previously reported and found a narrower distribution of G-quadruplex configurations compared to the parent Pu27 sequence. We could not definitively conclude whether these G-quadruplex structures were selected from the original ensemble or if they are new G-quadruplex structures. Since these sequences differ considerably from the wild-type promoter sequence, it is unclear whether their structures have any actual biological relevance. Additional studies are needed to examine how the polymorphic nature of G-quadruplexes affects the interpretation of in vitro data for c-Myc and other G-quadruplexes. The findings reported here demonstrate that experimental conditions contribute significantly to G-quadruplex formation and should be carefully considered, controlled, and reported in detail.
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Affiliation(s)
- Huy T. Le
- Department of Biochemistry & Molecular Biology, School of Medicine, University of Louisville, HSC-A Building, Room 616 Louisville, Kentucky 40292; Phone: (502) 852-6221; Fax: (502) 852-6222
| | - M. Clarke Miller
- James G. Brown Cancer Center, University of Louisville, 529 South Jackson Street Louisville, KY 40202; Phone:(502) 562-4375
| | - Robert Buscaglia
- Department of Biochemistry & Molecular Biology, School of Medicine, University of Louisville, HSC-A Building, Room 616 Louisville, Kentucky 40292; Phone: (502) 852-6221; Fax: (502) 852-6222
| | - William L. Dean
- James G. Brown Cancer Center, University of Louisville, 529 South Jackson Street Louisville, KY 40202; Phone:(502) 562-4375
- Department of Medicine, School of Medicine, University of Louisville, 550 South Jackson Street, Louisville, KY 40202; Phone: (502) 852-5241; Fax: (502) 852-6233
| | - Patrick A. Holt
- Department of Biochemistry & Molecular Biology, School of Medicine, University of Louisville, HSC-A Building, Room 616 Louisville, Kentucky 40292; Phone: (502) 852-6221; Fax: (502) 852-6222
| | - Jonathan B. Chaires
- Department of Biochemistry & Molecular Biology, School of Medicine, University of Louisville, HSC-A Building, Room 616 Louisville, Kentucky 40292; Phone: (502) 852-6221; Fax: (502) 852-6222
- James G. Brown Cancer Center, University of Louisville, 529 South Jackson Street Louisville, KY 40202; Phone:(502) 562-4375
- Department of Medicine, School of Medicine, University of Louisville, 550 South Jackson Street, Louisville, KY 40202; Phone: (502) 852-5241; Fax: (502) 852-6233
| | - John O. Trent
- Department of Biochemistry & Molecular Biology, School of Medicine, University of Louisville, HSC-A Building, Room 616 Louisville, Kentucky 40292; Phone: (502) 852-6221; Fax: (502) 852-6222
- James G. Brown Cancer Center, University of Louisville, 529 South Jackson Street Louisville, KY 40202; Phone:(502) 562-4375
- Department of Medicine, School of Medicine, University of Louisville, 550 South Jackson Street, Louisville, KY 40202; Phone: (502) 852-5241; Fax: (502) 852-6233
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149
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Chung CH, Kim JH, Jung J, Chung BH. Nuclease-resistant DNA aptamer on gold nanoparticles for the simultaneous detection of Pb2+ and Hg2+ in human serum. Biosens Bioelectron 2012; 41:827-32. [PMID: 23137944 DOI: 10.1016/j.bios.2012.10.026] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 10/08/2012] [Accepted: 10/08/2012] [Indexed: 10/27/2022]
Abstract
There has been great progress in the development of functional DNA-based sensors for the detection of metal ions. However, many functional DNAs are vulnerable to hydrolysis by nucleases in human blood. In addition, the detection methods that are based on DNA often exhibit interference due to the high blood concentrations of other ions, such as K(+) and Na(+). Therefore, we selected highly Pb(2+)-specific DNA-aptamer sequences based on CD spectroscopy of 4 G-rich DNA sequences and Hg(2+)-specific T-rich DNA sequences and immobilized them on gold nanoparticles for the simultaneous detection of Pb(2+) and Hg(2+) in human serum. We used gold nanoparticles because these have a superior fluorescence-quenching efficiency over a broad range of wavelengths compared with other organic quenchers. In addition, gold nanoparticles have a stabilizing effect on the immobilized DNA, which makes it more resistant to degradation by nucleases than free DNA. As a result, even in the presence of DNase, we were able to simultaneously detect Pb(2+) and Hg(2+) in serum at concentrations as low as 128 pM and 121 pM, respectively, within 10 min. These detection limits for Pb(2+) and Hg(2+) were 39-fold and 26.4-fold lower, respectively, than the detection limits that were obtained using free DNAs. Given the multi-color-fluorescence quenching capability of the gold nanoparticles and the possibility of developing functional nucleic acids for the detection of other metal ions, this study extends the application of oligonucleotides to a point-of-care detection system for the detection of multiple harmful metal ions in body fluids.
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Affiliation(s)
- Chan Ho Chung
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, 125, Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
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150
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Park S, Hwang D, Chung J. Cotinine-conjugated aptamer/anti-cotinine antibody complexes as a novel affinity unit for use in biological assays. Exp Mol Med 2012; 44:554-61. [PMID: 22809871 PMCID: PMC3465749 DOI: 10.3858/emm.2012.44.9.063] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2012] [Indexed: 01/12/2023] Open
Abstract
Aptamers are synthetic, relatively short (e.g., 20-80 bases) RNA or ssDNA oligonucleotides that can bind targets with high affinity and specificity, similar to antibodies, because they can fold into unique, three-dimensional shapes. For use in various assays and experiments, aptamers have been conjugated with biotin or digoxigenin to form complexes with avidin or anti-digoxigenin antibodies, respectively. In this study, we developed a method to label the 5' ends of aptamers with cotinine, which allows formation of a stable complex with anti-cotinine antibodies for the purpose of providing another affinity unit for the application in biological assays using aptamers. To demonstrate the functionality of this affinity unit in biological assays, we utilized two well-known aptamers: AS1411, which binds nucleolin, and pegaptanib, which binds vascular endothelial growth factor. Cotinine-conjugated AS1411/ anti-cotinine antibody complexes were successfully applied to immunoblot, immunoprecipitation, and flow cytometric analyses, and cotinine-conjugated pegaptanib/ anti-cotinine antibody complexes were used successfully in enzyme immunoassays. Our results show that cotinine-conjugated aptamer/anti-cotinine antibody complexes are an effective alternative and complementary technique for aptamer use in multiple assays and experiments.
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Affiliation(s)
- Sunyoung Park
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 110-799, Korea
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