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Simmons CR, Buchberger A, Henry SJW, Novacek A, Fahmi NE, MacCulloch T, Stephanopoulos N, Yan H. Site-Specific Arrangement and Structure Determination of Minor Groove Binding Molecules in Self-Assembled Three-Dimensional DNA Crystals. J Am Chem Soc 2023; 145:26075-26085. [PMID: 37987645 PMCID: PMC10789492 DOI: 10.1021/jacs.3c07802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The structural analysis of guest molecules in rationally designed and self-assembling DNA crystals has proven an elusive goal since its conception. Oligonucleotide frameworks provide an especially attractive route toward studying DNA-binding molecules by using three-dimensional lattices with defined sequence and structure. In this work, we site-specifically position a suite of minor groove binding molecules, and solve their structures via X-ray crystallography as a proof-of-principle toward scaffolding larger guest species. Two crystal motifs were used to precisely immobilize the molecules DAPI, Hoechst, and netropsin at defined positions in the lattice, allowing us to control occupancy within the crystal. We also solved the structure of a three-ring imidazole-pyrrole-pyrrole polyamide molecule, which sequence-specifically packs in an antiparallel dimeric arrangement within the minor groove. Finally, we engineered a crystal designed to position both netropsin and the polyamide at two distinct locations within the same lattice. Our work elucidates the design principles for the spatial arrangement of functional guests within lattices and opens new potential opportunities for the use of DNA crystals to display and structurally characterize small molecules, peptides, and ultimately proteins of unknown structure.
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Affiliation(s)
- Chad R Simmons
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
| | - Alex Buchberger
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287,United States
| | - Skylar J W Henry
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287,United States
| | - Alexandra Novacek
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287,United States
| | - Nour Eddine Fahmi
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
| | - Tara MacCulloch
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287,United States
| | - Nicholas Stephanopoulos
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287,United States
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287,United States
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2
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Simmons CR, Buchberger A, Henry SJW, Novacek A, Fahmi NE, MacCulloch T, Stephanopoulos N, Yan H. Site-specific arrangement and structure determination of minor groove binding molecules in self-assembled three-dimensional DNA crystals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561756. [PMID: 37873139 PMCID: PMC10592734 DOI: 10.1101/2023.10.10.561756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The structural analysis of guest molecules in rationally designed and self-assembling DNA crystals has proven elusive since its conception. Oligonucleotide frameworks provide an especially attractive route towards studying DNA-binding molecules by using three-dimensional lattices with defined sequence and structure. In this work, we site-specifically position a suite of minor groove binding molecules, and solve their structures via x-ray crystallography, as a proof-of-principle towards scaffolding larger guest species. Two crystal motifs were used to precisely immobilize the molecules DAPI, Hoechst, and netropsin at defined positions in the lattice, allowing us to control occupancy within the crystal. We also solved the structure of a three-ring imidazole-pyrrole-pyrrole polyamide molecule, which sequence-specifically packs in an anti-parallel dimeric arrangement within the minor groove. Finally, we engineered a crystal designed to position both netropsin and the polyamide at two distinct locations within the same lattice. Our work elucidates the design principles for the spatial arrangement of functional guests within lattices and opens new potential opportunities for the use of DNA crystals to display and structurally characterize small molecules, peptides, and ultimately proteins of unknown structure.
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3
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Pradhan S, Apaydin S, Bucevičius J, Gerasimaitė R, Kostiuk G, Lukinavičius G. Sequence-specific DNA labelling for fluorescence microscopy. Biosens Bioelectron 2023; 230:115256. [PMID: 36989663 DOI: 10.1016/j.bios.2023.115256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/04/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023]
Abstract
The preservation of nucleus structure during microscopy imaging is a top priority for understanding chromatin organization, genome dynamics, and gene expression regulation. In this review, we summarize the sequence-specific DNA labelling methods that can be used for imaging in fixed and/or living cells without harsh treatment and DNA denaturation: (i) hairpin polyamides, (ii) triplex-forming oligonucleotides, (iii) dCas9 proteins, (iv) transcription activator-like effectors (TALEs) and (v) DNA methyltransferases (MTases). All these techniques are capable of identifying repetitive DNA loci and robust probes are available for telomeres and centromeres, but visualizing single-copy sequences is still challenging. In our futuristic vision, we see gradual replacement of the historically important fluorescence in situ hybridization (FISH) by less invasive and non-destructive methods compatible with live cell imaging. Combined with super-resolution fluorescence microscopy, these methods will open the possibility to look into unperturbed structure and dynamics of chromatin in living cells, tissues and whole organisms.
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4
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Takubo C, Kimura S, Ichinomiya M, Hayakawa A, Murata M, Urushibara K, Masu H, Katagiri K, Kawahata M, Kudo M, Azumaya I, Kagechika H, Tanatani A. Conformational Properties of Aromatic Amides Bearing Imidazole Ring and Acid-Induced Trans- Cis Amide Switching. J Org Chem 2022. [PMID: 36169666 DOI: 10.1021/acs.joc.2c01295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aromatic amides bearing secondary amide bond exist in trans conformation both in the crystal and in solution, whereas the conformation of the N-methylated derivatives is cis in the crystal and predominantly cis in various solvents. The cis conformational preference of N-alkylated benzanilide provides access to aromatic foldamers such as oligo(N-alkyl-p-benzamide)s, which adopt dynamic helical structures. Here, the conformational properties of imidazole-substituted amide in the crystal and in solution were examined. Imidazole-substituted amides 2a and 4a existed mainly in the cis conformation in solution. The ratio of the cis conformer of N-methyl-N-(1-methyl-1H-imidazol-4-yl)benzamide (4a) was smaller than that of N,1-dimethyl-N-phenyl-1H-imidazole-2-carboxamide (2a) or N-methylbenzanilide, but the introduction of a substituent strongly affected the conformer ratio. Compounds 6a and 7a bearing an electron-withdrawing group on the imidazole ring existed predominantly in trans form. On the other hand, the introduction of an electron-withdrawing group on the phenyl ring or a bulky substituent on the amide nitrogen of 4a increased the ratio of cis conformer. Further, the major conformer of N-alkylated N-imidazolylamides was switched from cis to trans by the addition of acid. These results suggest that imidazole-substituted amides might be applicable as conformational switches in aromatic foldamers to enable environment-dependent structural change.
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Affiliation(s)
- Chiharu Takubo
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Sakiko Kimura
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Mami Ichinomiya
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Arisa Hayakawa
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Mako Murata
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Ko Urushibara
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Hyuma Masu
- Center for Analytical Instrumentation, Chiba University, Yayoi-cho, Chiba-shi, Chiba 263-8522, Japan
| | - Kosuke Katagiri
- Department of Chemistry, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada, Kobe, Hyogo 658-8501, Japan
| | - Masatoshi Kawahata
- Faculty of Pharmaceutical Sciences, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Mayumi Kudo
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan.,Department of Chemistry and Materials Science, National Institute of Technology, Gunma College, 580 Toribamachi, Maebashi, Gunma 371-8530, Japan
| | - Isao Azumaya
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Hiroyuki Kagechika
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Aya Tanatani
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
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5
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Tran YBN, Nguyen PTK. A New Zinc‐Based Metal‐Organic Framework for Catalytic Synthesis of
N
‐Substituted Pyrroles. ChemistrySelect 2022. [DOI: 10.1002/slct.202200592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Y B. N. Tran
- Future Materials & Devices Laboratory Institute of Fundamental and Applied Sciences Duy Tan University Ho Chi Minh City 700000 Vietnam
- Faculty of Natural Sciences Duy Tan University Da Nang 550000 Vietnam
| | - Phuong T. K. Nguyen
- Future Materials & Devices Laboratory Institute of Fundamental and Applied Sciences Duy Tan University Ho Chi Minh City 700000 Vietnam
- Faculty of Natural Sciences Duy Tan University Da Nang 550000 Vietnam
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6
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Redirection of the Transcription Factor SP1 to AT Rich Binding Sites by a Synthetic Adaptor Molecule. Helv Chim Acta 2021. [DOI: 10.1002/hlca.202100095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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7
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Troselj P, Bolgar P, Ballester P, Hunter CA. High-Fidelity Sequence-Selective Duplex Formation by Recognition-Encoded Melamine Oligomers. J Am Chem Soc 2021; 143:8669-8678. [PMID: 34081864 PMCID: PMC8213060 DOI: 10.1021/jacs.1c02275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Melamine oligomers composed of repeating triazine-piperidine units and equipped with phenol and phosphine oxide side-chains form H-bonded duplexes. The melamine backbone provides sufficient rigidity to prevent intramolecular folding of oligomers up to three recognition units in length, leading to reliable duplex formation between sequence complementary oligomers. NMR spectroscopy and isothermal titration calorimetry (ITC) were used to characterize the self-assembly properties of the oligomers. For length-complementary homo-oligomers, duplex formation in toluene is characterized by an increase in stability of an order of magnitude for every base-pair added to the chain. NMR spectra of dilute solutions of the AD 2-mer show that intramolecular H-bonding between neighboring recognition units on the chain (1,2-folding) does not occur. NMR spectra of dilute solutions of both the AAD and the ADD 3-mer show that 1,3-folding does not take place either. ITC was used to characterize interactions between all pairwise combinations of the six different 3-mer sequences, and the sequence complementary duplexes are approximately an order of magnitude more stable than duplexes with a single base mismatch. High-fidelity duplex formation combined with the synthetic accessibility of the monomer building blocks makes these systems attractive targets for further investigation.
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Affiliation(s)
- Pavle Troselj
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Peter Bolgar
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Pablo Ballester
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
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8
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Maeda R, Bando T, Sugiyama H. Application of DNA-Alkylating Pyrrole-Imidazole Polyamides for Cancer Treatment. Chembiochem 2021; 22:1538-1545. [PMID: 33453075 DOI: 10.1002/cbic.202000752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/28/2020] [Indexed: 12/13/2022]
Abstract
Pyrrole-imidazole (PI) polyamides, which target specific DNA sequences, have been studied as a class of DNA minor-groove-binding molecules. To investigate the potential of compounds for cancer treatment, PI polyamides were conjugated with DNA-alkylating agents, such as seco-CBI and chlorambucil. DNA-alkylating PI polyamides have attracted attention because of their sequence-specific alkylating activities, which contribute to reducing the severe side effects of current DNA-damaging drugs. Many of these types of conjugates have been developed as new candidates for anticancer drugs. Herein, we review recent progress into research on DNA-alkylating PI polyamides and their sequence-specific action on targets associated with cancer development.
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Affiliation(s)
- Rina Maeda
- Graduate School of Advanced Integrated Studies in Human Survivability, Kyoto University, Sakyo-ku, Kyoto, 606-8306, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Yoshida-Ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
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9
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Single position substitution of hairpin pyrrole-imidazole polyamides imparts distinct DNA-binding profiles across the human genome. PLoS One 2020; 15:e0243905. [PMID: 33351840 PMCID: PMC7755219 DOI: 10.1371/journal.pone.0243905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/01/2020] [Indexed: 01/21/2023] Open
Abstract
Pyrrole–imidazole (Py–Im) polyamides are synthetic molecules that can be rationally designed to target specific DNA sequences to both disrupt and recruit transcriptional machinery. While in vitro binding has been extensively studied, in vivo effects are often difficult to predict using current models of DNA binding. Determining the impact of genomic architecture and the local chromatin landscape on polyamide-DNA sequence specificity remains an unresolved question that impedes their effective deployment in vivo. In this report we identified polyamide–DNA interaction sites across the entire genome, by covalently crosslinking and capturing these events in the nuclei of human LNCaP cells. This technique confirms the ability of two eight ring hairpin-polyamides, with similar architectures but differing at a single ring position (Py to Im), to retain in vitro specificities and display distinct genome-wide binding profiles.
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10
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Hidaka T, Sugiyama H. Chemical Approaches to the Development of Artificial Transcription Factors Based on Pyrrole-Imidazole Polyamides. CHEM REC 2020; 21:1374-1384. [PMID: 33332727 DOI: 10.1002/tcr.202000158] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 12/19/2022]
Abstract
To maintain the functions of living organisms, cells have developed complex gene regulatory networks. Transcription factors have a central role in spatiotemporal control of gene expression and this has motivated us to develop artificial transcription factors that mimic their function. We found that three functions could be mimicked by applying our chemical approaches: i) efficient delivery into organelles that contain target DNA, ii) specific DNA binding to the target genomic region, and iii) regulation of gene expression by interaction with other transcription coregulators. We chose pyrrole-imidazole polyamides (PIPs), sequence-selective DNA binding molecules, as DNA binding domains, and have achieved each of the required functions by introducing other functional moieties. The developed artificial transcription factors have potential as chemical tools that can be used to artificially modulate gene expression to enable cell fate control and to correct abnormal gene regulation for therapeutic purposes.
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Affiliation(s)
- Takuya Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Sakyo-ku, Kyoto, 606-8501, Japan
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11
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Hidaka T, Tsubono Y, Hashiya K, Bando T, Pandian GN, Sugiyama H. Enhanced nuclear accumulation of pyrrole-imidazole polyamides by incorporation of the tri-arginine vector. Chem Commun (Camb) 2020; 56:12371-12374. [PMID: 32930253 DOI: 10.1039/d0cc05158f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The tri-arginine moiety enhanced nuclear accumulation of a 12-ring pyrrole-imidazole polyamide (PIP) without compromising sequence-selectivity and achieved efficient repression of SOX2-downstream genes and HER2 transcription in live cells. This simple vector expands the application of long PIPs in live cells by overcoming the compound delivery problems associated with them.
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Affiliation(s)
- Takuya Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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12
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Effects of Pyrrole-Imidazole Polyamides Targeting Human TGF-β1 on the Malignant Phenotypes of Liver Cancer Cells. Molecules 2020; 25:molecules25122883. [PMID: 32585841 PMCID: PMC7356887 DOI: 10.3390/molecules25122883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/12/2020] [Accepted: 06/20/2020] [Indexed: 02/06/2023] Open
Abstract
Synthetic pyrrole-imidazole (PI) polyamides bind to the minor groove of double-helical DNA with high affinity and specificity, and inhibit the transcription of corresponding genes. In liver cancer, transforming growth factor (TGF)-β expression is correlated with tumor grade, and high-grade liver cancer tissues express epithelial-mesenchymal transition markers. TGF-β1 was reported to be involved in cancer development by transforming precancer cells to cancer stem cells (CSCs). This study aimed to evaluate the effects of TGF-β1-targeting PI polyamide on the growth of liver cancer cells and CSCs and their TGF-β1 expression. We analyzed TGF-β1 expression level after the administration of GB1101, a PI polyamide that targets human TGF-β1 promoter, and examined its effects on cell proliferation, invasiveness, and TGF-β1 mRNA expression level. GB1101 treatment dose-dependently decreased TGF-β1 mRNA levels in HepG2 and HLF cells, and inhibited HepG2 colony formation associated with downregulation of TGF-β1 mRNA. Although GB1101 did not substantially inhibit the proliferation of HepG2 cells compared to untreated control cells, GB1101 significantly suppressed the invasion of HLF cells, which displayed high expression of CD44, a marker for CSCs. Furthermore, GB1101 significantly inhibited HLF cell sphere formation by inhibiting TGF-β1 expression, in addition to suppressing the proliferation of HLE and HLF cells. Taken together, GB1101 reduced TGF-β1 expression in liver cancer cells and suppressed cell invasion; therefore, GB1101 is a novel candidate drug for the treatment of liver cancer.
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Müller S, Paulus J, Mattay J, Ihmels H, Dodero VI, Sewald N. Photocontrolled DNA minor groove interactions of imidazole/pyrrole polyamides. Beilstein J Org Chem 2020; 16:60-70. [PMID: 31976017 PMCID: PMC6964667 DOI: 10.3762/bjoc.16.8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 12/20/2019] [Indexed: 12/21/2022] Open
Abstract
Azobenzenes are photoswitchable molecules capable of generating significant structural changes upon E-to-Z photoisomerization in peptides or small molecules, thereby controlling geometry and functionality. E-to-Z photoisomerization usually is achieved upon irradiation at 350 nm (π–π* transition), while the Z-to-E isomerization proceeds photochemically upon irradiation at >400 nm (n–π* transition) or thermally. Photoswitchable compounds have frequently been employed as modules, e.g., to control protein–DNA interactions. However, their use in conjunction with minor groove-binding imidazole/pyrrole (Im/Py) polyamides is yet unprecedented. Dervan-type Im/Py polyamides were equipped with an azobenzene unit, i.e., 3-(3-(aminomethyl)phenyl)azophenylacetic acid, as the linker between two Im/Py polyamide strands. Only the (Z)-azobenzene-containing polyamides bound to the minor groove of double-stranded DNA hairpins. Photoisomerization was exemplarily evaluated by 1H NMR experiments, while minor groove binding of the (Z)-azobenzene derivatives was proven by CD titration experiments. The resulting induced circular dichroism (ICD) bands of the bound ligands, together with the photometric determination of the dsDNA melting temperature, revealed a significant stabilization of the DNA upon association with the ligand. The (Z)-azobenzene acted as a building block inducing a reverse turn, which favored hydrogen bonds between the pyrrole/imidazole amide and the DNA bases. In contrast, the E-configured polyamides did not induce any ICD characteristic for minor groove binding. The incorporation of the photoswitchable azobenzene unit is a promising strategy to obtain photoswitchable Im/Py hairpin polyamides capable of interacting with the dsDNA minor groove only in the Z-configuration.
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Affiliation(s)
- Sabrina Müller
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, PO Box 100131, D-33501 Bielefeld, Germany
| | - Jannik Paulus
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, PO Box 100131, D-33501 Bielefeld, Germany
| | - Jochen Mattay
- Organic Chemistry I, Department of Chemistry, Bielefeld University, PO Box 100131, D-33501 Bielefeld, Germany
| | - Heiko Ihmels
- Organic Chemistry II, Department Chemistry - Biology, Siegen University, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Veronica I Dodero
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, PO Box 100131, D-33501 Bielefeld, Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, PO Box 100131, D-33501 Bielefeld, Germany
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14
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Heinrich B, Vázquez O. 4-Methyltrityl-Protected Pyrrole and Imidazole Building Blocks for Solid Phase Synthesis of DNA-Binding Polyamides. Org Lett 2020; 22:533-536. [PMID: 31904984 DOI: 10.1021/acs.orglett.9b04288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-binding polyamides are synthetic oligomers of pyrrole/imidazole units with high specificity and affinity for double-stranded DNA. To increase their synthetic diversity, we report a mild methodology based on 4-methyltrityl (Mtt) solid phase peptide synthesis (SPPS), whose building blocks are more accessible than the standard Fmoc and Boc SPPS ones. We demonstrate the robustness of the approach by preparing and studying a hairpin with all precursors. Importantly, our strategy is orthogonal and compatible with sensitive molecules and could be readily automated.
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Affiliation(s)
- Benedikt Heinrich
- Fachbereich Chemie , Philipps-Universität Marburg , Hans-Meerwein-Straße 4 , 35043 Marburg , Germany
| | - Olalla Vázquez
- Fachbereich Chemie , Philipps-Universität Marburg , Hans-Meerwein-Straße 4 , 35043 Marburg , Germany
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15
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Enrichment technique to allow early detection and monitor emergence of KRAS mutation in response to treatment. Sci Rep 2019; 9:11346. [PMID: 31383871 PMCID: PMC6683117 DOI: 10.1038/s41598-019-47700-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 07/18/2019] [Indexed: 02/08/2023] Open
Abstract
Sensitivity of cell-free circulating tumour DNA (ctDNA) assays is often hampered by the limited quantity of intact mutant nucleotide fragments. To overcome the issue of substrate limitation in clinical applications, we developed an enrichment method utilizing pyrrole-imidazole (PI) polyamides and their ability to bind the minor groove of B-DNA. We present here a proof-of-concept experiment to enrich specific mutant KRAS alleles with biotinylated PI polyamides. We investigated the clinical feasibility of incorporating PI polyamides to detect KRAS mutations in ctDNA from 40 colorectal cancer (CRC) patients, of whom 17 carried mutations in KRAS. After enriching ctDNA with those polyamides, we used digital PCR to detect several common KRAS codon 12 mutations. Enrichment by biotinylated PI polyamides improved the sensitivity of ctDNA analysis (88.9% vs. 11.1%, P < 0.01) in 9 non-metastatic mutation-positive patients. We observed no differences in performance for the 8 metastatic subjects (100% vs. 75%, P = 0.47). In the remaining 23/40 patients with wild type KRAS codon 12, no mutant alleles were detected with or without polyamide-facilitated enrichment. Enriching B-form of ctDNA with PI polyamides significantly improved the assay sensitivity in detecting KRAS mutations in non-metastatic CRC patient samples.
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16
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Yu Z, Pandian GN, Hidaka T, Sugiyama H. Therapeutic gene regulation using pyrrole-imidazole polyamides. Adv Drug Deliv Rev 2019; 147:66-85. [PMID: 30742856 DOI: 10.1016/j.addr.2019.02.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/22/2018] [Accepted: 02/04/2019] [Indexed: 12/13/2022]
Abstract
Recent innovations in cutting-edge sequencing platforms have allowed the rapid identification of genes associated with communicable, noncommunicable and rare diseases. Exploitation of this collected biological information has facilitated the development of nonviral gene therapy strategies and the design of several proteins capable of editing specific DNA sequences for disease control. Small molecule-based targeted therapeutic approaches have gained increasing attention because of their suggested clinical benefits, ease of control and lower costs. Pyrrole-imidazole polyamides (PIPs) are a major class of DNA minor groove-binding small molecules that can be predesigned to recognize specific DNA sequences. This programmability of PIPs allows the on-demand design of artificial genetic switches and fluorescent probes. In this review, we detail the progress in the development of PIP-based designer ligands and their prospects as advanced DNA-based small-molecule drugs for therapeutic gene modulation.
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17
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Heinrich B, Bouazoune K, Wojcik M, Bakowsky U, Vázquez O. ortho-Fluoroazobenzene derivatives as DNA intercalators for photocontrol of DNA and nucleosome binding by visible light. Org Biomol Chem 2019; 17:1827-1833. [PMID: 30604825 DOI: 10.1039/c8ob02343c] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We report a high-affinity photoswitchable DNA binder, which displays different nucleosome-binding capacities upon visible-light irradiation. Both photochemical and DNA-recognition properties were examined by UV-Vis, HPLC, CD spectroscopy, NMR, FID assays, EMSA and DLS. Our probe sets the basis for developing new optoepigenetic tools for conditional modulation of nucleosomal DNA accessibility.
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Affiliation(s)
- Benedikt Heinrich
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043, Marburg, Germany.
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18
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Saha HR, Kaneda-Nakashima K, Shimosaki S, Suekane A, Sarkar B, Saito Y, Ogoh H, Nakahata S, Inoue K, Watanabe T, Nagase H, Morishita K. Suppression of GPR56 expression by pyrrole-imidazole polyamide represents a novel therapeutic drug for AML with high EVI1 expression. Sci Rep 2018; 8:13741. [PMID: 30214063 PMCID: PMC6137133 DOI: 10.1038/s41598-018-32205-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 09/04/2018] [Indexed: 12/14/2022] Open
Abstract
G protein-coupled receptor 56 (GPR56) is highly expressed in acute myeloid leukemia (AML) cells with high EVI1 expression (EVI1high AML). Because GPR56 is a transcriptional target of EVI1 and silencing of GPR56 expression induces apoptosis, we developed a novel drug to suppress GPR56 expression in EVI1high AML cells. For this purpose, we generated pyrrole-imidazole (PI) polyamides specific to GPR56 (PIP/56-1 or PIP/56-2) as nuclease-resistant novel compounds that interfere with the binding of EVI1 to the GPR56 promoter in a sequence-specific manner. Treatment of EVI1high AML cell lines (UCSD/AML1 and Kasumi-3) with PIP/56-1 or PIP/56-2 effectively suppressed GPR56 expression by inhibiting binding of EVI1 to its promoter, leading to suppression of cell growth with increased rates of apoptosis. Moreover, intravenous administration of PIP/56-1 into immunodeficient Balb/c-RJ mice subcutaneously transplanted with UCSD/AML1 cells significantly inhibited tumor growth and extended survival. Furthermore, organ infiltration by leukemia cells in immunodeficient Balb/c-RJ mice, which were intravenously transplanted using UCSD/AML1 cells, was successfully inhibited by PIP/56-1 treatment with no apparent effects on murine hematopoietic cells. In addition, PIP treatment did not inhibit colony formation of human CD34+ progenitor cells. Thus, PI polyamide targeting of GPR56 using our compound is promising, useful, and safe for the treatment of EVI1high AML.
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Affiliation(s)
- Hasi Rani Saha
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Kazuko Kaneda-Nakashima
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Shunsuke Shimosaki
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Akira Suekane
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Bidhan Sarkar
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yusuke Saito
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Honami Ogoh
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Shingo Nakahata
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Kentaro Inoue
- Department of Computer Science and Systems Engineering, Faculty of Engineering, University of Miyazaki, Miyazaki, Japan
| | - Takayoshi Watanabe
- Division of Innovative Cancer Therapeutics, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Hiroki Nagase
- Division of Innovative Cancer Therapeutics, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Kazuhiro Morishita
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
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19
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Wu C, Wang W, Fang L, Su W. Programmable pyrrole-imidazole polyamides: A potent tool for DNA targeting. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.05.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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20
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Bhaduri S, Ranjan N, Arya DP. An overview of recent advances in duplex DNA recognition by small molecules. Beilstein J Org Chem 2018; 14:1051-1086. [PMID: 29977379 PMCID: PMC6009268 DOI: 10.3762/bjoc.14.93] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 04/06/2018] [Indexed: 12/13/2022] Open
Abstract
As the carrier of genetic information, the DNA double helix interacts with many natural ligands during the cell cycle, and is amenable to such intervention in diseases such as cancer biogenesis. Proteins bind DNA in a site-specific manner, not only distinguishing between the geometry of the major and minor grooves, but also by making close contacts with individual bases within the local helix architecture. Over the last four decades, much research has been reported on the development of small non-natural ligands as therapeutics to either block, or in some cases, mimic a DNA–protein interaction of interest. This review presents the latest findings in the pursuit of novel synthetic DNA binders. This article provides recent coverage of major strategies (such as groove recognition, intercalation and cross-linking) adopted in the duplex DNA recognition by small molecules, with an emphasis on major works of the past few years.
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Affiliation(s)
| | - Nihar Ranjan
- National Institute of Pharmaceutical Education and Research (NIPER), Raebareli 122003, India
| | - Dev P Arya
- NUBAD, LLC, 900B West Faris Rd., Greenville 29605, SC, USA.,Clemson University, Hunter Laboratory, Clemson 29634, SC, USA
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21
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Asamitsu S, Obata S, Phan AT, Hashiya K, Bando T, Sugiyama H. Simultaneous Binding of Hybrid Molecules Constructed with Dual DNA-Binding Components to a G-Quadruplex and Its Proximal Duplex. Chemistry 2018; 24:4428-4435. [DOI: 10.1002/chem.201705945] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Sefan Asamitsu
- Department of Chemistry; Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo; Kyoto 606-8502 Japan
| | - Shunsuke Obata
- Department of Chemistry; Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo; Kyoto 606-8502 Japan
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
| | - Kaori Hashiya
- Department of Chemistry; Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo; Kyoto 606-8502 Japan
| | - Toshikazu Bando
- Department of Chemistry; Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo; Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry; Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo; Kyoto 606-8502 Japan
- Institute for Integrated Cell-Material Science (WPI-iCeMS); Kyoto University, Sakyo; Kyoto 606-8501 Japan
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22
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Kawamoto Y, Bando T, Sugiyama H. Sequence-specific DNA binding Pyrrole-imidazole polyamides and their applications. Bioorg Med Chem 2018; 26:1393-1411. [PMID: 29439914 DOI: 10.1016/j.bmc.2018.01.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/25/2018] [Accepted: 01/28/2018] [Indexed: 12/25/2022]
Abstract
Pyrrole-imidazole polyamides (Py-Im polyamides) are cell-permeable compounds that bind to the minor groove of double-stranded DNA in a sequence-specific manner without causing denaturation of the DNA. These compounds can be used to control gene expression and to stain specific sequences in cells. Here, we review the history, structural variations, and functional investigations of Py-Im polyamides.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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23
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Synthesis of pyrrole-imidazole polyamide oligomers based on a copper-catalyzed cross-coupling strategy. Bioorg Med Chem Lett 2017; 27:2197-2200. [PMID: 28389153 DOI: 10.1016/j.bmcl.2017.03.052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 02/08/2023]
Abstract
Pyrrole-imidazole (Py-Im) polyamides are useful tools for chemical biology and medicinal chemistry studies due to their unique binding properties to the minor groove of DNA. We developed a novel method of synthesizing Py-Im polyamide oligomers based on a Cu-catalyzed cross-coupling strategy. All four patterns of dimer fragments could be synthesized using a Cu-catalyzed Ullmann-type cross-coupling with easily prepared monomer units. Moreover, we demonstrated that pyrrole dimer, trimer, and tetramer building blocks for Py-Im polyamide synthesis were accessible by combining site selective iodination of the pyrrole/pyrrole coupling adduct.
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24
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Dendritic Amine on Mesoporous Silica: First Organo Base Catalyst for Paal Knorr Reaction under Solvent Free Condition, A green approach. Catal Letters 2017. [DOI: 10.1007/s10562-017-1975-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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25
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Abstract
Bio-inspired synthetic backbones leading to foldamers can provide effective biopolymer mimics with new and improved properties in a physiological environment, and in turn could serve as useful tools to study biology and lead to practical applications in the areas of diagnostics or therapeutics. Remarkable progress has been accomplished over the past 20 years with the discovery of many potent bioactive foldamers originating from diverse backbones and targeting a whole spectrum of bio(macro)molecules such as membranes, protein surfaces, and nucleic acids. These current achievements, future opportunities, and key challenges that remain are discussed in this article.
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26
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Kawamoto Y, Sasaki A, Chandran A, Hashiya K, Ide S, Bando T, Maeshima K, Sugiyama H. Targeting 24 bp within Telomere Repeat Sequences with Tandem Tetramer Pyrrole–Imidazole Polyamide Probes. J Am Chem Soc 2016; 138:14100-14107. [DOI: 10.1021/jacs.6b09023] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yusuke Kawamoto
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Asuka Sasaki
- Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Anandhakumar Chandran
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Satoru Ide
- Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Toshikazu Bando
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kazuhiro Maeshima
- Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Hiroshi Sugiyama
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material
Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
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27
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Abstract
Aromatic amide foldamers constitute a growing class of oligomers that adopt remarkably stable folded conformations. The folded structures possess largely predictable shapes and open the way toward the design of synthetic mimics of proteins. Important examples of aromatic amide foldamers include oligomers of 7- or 8-amino-2-quinoline carboxylic acid that have been shown to exist predominantly as well-defined helices, including when they are combined with α-amino acids to which they may impose their folding behavior. To rapidly iterate their synthesis, solid phase synthesis (SPS) protocols have been developed and optimized for overcoming synthetic difficulties inherent to these backbones such as low nucleophilicity of amine groups on electron poor aromatic rings and a strong propensity of even short sequences to fold on the solid phase during synthesis. For example, acid chloride activation and the use of microwaves are required to bring coupling at aromatic amines to completion. Here, we report detailed SPS protocols for the rapid production of: (1) oligomers of 8-amino-2-quinolinecarboxylic acid; (2) oligomers containing 7-amino-8-fluoro-2-quinolinecarboxylic acid; and (3) heteromeric oligomers of 8-amino-2-quinolinecarboxylic acid and α-amino acids. SPS brings the advantage to quickly produce sequences having varied main chain or side chain components without having to purify multiple intermediates as in solution phase synthesis. With these protocols, an octamer could easily be synthesized and purified within one to two weeks from Fmoc protected amino acid monomer precursors.
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28
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Jewginski M, Fischer L, Colombo C, Huc I, Mackereth CD. Solution Observation of Dimerization and Helix Handedness Induction in a Human Carbonic Anhydrase-Helical Aromatic Amide Foldamer Complex. Chembiochem 2016; 17:727-36. [PMID: 26807531 DOI: 10.1002/cbic.201500619] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Indexed: 12/18/2022]
Abstract
The design of synthetic foldamers to selectively bind proteins is currently hindered by the limited availability of molecular data to establish key features of recognition. Previous work has described dimerization of human carbonic anhydrase II (HCA) through self-association of a quinoline oligoamide helical foldamer attached to a tightly binding HCA ligand. A crystal structure of the complex provided atomic details to explain the observed induction of single foldamer helix handedness and revealed an unexpected foldamer-mediated dimerization. Here, we investigated the detailed behavior of the HCA-foldamer complex in solution by using NMR spectroscopy. We found that the ability to dimerize is buffer-dependent and uses partially distinct intermolecular contacts. The use of a foldamer variant incapable of self-association confirmed the ability to induce helix handedness separately from dimer formation and provided insight into the dynamics of enantiomeric selection.
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Affiliation(s)
- Michal Jewginski
- University of Bordeaux, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France.,CNRS, CBMN (UMR 5248).,Bordeaux Institut National Polytechnique, CBMN (UMR 5248).,Wrocław University of Technology, Faculty of Chemistry, Wrocław, Poland
| | - Lucile Fischer
- University of Bordeaux, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France.,CNRS, CBMN (UMR 5248).,Bordeaux Institut National Polytechnique, CBMN (UMR 5248)
| | - Cinzia Colombo
- University of Bordeaux, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France.,CNRS, CBMN (UMR 5248).,Bordeaux Institut National Polytechnique, CBMN (UMR 5248)
| | - Ivan Huc
- University of Bordeaux, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France. .,CNRS, CBMN (UMR 5248). .,Bordeaux Institut National Polytechnique, CBMN (UMR 5248).
| | - Cameron D Mackereth
- University of Bordeaux, ARNA (U1212), Institut Européen de Chimie et Biologie. .,INSERM, ARNA (U1212). .,CNRS, ARNA (UMR 5320), 2 rue Escarpit, 33600, Pessac, France.
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29
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Pauff SM, Fallows AJ, Mackay SP, Su W, Cullis PM, Burley GA. Pyrrole‐Imidazole Polyamides: Manual Solid‐Phase Synthesis. ACTA ACUST UNITED AC 2015; 63:8.10.1-8.10.41. [DOI: 10.1002/0471142700.nc0810s63] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Steven M. Pauff
- Department of Pure and Applied Chemistry, University of Strathclyde Glasgow United Kingdom
| | - Andrew J. Fallows
- Department of Chemistry, University of Leicester Leicester United Kingdom
| | - Simon P. Mackay
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde Glasgow United Kingdom
| | - Wu Su
- Guangdong Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences Shenzhen Guangdong People's Republic of China
| | - Paul M. Cullis
- Department of Chemistry, University of Leicester Leicester United Kingdom
| | - Glenn A. Burley
- Department of Pure and Applied Chemistry, University of Strathclyde Glasgow United Kingdom
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30
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Taylor RD, Chandran A, Kashiwazaki G, Hashiya K, Bando T, Nagase H, Sugiyama H. Selective Targeting of the KRAS Codon 12 Mutation Sequence by Pyrrole-Imidazole Polyamideseco-CBI Conjugates. Chemistry 2015; 21:14996-5003. [DOI: 10.1002/chem.201501870] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Indexed: 12/16/2022]
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31
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Janssen BMG, van Ommeren SPFI, Merkx M. Efficient Synthesis of Peptide and Protein Functionalized Pyrrole-Imidazole Polyamides Using Native Chemical Ligation. Int J Mol Sci 2015; 16:12631-47. [PMID: 26053396 PMCID: PMC4490465 DOI: 10.3390/ijms160612631] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/25/2015] [Accepted: 05/28/2015] [Indexed: 01/02/2023] Open
Abstract
The advancement of DNA-based bionanotechnology requires efficient strategies to functionalize DNA nanostructures in a specific manner with other biomolecules, most importantly peptides and proteins. Common DNA-functionalization methods rely on laborious and covalent conjugation between DNA and proteins or peptides. Pyrrole-imidazole (Py-Im) polyamides, based on natural minor groove DNA-binding small molecules, can bind to DNA in a sequence specific fashion. In this study, we explore the use of Py-Im polyamides for addressing proteins and peptides to DNA in a sequence specific and non-covalent manner. A generic synthetic approach based on native chemical ligation was established that allows efficient conjugation of both peptides and recombinant proteins to Py-Im polyamides. The effect of Py-Im polyamide conjugation on DNA binding was investigated by Surface Plasmon Resonance (SPR). Although the synthesis of different protein-Py-Im-polyamide conjugates was successful, attenuation of DNA affinity was observed, in particular for the protein-Py-Im-polyamide conjugates. The practical use of protein-Py-Im-polyamide conjugates for addressing DNA structures in an orthogonal but non-covalent manner, therefore, remains to be established.
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Affiliation(s)
- Brian M G Janssen
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5600 MB Eindhoven, The Netherlands.
| | - Sven P F I van Ommeren
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5600 MB Eindhoven, The Netherlands.
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5600 MB Eindhoven, The Netherlands.
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32
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Kawamoto Y, Sasaki A, Hashiya K, Ide S, Bando T, Maeshima K, Sugiyama H. Tandem trimer pyrrole-imidazole polyamide probes targeting 18 base pairs in human telomere sequences. Chem Sci 2015; 6:2307-2312. [PMID: 29308145 PMCID: PMC5645774 DOI: 10.1039/c4sc03755c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 01/20/2015] [Indexed: 01/06/2023] Open
Abstract
The novel tandem trimer pyrrole-imidazole polyamide probe targeting 18 bp in telomeric repeats visualized telomeres in human cells selectively.
The binding of molecules to specific DNA sequences is important for imaging genome DNA and for studying gene expression. Increasing the number of base pairs targeted by these molecules would provide greater specificity. N-Methylpyrrole–N-methylimidazole (Py–Im) polyamides are one type of such molecules and can bind to the minor groove of DNA in a sequence-specific manner without causing denaturation of DNA. Our recent work has demonstrated that tandem hairpin Py–Im polyamides conjugated with a fluorescent dye can be synthesized easily and can serve as new probes for studying human telomeres under mild conditions. Herein, to improve their selectivities to telomeres by targeting longer sequences, we designed and synthesized a fluorescent tandem trimer Py–Im polyamide probe, comprising three hairpins and two connecting regions (hinges). The new motif bound to 18 bp dsDNA in human telomeric repeats (TTAGGG)n, the longest sequence for specific binding reported for Py–Im polyamides. We compared the binding affinities and the abilities to discriminate mismatch, the UV-visible absorption and fluorescence spectra, and telomere staining in human cells between the tandem trimer and a previously developed tandem hairpin. We found that the tandem trimer Py–Im polyamide probe has higher ability to recognize telomeric repeats and stains telomeres in chemically fixed cells with lower background signal.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Chemistry , Graduate School of Science , Kyoto University , Kyoto 606-8502 , Sakyo , Japan . ;
| | - Asuka Sasaki
- Biological Macromolecules Laboratory , Structural Biology Center , National Institute of Genetics, and Department of Genetics , School of Life Science , Graduate University for Advanced Studies (Sokendai) , Mishima , Shizuoka 411-8540 , Japan .
| | - Kaori Hashiya
- Department of Chemistry , Graduate School of Science , Kyoto University , Kyoto 606-8502 , Sakyo , Japan . ;
| | - Satoru Ide
- Biological Macromolecules Laboratory , Structural Biology Center , National Institute of Genetics, and Department of Genetics , School of Life Science , Graduate University for Advanced Studies (Sokendai) , Mishima , Shizuoka 411-8540 , Japan .
| | - Toshikazu Bando
- Department of Chemistry , Graduate School of Science , Kyoto University , Kyoto 606-8502 , Sakyo , Japan . ;
| | - Kazuhiro Maeshima
- Biological Macromolecules Laboratory , Structural Biology Center , National Institute of Genetics, and Department of Genetics , School of Life Science , Graduate University for Advanced Studies (Sokendai) , Mishima , Shizuoka 411-8540 , Japan .
| | - Hiroshi Sugiyama
- Department of Chemistry , Graduate School of Science , Kyoto University , Kyoto 606-8502 , Sakyo , Japan . ; .,Institute for Integrated Cell-Material Science (WPI-iCeMS) , Kyoto University , Kyoto 606-8501 , Sakyo , Japan
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33
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Guo C, Kawamoto Y, Asamitsu S, Sawatani Y, Hashiya K, Bando T, Sugiyama H. Rational design of specific binding hairpin Py-Im polyamides targeting human telomere sequences. Bioorg Med Chem 2014; 23:855-60. [PMID: 25614111 DOI: 10.1016/j.bmc.2014.12.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 12/12/2014] [Accepted: 12/13/2014] [Indexed: 02/03/2023]
Abstract
N-Methylpyrrole (Py)-N-methylimidazole (Im) polyamides are organic molecules that can recognize predetermined DNA sequences in a sequence-specific manner. Human telomeres contain regions of (TTAGGG)n repetitive nucleotide sequences at each end of chromosomes, and these regions protect the chromosome from deterioration or from fusion with neighboring chromosomes. The telomeres are disposable buffers at the ends of chromosomes that are truncated during cell division. Tandem hairpin Py-Im polyamide TH59, which recognizes human telomere sequences, was reported by Laemmli's group in 2001. Here, we synthesized three types of Py-Im polyamides 1-3 based on TH59 for specific recognition of human telomere repeat sequences. Thermal melting temperature (Tm) measurements and surface plasmon resonance analysis were used to evaluate the abilities of the three types of Py-Im polyamides to discriminate between three kinds of DNA sequences. Significantly, the results showed that polyamides 1 and 2 have better affinities to TTAAGG than to TTAGGG. In contrast, polyamide 3 displayed good specificity to human telomere sequence, TTAGGG, as expected on the basis of Py-Im binding rules.
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Affiliation(s)
- Chuanxin Guo
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Sefan Asamitsu
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yoshito Sawatani
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; Institute for Integrated Cell-Materials Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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Fang L, Yao G, Pan Z, Wu C, Wang HS, Burley GA, Su W. Fully Automated Synthesis of DNA-Binding Py-Im Polyamides Using a Triphosgene Coupling Strategy. Org Lett 2014; 17:158-61. [DOI: 10.1021/ol503388a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lijing Fang
- Guangdong
Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology,
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P. R. China
| | - Guiyang Yao
- Key Laboratory for the Chemistry and Molecular Engineer of Medicinal Resources, School of Chemistry & Pharmaceutical Sciences of Guangxi Normal University, Guilin 541004, P. R. China
| | - Zhengyin Pan
- Guangdong
Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology,
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P. R. China
| | - Chunlei Wu
- Guangdong
Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology,
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P. R. China
| | - Heng-Shan Wang
- Key Laboratory for the Chemistry and Molecular Engineer of Medicinal Resources, School of Chemistry & Pharmaceutical Sciences of Guangxi Normal University, Guilin 541004, P. R. China
| | - Glenn A Burley
- Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Wu Su
- Guangdong
Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology,
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P. R. China
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Kawamoto Y, Bando T, Kamada F, Li Y, Hashiya K, Maeshima K, Sugiyama H. Development of a new method for synthesis of tandem hairpin pyrrole-imidazole polyamide probes targeting human telomeres. J Am Chem Soc 2014; 135:16468-77. [PMID: 24083880 DOI: 10.1021/ja406737n] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Pyrrole–imidazole (PI) polyamides bind to the minor groove of DNA in a sequence-specific manner without causing denaturation of DNA. To visualize telomeres specifically, tandem hairpin PI polyamides conjugated with a fluorescent dye have been synthesized, but the study of telomeres using these PI polyamides has not been reported because of difficulties synthesizing these tandem hairpin PI polyamides. To synthesize tandem hairpin PI polyamides more easily, we have developed new PI polyamide fragments and have used them as units in Fmoc solid-phase peptide synthesis. Using this new method, we synthesized four fluorescent polyamide probes for the human telomeric repeat TTAGGG, and we examined the binding affinities and specificities of the tandem hairpin PI polyamides, the UV–vis absorption and fluorescence spectra of the fluorescent polyamide probes, and telomere staining in mouse MC12 and human HeLa cells. The polyamides synthesized using the new method successfully targeted to human and mouse telomeres under mild conditions and allow easier labeling of telomeres in the cells while maintaining the telomere structure. Using the fluorescent polyamides, we demonstrated that the telomere length at a single telomere level is related to the abundance of TRF1 protein, a shelterin complex component in the telomere.
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Shang J, Gan Q, Dawson SJ, Rosu F, Jiang H, Ferrand Y, Huc I. Self-Association of Aromatic Oligoamide Foldamers into Double Helices in Water. Org Lett 2014; 16:4992-5. [DOI: 10.1021/ol502259y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Jie Shang
- Université Bordeaux, CBMN, UMR 5248, Institut Européen de
Chimie Biologie, 2 rue Robert Escarpit 33607 Pessac, France
- CNRS, CBMN, UMR 5248, 33607 Pessac, France
- Beijing
National Laboratory for Molecular Sciences, CAS Key Laboratory of
Photochemistry, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190, China
| | - Quan Gan
- Université Bordeaux, CBMN, UMR 5248, Institut Européen de
Chimie Biologie, 2 rue Robert Escarpit 33607 Pessac, France
- CNRS, CBMN, UMR 5248, 33607 Pessac, France
| | - Simon J. Dawson
- Université Bordeaux, CBMN, UMR 5248, Institut Européen de
Chimie Biologie, 2 rue Robert Escarpit 33607 Pessac, France
- CNRS, CBMN, UMR 5248, 33607 Pessac, France
| | - Frédéric Rosu
- Université Bordeaux, UMS 3033/US 001, IECB, 2 rue Robert Escarpit 33607 Pessac, France
- CNRS, IECB, UMS 3033, 33607 Pessac, France
| | - Hua Jiang
- Beijing
National Laboratory for Molecular Sciences, CAS Key Laboratory of
Photochemistry, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190, China
| | - Yann Ferrand
- Université Bordeaux, CBMN, UMR 5248, Institut Européen de
Chimie Biologie, 2 rue Robert Escarpit 33607 Pessac, France
- CNRS, CBMN, UMR 5248, 33607 Pessac, France
| | - Ivan Huc
- Université Bordeaux, CBMN, UMR 5248, Institut Européen de
Chimie Biologie, 2 rue Robert Escarpit 33607 Pessac, France
- CNRS, CBMN, UMR 5248, 33607 Pessac, France
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37
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Asamitsu S, Kawamoto Y, Hashiya F, Hashiya K, Yamamoto M, Kizaki S, Bando T, Sugiyama H. Sequence-specific DNA alkylation and transcriptional inhibition by long-chain hairpin pyrrole–imidazole polyamide–chlorambucil conjugates targeting CAG/CTG trinucleotide repeats. Bioorg Med Chem 2014; 22:4646-57. [DOI: 10.1016/j.bmc.2014.07.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/13/2014] [Accepted: 07/14/2014] [Indexed: 01/06/2023]
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38
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Fallows AJ, Singh I, Dondi R, Cullis PM, Burley GA. Highly efficient synthesis of DNA-binding polyamides using a convergent fragment-based approach. Org Lett 2014; 16:4654-7. [PMID: 25162625 DOI: 10.1021/ol502203y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Two advances in the synthesis of hairpin pyrrole-imidazole polyamides (PAs) are described. First, the application of a convergent synthetic strategy is shown, involving the Boc-based solid phase synthesis of a C-terminal fragment and the solution phase synthesis of the N-terminal fragment. Second a new hybrid resin is developed that allows for the preparation of hairpin PAs lacking a C-terminal β-alanine tail. Both methods are compatible with a range of coupling reagents and provide a facile, modular route to prepare PA libraries in high yield and crude purity.
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Affiliation(s)
- Andrew J Fallows
- Department of Chemistry, University of Leicester , University Road, Leicester, LE1 7RH, U.K
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39
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Hirata A, Nokihara K, Kawamoto Y, Bando T, Sasaki A, Ide S, Maeshima K, Kasama T, Sugiyama H. Structural Evaluation of Tandem Hairpin Pyrrole–Imidazole Polyamides Recognizing Human Telomeres. J Am Chem Soc 2014; 136:11546-54. [DOI: 10.1021/ja506058e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Akiyoshi Hirata
- HiPep Laboratories, Nakatsukasa-cho 486-46, Kamigyo-ku Kyoto, 602-8158, Japan
| | - Kiyoshi Nokihara
- HiPep Laboratories, Nakatsukasa-cho 486-46, Kamigyo-ku Kyoto, 602-8158, Japan
| | - Yusuke Kawamoto
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Asuka Sasaki
- Biological
Macromolecules Laboratory, Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Satoru Ide
- Biological
Macromolecules Laboratory, Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Kazuhiro Maeshima
- Biological
Macromolecules Laboratory, Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Takeshi Kasama
- Research
Center for Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroshi Sugiyama
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute
for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
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40
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Taylor RD, Kawamoto Y, Hashiya K, Bando T, Sugiyama H. Sequence-Specific DNA Alkylation by Tandem Py-Im Polyamide Conjugates. Chem Asian J 2014; 9:2527-33. [DOI: 10.1002/asia.201402331] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Indexed: 12/13/2022]
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41
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Mäde V, Els-Heindl S, Beck-Sickinger AG. Automated solid-phase peptide synthesis to obtain therapeutic peptides. Beilstein J Org Chem 2014; 10:1197-212. [PMID: 24991269 PMCID: PMC4077397 DOI: 10.3762/bjoc.10.118] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 04/16/2014] [Indexed: 12/17/2022] Open
Abstract
The great versatility and the inherent high affinities of peptides for their respective targets have led to tremendous progress for therapeutic applications in the last years. In order to increase the drugability of these frequently unstable and rapidly cleared molecules, chemical modifications are of great interest. Automated solid-phase peptide synthesis (SPPS) offers a suitable technology to produce chemically engineered peptides. This review concentrates on the application of SPPS by Fmoc/t-Bu protecting-group strategy, which is most commonly used. Critical issues and suggestions for the synthesis are covered. The development of automated methods from conventional to essentially improved microwave-assisted instruments is discussed. In order to improve pharmacokinetic properties of peptides, lipidation and PEGylation are described as covalent conjugation methods, which can be applied by a combination of automated and manual synthesis approaches. The synthesis and application of SPPS is described for neuropeptide Y receptor analogs as an example for bioactive hormones. The applied strategies represent innovative and potent methods for the development of novel peptide drug candidates that can be manufactured with optimized automated synthesis technologies.
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Affiliation(s)
- Veronika Mäde
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Universität Leipzig, Brüderstraße 34, D-04103 Leipzig, Germany
| | - Sylvia Els-Heindl
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Universität Leipzig, Brüderstraße 34, D-04103 Leipzig, Germany
| | - Annette G Beck-Sickinger
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Universität Leipzig, Brüderstraße 34, D-04103 Leipzig, Germany
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42
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Tsunemi A, Ueno T, Fukuda N, Watanabe T, Tahira K, Haketa A, Hatanaka Y, Tanaka S, Matsumoto T, Matsumoto Y, Nagase H, Soma M. A novel gene regulator, pyrrole-imidazole polyamide targeting ABCA1 gene increases cholesterol efflux from macrophages and plasma HDL concentration. J Mol Med (Berl) 2014; 92:509-21. [PMID: 24463557 DOI: 10.1007/s00109-013-1118-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 11/29/2013] [Accepted: 12/16/2013] [Indexed: 01/08/2023]
Abstract
UNLABELLED Pyrrole-imidazole (PI) polyamides are nuclease-resistant novel compounds that inhibit transcription factors by binding to the minor groove of DNA. A PI polyamide that targets mouse ABCA1 and increases ABCA1 gene expression was designed and evaluated as an agent to increase plasma HDL concentration. A PI polyamide was designed to bind the activator protein-2 binding site of the mouse ABCA1 promoter. The effect of this PI polyamide on ABCA1 expression was evaluated by real-time RT-PCR and Western blotting using RAW264 cells. In vivo effects of this polyamide on ABCA1 gene expression and plasma HDL level were examined in C57B6 mice. One milligram per kilogram of body weight of PI polyamide was injected via the tail veins every 2 days for 1 week, and plasma lipid profiles were evaluated. PI polyamide showed a specific binding to the target DNA in gel mobility shift assay. Treatment of RAW264 cells with 1.0 μM PI polyamide significantly increased ABCA1 mRNA expression. PI polyamide also significantly increased apolipoprotein AI-mediated HDL biogenesis in RAW264 cells. Cellular cholesterol efflux mediated by apolipoprotein AI was significantly increased by the PI polyamide treatment. PI polyamide significantly increased expression of ABCA1 mRNA in the liver of C57B6 mice. Plasma HDL concentration was increased by PI polyamide administration. All of the HDL sub-fractions showed a tendency to increase after PI polyamide administration. The designed PI polyamide that targeted ABCA1 successfully increased ABCA1 expression and HDL biogenesis. This novel gene-regulating agent is promising as a useful compound to increase plasma HDL concentration. KEY MESSAGES A novel pyrrole-imidazole (PI) polyamide binds to ABCA1. PI polyamide interfered with binding of AP-2ɑ protein to the ABCA1 gene promoter. PI polyamide inhibited the AP-2ɑ-mediated reduction of ABCA1 gene and protein expression. PI polyamide increased ABCA1 protein and apolipoprotein AI mediated HDL biogenesis. PI polyamide is a new gene regulator for the prevention of atherosclerotic diseases.
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Affiliation(s)
- Akiko Tsunemi
- Department of Medicine, Division of Nephrology, Hypertension and Endocrinology, Nihon University School of Medicine, 30-1 Oyaguchi-kami, Itabashi, Tokyo, Japan
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43
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Taylor RD, Asamitsu S, Takenaka T, Yamamoto M, Hashiya K, Kawamoto Y, Bando T, Nagase H, Sugiyama H. Sequence-Specific DNA Alkylation Targeting for Kras Codon 13 Mutation by Pyrrole-Imidazole Polyamideseco-CBI Conjugates. Chemistry 2013; 20:1310-7. [DOI: 10.1002/chem.201303295] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 10/31/2013] [Indexed: 12/13/2022]
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44
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Taladriz-Sender A, Vicent C. Synthesis of cationic glyco-oligoamide for DNA–carbohydrate interaction studies. Supramol Chem 2013. [DOI: 10.1080/10610278.2013.814776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Andrea Taladriz-Sender
- Departamento de Síntesis, Estructura y Propiedades de los Compuestos Orgánicos (SEPCO), Instituto de Química Orgánica General, CSIC, C/Juan de la Cierva 3, 28006 Madrid, Spain
| | - Cristina Vicent
- Departamento de Síntesis, Estructura y Propiedades de los Compuestos Orgánicos (SEPCO), Instituto de Química Orgánica General, CSIC, C/Juan de la Cierva 3, 28006 Madrid, Spain
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45
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Blackledge MS, Melander C. Programmable DNA-binding small molecules. Bioorg Med Chem 2013; 21:6101-14. [PMID: 23665141 DOI: 10.1016/j.bmc.2013.04.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/29/2013] [Accepted: 04/05/2013] [Indexed: 10/26/2022]
Abstract
Aberrant gene expression is responsible for a myriad of human diseases from infectious diseases to cancer. Precise regulation of these genes via specific interactions with the DNA double helix could pave the way for novel therapeutics. Pyrrole-imidazole polyamides are small molecules capable of binding to pre-determined DNA sequences up to 16 base pairs with affinity and specificity comparable to natural transcription factors. In the three decades since their development, great strides have been made relating to synthetic accessibility and improved sequence specificity and binding affinity. This perspective presents a brief history of early seminal developments in the field and highlights recent reports of the utility of polyamides as both genetic modulators and molecular probes.
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Affiliation(s)
- Meghan S Blackledge
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8024, United States
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46
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Murphy NS, Prabhakaran P, Azzarito V, Plante JP, Hardie MJ, Kilner CA, Warriner SL, Wilson AJ. Solid-phase methodology for synthesis of O-alkylated aromatic oligoamide inhibitors of α-helix-mediated protein-protein interactions. Chemistry 2013; 19:5546-50. [PMID: 23508712 PMCID: PMC3743211 DOI: 10.1002/chem.201204098] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Indexed: 01/18/2023]
Abstract
Rapid access to rigid rods: A method is described for the synthesis of 3-O-alkylated aromatic oligobenzamide foldamers that could be used for assembly of libraries of α-helix mimetic inhibitors of protein-protein interactions (see scheme; Fmoc=9-fluorenylmethoxycarbonyl).
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Affiliation(s)
- Natasha S Murphy
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, UK
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47
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Xu X, Zavalij PY, Hu W, Doyle MP. Vinylogous reactivity of enol diazoacetates with donor-acceptor substituted hydrazones. Synthesis of substituted pyrazole derivatives. J Org Chem 2013; 78:1583-8. [PMID: 23301562 DOI: 10.1021/jo302696y] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A regiospecific synthesis of multifunctional pyrazoleshas been developed from a cascade process triggered by Rh(II)-catalyzed dinitrogen extrusion from enol diazoacetates with vinylogous nucleophilic addition followed by Lewis acid catalyzed cyclization and aromatization.
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Affiliation(s)
- Xinfang Xu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
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48
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Iyer P, Srinivasan A, Singh SK, Mascara GP, Zayitova S, Sidone B, Fouquerel E, Svilar D, Sobol RW, Bobola MS, Silber JR, Gold B. Synthesis and characterization of DNA minor groove binding alkylating agents. Chem Res Toxicol 2013; 26:156-68. [PMID: 23234400 PMCID: PMC3618862 DOI: 10.1021/tx300437x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Derivatives of methyl 3-(1-methyl-5-(1-methyl-5-(propylcarbamoyl)-1H-pyrrol-3-ylcarbamoyl)-1H-pyrrol-3-ylamino)-3-oxopropane-1-sulfonate (1), a peptide-based DNA minor groove binding methylating agent, were synthesized and characterized. In all cases, the N-terminus was appended with an O-methyl sulfonate ester, while the C-terminus group was varied with nonpolar and polar side chains. In addition, the number of pyrrole rings was varied from 2 (dipeptide) to 3 (tripeptide). The ability of the different analogues to efficiently generate N3-methyladenine was demonstrated as was their selectivity for minor groove (N3-methyladenine) versus major groove (N7-methylguanine) methylation. Induced circular dichroism studies were used to measure the DNA equilibrium binding properties of the stable sulfone analogues; the tripeptide binds with affinity that is >10-fold higher than that of the dipeptide. The toxicities of the compounds were evaluated in alkA/tag glycosylase mutant E. coli and in human WT glioma cells and in cells overexpressing and under-expressing N-methylpurine-DNA glycosylase, which excises N3-methyladenine from DNA. The results show that equilibrium binding correlates with the levels of N3-methyladenine produced and cellular toxicity. The toxicity of 1 was inversely related to the expression of MPG in both the bacterial and mammalian cell lines. The enhanced toxicity parallels the reduced activation of PARP and the diminished rate of formation of aldehyde reactive sites observed in the MPG knockdown cells. It is proposed that unrepaired N3-methyladenine is toxic due to its ability to directly block DNA polymerization.
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Affiliation(s)
- Prema Iyer
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261
| | - Ajay Srinivasan
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261
| | - Sreelekha K. Singh
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261
| | - Gerard P. Mascara
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261
| | - Sevara Zayitova
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261
| | - Brian Sidone
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261
| | - Elise Fouquerel
- University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh PA 15232
| | - David Svilar
- University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh PA 15232
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261
| | - Robert W. Sobol
- University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh PA 15232
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261
- Department of Human Genetics, University of Pittsburgh 15213
| | - Michael S. Bobola
- Department of Neurological Surgery, University of Washington, Seattle, WA 98105
| | - John R. Silber
- Department of Neurological Surgery, University of Washington, Seattle, WA 98105
| | - Barry Gold
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261
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49
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Liu JY, Li QY, Jiang B, Tu SJ. Three-component domino reactions providing rapid and efficient routes to fully substituted pyrroles. RSC Adv 2013. [DOI: 10.1039/c3ra40252e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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50
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Design of a new fluorescent probe: pyrrole/imidazole hairpin polyamides with pyrene conjugation at their γ-turn. Bioorg Med Chem 2012; 21:852-5. [PMID: 23313608 DOI: 10.1016/j.bmc.2012.12.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 12/14/2012] [Accepted: 12/15/2012] [Indexed: 12/24/2022]
Abstract
Fluorophores that are conjugated with N-methylpyrrole-N-methylimidazole (Py-Im) polyamides postulates versatile applications in biological and physicochemical studies. Here, we show the design and synthesis of new types of pyrene-conjugated hairpin Py-Im polyamides (1-5). We evaluated the steady state fluorescence of the synthesized conjugates (1-5) in the presence and absence of oligodeoxynucleotides 5'-CGTATGGACTCGG-3' (ODN 1) and 5'-CCGAGTCCATACG-3' (ODN 2) and observed a distinct increase in emission at 386nm with conjugates 4 and 5. Notably, conjugate 5 that contains a β-alanine linker had a stronger binding affinity (K(D)=1.73×10(-8)M) than that of conjugate 4 (K(D)=1.74×10(-6)M). Our data suggests that Py-Im polyamides containing pyrene fluorophore with a β-alanine linker at the γ-turn NH(2) position can be developed as the competent fluorescent DNA-binding probes.
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