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Yang L, Luo L, Cai W, Chen Z, Luo X, Chen Y. Changes in carbohydrate metabolism and soil microorganisms under the stress of polyamide and polyethylene nanoplastics during rice (Oryza sativa L.) growth. Sci Total Environ 2024; 912:169183. [PMID: 38092212 DOI: 10.1016/j.scitotenv.2023.169183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/18/2024]
Abstract
Nanoplastics (NPs) presence in agricultural soils can affect plant growth and impact the quality of agricultural products. To investigate the effect of polyamide (PA) NPs and polyethylene (PE) NPs on carbohydrate metabolism and soil microorganisms during rice growth, rice seedlings were exposed to soil containing 2 g/kg of 100 nm PA or 100 nm PE powder for 33 d. The results revealed that 100 nm PE reduced shoot length and dry weight of rice by 4.14 % and 15.68 %, respectively. Analyzing the expression of hexokinase-2 (HXK), phosphofructokinase-1 (PFK), pyruvate kinase (PK) and isocitrate dehydrogenase (IDH), which are four genes related to carbohydrate metabolism, 100 nm PA decreased the expression of PFK and increased the expression of PK and IDH. 100 nm PE increased the expression of HXK, PFK, PK, and IDH. The results of soil microorganisms showed that 100 nm PA significantly effects on 3 bacterial phyla (Bacteroidota, Deinococcota, and Desulfobacterota), whereas 100 nm PE significantly effects on phylum Rozellomycota, class Umbelopsidomycetes, and an unclassified Firmicutes. Our study provides direct evidence of the negative effects of PA and PE on rice, which may be important for assessing the risk of NPs on agroecosystems.
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Affiliation(s)
- Limin Yang
- College of Life Science, Jiangxi Normal University, Jiangxi 330000, China; Institute of High Energy Physics, Chinese Academy of Sciences, China
| | - Lili Luo
- College of Life Science, Jiangxi Normal University, Jiangxi 330000, China
| | - Wenshan Cai
- College of Life Science, Jiangxi Normal University, Jiangxi 330000, China
| | - Zheng Chen
- College of Life Science, Jiangxi Normal University, Jiangxi 330000, China
| | - Xiangdong Luo
- College of Life Science, Jiangxi Normal University, Jiangxi 330000, China.
| | - Yaling Chen
- College of Life Science, Jiangxi Normal University, Jiangxi 330000, China.
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Choi JH, Kim JH. Toxic effects of sub-acute microplastic (polyamide) exposure on the accumulation, hematological, and antioxidant responses in crucian carp, Carassius carassius. Environ Toxicol Pharmacol 2023; 102:104199. [PMID: 37391052 DOI: 10.1016/j.etap.2023.104199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/26/2023] [Accepted: 06/24/2023] [Indexed: 07/02/2023]
Abstract
The purpose of this study is to investigate the impact of microplastics (MPs) on fish and to confirm the toxic effects of MPs on fish, as well as to clarify the standard indicators. MPs are present in a large amount in the aquatic environment and can have various adverse effects on aquatic animals. Crucian carp, Carassius carassius (mean weight, 23.7 ± 1.6 g; mean length, 13.9 ± 1.4 cm), were exposed to PA (Polyamide) concentrations of 0, 4, 8, 16, 32 and 64 mg/L for 2 weeks. The PA accumulation profile in C. carassius decreased from the intestine to the gill to the liver. Hematological parameters such as red blood cell (RBC) counts, hemoglobin (Hb), and hematocrit (Ht) notably decreased at high levels of PA exposure. Plasma components such as calcium, magnesium, glucose, cholesterol, total protein, aspartate aminotransferase (AST), alanine aminotransferase (ALT), and alkaline phosphatase (ALP) were significantly altered by PA exposure. The activities of superoxide dismutase (SOD), catalase (CAT), glutathione S-transferase (GST) and glutathione (GSH) of liver, gill and intestine significantly increased following PA exposure. The results of this study suggest that MP exposure affects the hematological physiology and antioxidant responses in C. carassius as well as accumulation in specific tissues.
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Affiliation(s)
- Jae-Ho Choi
- Department of Aquatic Life Medicine, Pukyong National University, Busan 608-737, the Republic of Korea
| | - Jun-Hwan Kim
- Department of Marine Life Sciences, Jeju National University, Jeju 63243, Korea.
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Han T, Lee SY. Metabolic engineering of Corynebacterium glutamicum for the high-level production of valerolactam, a nylon-5 monomer. Metab Eng 2023; 79:78-85. [PMID: 37451533 DOI: 10.1016/j.ymben.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Valerolactam (VL) is an important precursor chemical for nylon-5 and nylon 6,5. It has been produced by petroleum-based route involving harsh reaction conditions and generating toxic wastes. Here, we report the complete biosynthesis of VL by metabolically engineered Corynebacterium glutamicum overproducing L-lysine. The pathway comprising L-lysine monooxygenase (davB) and 5-aminovaleramide amidohydrolase (davA) from Pseudomonas putida, and β-alanine CoA transferase (act) from Clostridium propionicum was introduced into the C. glutamicum GA16 strain. To increase the VL flux, competitive pathways predicted from sRNA knockdown target screening were deleted. This engineered C. glutamicum strain produced VL as a major product, but still secreted significant amount of its precursor, 5-aminovaleric acid (5AVA). To circumvent this problem, putative 5AVA transporter genes were screened and engineered in the genome, thereby reuptaking 5AVA excreted. Also, multiple copies of the act gene were integrated into the genome to strengthen the conversion of 5AVA to VL. The final VL10 (pVL1) strain was constructed by enhancing glucose uptake system, which produced 9.68 g/L of VL in flask culture. Fed-batch fermentation of the VL10 (pVL1) strain produced 76.1 g/L of VL from glucose with the yield and productivity of 0.28 g/g and 0.99 g/L/h, respectively, showcasing a high potential for bio-based production of VL from renewable resources.
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Affiliation(s)
- Taehee Han
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea; KAIST Institute for the BioCentury and KAIST Institute for Artificial Intelligence, KAIST, Daejeon, 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, 34141, Daejeon, Republic of Korea.
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea; KAIST Institute for the BioCentury and KAIST Institute for Artificial Intelligence, KAIST, Daejeon, 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, 34141, Daejeon, Republic of Korea.
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Abstract
Bacteria are prime cell factories that can efficiently convert carbon and nitrogen sources into a large diversity of intracellular and extracellular biopolymers, such as polysaccharides, polyamides, polyesters, polyphosphates, extracellular DNA and proteinaceous components. Bacterial polymers have important roles in pathogenicity, and their varied chemical and material properties make them suitable for medical and industrial applications. The same biopolymers when produced by pathogenic bacteria function as major virulence factors, whereas when they are produced by non-pathogenic bacteria, they become food ingredients or biomaterials. Interdisciplinary research has shed light on the molecular mechanisms of bacterial polymer synthesis, identified new targets for antibacterial drugs and informed synthetic biology approaches to design and manufacture innovative materials. This Review summarizes the role of bacterial polymers in pathogenesis, their synthesis and their material properties as well as approaches to design cell factories for production of tailor-made bio-based materials suitable for high-value applications.
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Affiliation(s)
- M Fata Moradali
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Bernd H A Rehm
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, Australia.
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Ferrand-Drake Del Castillo G, Koenig M, Müller M, Eichhorn KJ, Stamm M, Uhlmann P, Dahlin A. Enzyme Immobilization in Polyelectrolyte Brushes: High Loading and Enhanced Activity Compared to Monolayers. Langmuir 2019; 35:3479-3489. [PMID: 30742441 DOI: 10.1021/acs.langmuir.9b00056] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Catalysis by enzymes on surfaces has many applications. However, strategies for efficient enzyme immobilization with preserved activity are still in need of further development. In this work, we investigate polyelectrolyte brushes prepared by both grafting-to and grafting-from with the aim to achieve high catalytic activity. For comparison, self-assembled monolayers that bind enzymes with the same chemical interactions are included. We use the model enzyme glucose oxidase and two kinds of polymers: anionic poly(acrylic acid) and cationic poly(diethylamino)methyl methacrylate. Surface plasmon resonance and spectroscopic ellipsometry are used for accurate quantification of surface coverage. Besides binding more enzymes, the "3D-like" brush environment enhances the specific activity compared to immobilization on self-assembled monolayers. For grafting-from brushes, multilayers of enzymes were spontaneously and irreversibly immobilized without conjugation chemistry. When the pH was between the pI of the enzyme and the p Ka of the polymer, binding was considerable (thousands of ng/cm2 or up to 50% of the polymer mass), even at physiological ionic strength. However, binding was observed also when the brushes were neutrally charged. For acidic brushes (both grafting-to and grafting-from), the activity was higher for covalent immobilization compared to noncovalent. For grafting-from brushes, a fully preserved specific activity compared to enzymes in the liquid bulk was achieved, both with covalent (acidic brush) and noncovalent (basic brush) immobilization. Catalytic activity of hundreds of pmol cm-2 s-1 was easily obtained for polybasic brushes only tens of nanometers in dry thickness. This study provides new insights for designing functional interfaces based on enzymatic catalysis.
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Affiliation(s)
| | - Meike Koenig
- Leibniz Institute of Polymer Research Dresden , Hohe Str. 6 , D-01069 Dresden , Germany
| | - Martin Müller
- Leibniz Institute of Polymer Research Dresden , Hohe Str. 6 , D-01069 Dresden , Germany
- Technische Universität Dresden, Physical Chemistry of Polymer Materials, Dresden , Germany
| | - Klaus-Jochen Eichhorn
- Leibniz Institute of Polymer Research Dresden , Hohe Str. 6 , D-01069 Dresden , Germany
| | - Manfred Stamm
- Leibniz Institute of Polymer Research Dresden , Hohe Str. 6 , D-01069 Dresden , Germany
- Technische Universität Dresden, Physical Chemistry of Polymer Materials, Dresden , Germany
| | - Petra Uhlmann
- Leibniz Institute of Polymer Research Dresden , Hohe Str. 6 , D-01069 Dresden , Germany
- Department of Chemistry , University of Nebraska-Lincoln , Hamilton Hall, 639 North 12th Street , Lincoln , Nebraska 68588 , United States
| | - Andreas Dahlin
- Department of Chemistry and Chemical Engineering , Chalmers University of Technology , 41296 Göteborg , Sweden
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Kyselka J, Bleha R, Dragoun M, Bialasová K, Horáčková Š, Schätz M, Sluková M, Filip V, Synytsya A. Antifungal Polyamides of Hydroxycinnamic Acids from Sunflower Bee Pollen. J Agric Food Chem 2018; 66:11018-11026. [PMID: 30296072 DOI: 10.1021/acs.jafc.8b03976] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The aim of the bioassay-guided fractionation was the selection of the most potent group of compounds responsible for the protection of sunflower bee pollen grains. Synthesis of prospective antifungal polyamides of hydroxycinnamic acids was based on previous structural elucidation of ethanol soluble fraction by 1H,1H-PFG-COSY, 1H,13C-HSQC, FT-IR, FT-Raman, and LC-MS experiments. The main compounds found were tri- p-coumaroylspermidines accompanied by other HCAA of spermidine and putrescine. Several model HCAA derivatives were prepared to test their antifungal activity against widespread spoilage fungi ( A. niger 42 CCM 8189, F. culmorum DMF 0103, and P. verrucosum DMF 0023). A. niger CCM 8189 and F. culmorum DMF 0103 exhibited higher resistance to the antifungal effects of hydroxycinnamic acid amides, whereas P. verrucosum DMF 0023 was the most sensitive strain. It has been discovered the effect of HCAA polarity on the role of secondary metabolites in the microbial protection of pollen grains. The combination of bioassay-guided fractionation, structural elucidation, selection of prospective compounds, and their synthesis to determine their antifungal properties could be considered as an original approach.
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Olden BR, Cheng Y, Yu JL, Pun SH. Cationic polymers for non-viral gene delivery to human T cells. J Control Release 2018; 282:140-147. [PMID: 29518467 PMCID: PMC6008197 DOI: 10.1016/j.jconrel.2018.02.043] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/16/2018] [Accepted: 02/28/2018] [Indexed: 12/20/2022]
Abstract
The clinical success of chimeric antigen receptor (CAR) T cell immunotherapy in treating multiple blood cancers has created a need for efficient methods of ex vivo gene delivery to primary human T cells for cell engineering. Here, we synthesize and evaluate a panel of cationic polymers for gene delivery to both cultured and primary human T cells. We show that a subset of comb- and sunflower-shaped pHEMA-g-pDMAEMA polymers can mediate transfection with efficiencies up to 50% in the Jurkat human T cell line with minimal concomitant toxicity (>90% viability). We then optimize primary human T cell transfection conditions including activation time, cell density, DNA dose, culture media, and cytokine treatment. We demonstrate transfection of both CD4+ and CD8+ primary human T cells with messenger RNA and plasmid DNA at efficiencies up to 25 and 18%, respectively, with similarly high viability.
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Affiliation(s)
- Brynn R Olden
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98195, USA
| | - Yilong Cheng
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98195, USA
| | - Jonathan L Yu
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98195, USA
| | - Suzie H Pun
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98195, USA.
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Inoue T, Shimozato O, Matsuo N, Mori Y, Shinozaki Y, Lin J, Watanabe T, Takatori A, Koshikawa N, Ozaki T, Nagase H. Hydrophobic structure of hairpin ten-ring pyrrole-imidazole polyamides enhances tumor tissue accumulation/retention in vivo. Bioorg Med Chem 2018; 26:2337-2344. [PMID: 29622411 DOI: 10.1016/j.bmc.2018.03.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/15/2018] [Accepted: 03/17/2018] [Indexed: 11/18/2022]
Abstract
To examine the hydrophobic structure of PI polyamides on tumor accumulation in vivo, PI polyamide-fluorescein conjugates 1-5 with the distinct number of N-methylimidazole (Im) units were synthesized. There existed an inverse relationship between the Im unit number of the compounds and their hydrophobicity. Compound 1 with one Im unit and 3 with three Im units accumulated and retained preferentially in tumor tissues compared to 5 with five Im units. These results suggest the importance of a PI polyamide's primary structure, which partly contributes to its hydrophobic property, on its accumulation and/or retention in tumor tissues in vivo.
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Affiliation(s)
- Takahiro Inoue
- Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuo-ku, Chiba 260-8717, Japan
| | - Osamu Shimozato
- Laboratory of DNA Damage Signaling, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuo-ku, Chiba 260-8717, Japan.
| | - Nina Matsuo
- Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuo-ku, Chiba 260-8717, Japan
| | - Yusuke Mori
- Laboratory of DNA Damage Signaling, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuo-ku, Chiba 260-8717, Japan
| | - Yoshinao Shinozaki
- Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuo-ku, Chiba 260-8717, Japan
| | - Jason Lin
- Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuo-ku, Chiba 260-8717, Japan
| | - Takayoshi Watanabe
- Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuo-ku, Chiba 260-8717, Japan
| | - Atsushi Takatori
- Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuo-ku, Chiba 260-8717, Japan
| | - Nobuko Koshikawa
- Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuo-ku, Chiba 260-8717, Japan
| | - Toshinori Ozaki
- Laboratory of DNA Damage Signaling, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuo-ku, Chiba 260-8717, Japan
| | - Hiroki Nagase
- Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuo-ku, Chiba 260-8717, Japan
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Welden NA, Cowie PR. Degradation of common polymer ropes in a sublittoral marine environment. Mar Pollut Bull 2017; 118:248-253. [PMID: 28267994 DOI: 10.1016/j.marpolbul.2017.02.072] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/23/2017] [Accepted: 02/24/2017] [Indexed: 05/22/2023]
Abstract
Contamination by microplastic particles and fibres has been observed in sediment and animals sampled from the Firth of Clyde, West Scotland. In addition to microplastics released during clothes washing, a probable source is polymer ropes in abandoned, lost and discarded fishing and recreational sailing gear. The fragmentation of polypropylene, polyethylene, and nylon exposed to benthic conditions at 10m depth over 12months was monitored using changes in weight and tensile properties. Water temperature and light levels were continuously monitored. The degree of biofouling was measured using chlorophyll a, the weight of attached macroalgae, and colonising fauna. Results indicate microplastic fibres and particles may be formed in benthic environments despite reduced photodegradation. Polypropylene, Nylon, and polyethylene lost an average of 0.39%, 1.02%, and 0.45% of their mass per month respectively. Microscope images of the rope surface revealed notable surface roughening believed to be caused by abrasion by substrate and the action of fouling organisms.
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Affiliation(s)
- Natalie A Welden
- Department of Science, Technology and Mathematics, Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom.
| | - Phillip R Cowie
- Field Studies Council Millport, Marine Parade, Millport, Isle of Cumbrae KA28 0EG, United Kingdom
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Szymanowski F, Hugo AA, Alves P, Simões PN, Gómez-Zavaglia A, Pérez PF. Endocytosis and intracellular traffic of cholesterol-PDMAEMA liposome complexes in human epithelial-like cells. Colloids Surf B Biointerfaces 2017; 156:38-43. [PMID: 28500977 DOI: 10.1016/j.colsurfb.2017.04.058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/04/2017] [Accepted: 04/29/2017] [Indexed: 12/22/2022]
Abstract
Liposomes are generally used as delivery systems, as they are capable of encapsulating a wide variety of molecules (i.e. plasmids, recombinant proteins, therapeutic drugs). However, liposomal drug delivery have to fulfill different requirements, such as the effective internalization by the target cells and avoidance of the degradative activity of the intracellular compartments. The use of polymer lipid complexes (PLCs), by including different polymers in the liposome formulation, could improve internalization and intracellular release of drugs. The aim of the present work is to study the mechanisms of cellular uptaking and the intracellular trafficking of PLCs formed with cholesterol-poly(2-(dimethylamino)ethyl methacrylate) CHO-PDMAEMA and lecithin (LC CHO-PD). Calcein-loaded liposomes were used to determine cellular uptake and intracellular localization by flow cytometry and confocal microscopy. Incorporation of CHO-PDMAEMA to lecithin liposomes enhanced the internalization capacity of PLCs. Internalization of PLCs by human epithelial-like cells (HEK-293) diminished at 4°C, suggesting uptake by endocytosis. PLCs showed no co-localization with acidic compartments after internalization. Experiments with endocytosis inhibitors and co-localization of liposomes and albumin, suggested the caveolae endocytic pathway as the most probable route for intracellular trafficking of PLCs. In this work, we demonstrated an efficient uptake of LC CHO-PDs by human epithelial-like cells (HEK-293) through the non-degradative caveolae endocytic pathway. The mode of internalization and the intracellular fate of liposomes under study, suggest a promising use of LC CHO-PDs as drug delivery systems.
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Affiliation(s)
- F Szymanowski
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos (CIDCA,-CCT-CONICET La Plata), 47 y 116 (s/n) B1900AJI. La Plata, Argentina
| | - A A Hugo
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos (CIDCA,-CCT-CONICET La Plata), 47 y 116 (s/n) B1900AJI. La Plata, Argentina
| | - P Alves
- Department of Chemical Engineering, University of Coimbra, P-3030-790 Coimbra, Portugal
| | - P N Simões
- Department of Chemical Engineering, University of Coimbra, P-3030-790 Coimbra, Portugal
| | - A Gómez-Zavaglia
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos (CIDCA,-CCT-CONICET La Plata), 47 y 116 (s/n) B1900AJI. La Plata, Argentina
| | - Pablo F Pérez
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos (CIDCA,-CCT-CONICET La Plata), 47 y 116 (s/n) B1900AJI. La Plata, Argentina; Cátedra de Microbiología, Facultad de Ciencias Exactas (FCE), UNLP, 47 y 115 (s/n) 1900 La Plata, Argentina.
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Blarer P, Burkhardt-Holm P. Microplastics affect assimilation efficiency in the freshwater amphipod Gammarus fossarum. Environ Sci Pollut Res Int 2016; 23:23522-23532. [PMID: 27614640 DOI: 10.1007/s11356-016-7584-2] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 09/02/2016] [Indexed: 05/20/2023]
Abstract
An important issue in assessing microplastics is whether this newly emerging type of pollution affects freshwater invertebrates. This study was designed to examine the interactions between the amphipod Gammarus fossarum and two types of microplastics. To determine the ingestion and egestion of polyamide (PA) fibres (500 × 20 μm), amphipods were exposed to four concentrations (100, 540, 2680, 13,380 PA fibres cm-2 base area of glass beakers) and four exposure times (0.5, 2, 8, 32 h) as well as four post-exposure times (1, 2, 4, 16 h). We demonstrate a positive correlation between concentration and ingestion of PA fibres. Fibres were found in the gut after 0.5 h of exposure. Egestion was rapid and the digestive tract was empty 16 h after exposure ended. To investigate whether polystyrene (PS) beads (1.6 μm) can be taken up in the epithelial cells of the gut and the midgut glands, four concentrations (500, 2500, 12,500, 60,000 PS beads mL-1) were tested. Cryosections exhibited fluorescent PS beads only within the gut lumen. In a 28-day feeding experiment with both, fibres and beads, we studied the amphipod's feeding rate, assimilation efficiency and wet weight change. The exposure to PA fibres (2680 PA fibres cm-2 base area of glass beakers) significantly reduced the assimilation efficiency of the animals. While both tested polymer types are ingested and egested, PA fibres can impair the health and ecological functions of freshwater amphipods under continuous exposure.
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Affiliation(s)
- Pascal Blarer
- Man-Society-Environment (Programme MGU), Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Patricia Burkhardt-Holm
- Man-Society-Environment (Programme MGU), Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
- Department of Biological Sciences, University of Alberta, Edmonton, Canada.
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12
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Patel S, Chueng STD, Yin PT, Dardir K, Song Z, Pasquale N, Kwan K, Sugiyama H, Lee KB. Induction of stem-cell-derived functional neurons by NanoScript-based gene repression. Angew Chem Int Ed Engl 2015; 54:11983-8. [PMID: 26292201 PMCID: PMC5568028 DOI: 10.1002/anie.201504902] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Indexed: 01/22/2023]
Abstract
Even though gene repression is a powerful approach to exogenously regulate cellular behavior, developing a platform to effectively repress targeted genes, especially for stem-cell applications, remains elusive. Herein, we introduce a nanomaterial-based platform that is capable of mimicking the function of transcription repressor proteins to downregulate gene expression at the transcriptional level for enhancing stem-cell differentiation. We developed the "NanoScript" platform by integrating multiple gene repression molecules with a nanoparticle. First, we show a proof-of-concept demonstration using a GFP-specific NanoScript to knockdown GFP expression in neural stem cells (NSCs-GFP). Then, we show that a Sox9-specific NanoScript can repress Sox9 expression to initiate enhanced differentiation of NSCs into functional neurons. Overall, the tunable properties and gene-knockdown capabilities of NanoScript enables its utilization for gene-repression applications in stem cell biology.
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Affiliation(s)
- Sahishnu Patel
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 (USA) http://kblee.rutgers.edu/
| | - Sy-Tsong Dean Chueng
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 (USA) http://kblee.rutgers.edu/
| | - Perry T Yin
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 (USA)
| | - Kholud Dardir
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 (USA) http://kblee.rutgers.edu/
| | - Zhichao Song
- Department of Cell Biology & Neuroscience, W. M. Keck Center for Collaborative Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 (USA)
| | - Nicholas Pasquale
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 (USA) http://kblee.rutgers.edu/
| | - Kelvin Kwan
- Department of Cell Biology & Neuroscience, W. M. Keck Center for Collaborative Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 (USA)
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, 606-8501 (Japan)
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 (USA) http://kblee.rutgers.edu/.
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 (USA).
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13
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Hovakeemian SG, Liu R, Gellman SH, Heerklotz H. Correlating antimicrobial activity and model membrane leakage induced by nylon-3 polymers and detergents. Soft Matter 2015; 11:6840-51. [PMID: 26234884 PMCID: PMC4666704 DOI: 10.1039/c5sm01521a] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Most antimicrobial peptides act upon target microorganisms by permeabilizing their membranes. The mode of action is often assessed by vesicle leakage experiments that use model membranes, with the assumption that biological activity correlates with the permeabilization of the lipid bilayer. The current work aims to extend the interpretation of vesicle leakage results and examine the correlation between vesicle leakage and antimicrobial activity. To this end, we used a lifetime-based leakage assay with calcein-loaded vesicles to study the membrane permeabilizing properties of a novel antifungal polymer poly-NM, two of its analogs, and a series of detergents. In conjunction, the biological activities of these compounds against Candida albicans were assessed and correlated with data from vesicle leakage. Poly-NM induces all-or-none leakage in polar yeast lipid vesicles at the polymer's MIC, 3 μg mL(-1). At this and higher concentrations, complete leakage after an initial lag time was observed. Concerted activity tests imply that this polymer acts independently of the detergent octyl glucoside (OG) for both vesicle leakage and activity against C. albicans spheroplasts. In addition, poly-NM was found to have negligible activity against zwitterionic vesicles and red blood cells. Our results provide a consistent, detailed picture of the mode of action of poly-NM: this polymer induces membrane leakage by electrostatic lipid clustering. In contrast, poly-MM:CO, a nylon-3 polymer comprised of both cationic and hydrophobic segments, seems to act by a different mechanism that involves membrane asymmetry stress. Vesicle leakage for this polymer is transient (limited to <100%) and graded, non-specific among zwitterionic and polar yeast lipid vesicles, additive with detergent action, and correlates poorly with biological activity. Based on these results, we conclude that comprehensive leakage experiments can provide a detailed description of the mode of action of membrane permeabilizing compounds. Without this thorough approach, it would have been logical to assume that the two nylon-3 polymers we examined act via similar mechanisms; it is surprising that their mechanisms are so distinct. Some, but not all mechanisms of vesicle permeabilization allow for antimicrobial activity.
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14
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Kirmair L, Seiler DL, Skerra A. Stability engineering of the Geobacillus stearothermophilus alcohol dehydrogenase and application for the synthesis of a polyamide 12 precursor. Appl Microbiol Biotechnol 2015; 99:10501-13. [PMID: 26329849 DOI: 10.1007/s00253-015-6930-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 08/05/2015] [Accepted: 08/08/2015] [Indexed: 10/23/2022]
Abstract
The thermostable NAD(+)-dependent alcohol dehydrogenase from Geobacillus stearothermophilus (BsADH) was exploited with regard to the biocatalytic synthesis of ω-oxo lauric acid methyl ester (OLAMe), a key intermediate for biobased polyamide 12 production, from the corresponding long-chain alcohol. Recombinant BsADH was produced in Escherichia coli as a homogeneous tetrameric enzyme and showed high activity towards the industrially relevant substrate ω-hydroxy lauric acid methyl ester (HLAMe) with K M = 86 μM and 44 U mg(-1). The equilibrium constant for HLAMe oxidation to the aldehyde (OLAMe) with NAD(+) was determined as 2.16 × 10(-3) from the kinetic parameters of the BsADH-catalyzed forward and reverse reactions. Since BsADH displayed limited stability under oxidizing conditions, the predominant oxidation-prone residue Cys257 was mutated to Leu based on sequence homology with related enzymes and computational simulation. This substitution resulted in an improved BsADH variant exhibiting prolonged stability and an elevated inactivation temperature. Semi-preparative biocatalysis at 60 °C using the stabilized enzyme, employing butyraldehyde for in situ cofactor regeneration with only catalytic amounts of NAD(+), yielded up to 23 % conversion of HLAMe to OLAMe after 30 min. In contrast to other oxidoreductases, no overoxidation to the dodecanoic diacid monomethyl ester was detected. Thus, the mutated BsADH offers a promising biocatalyst for the selective oxidation of fatty alcohols to yield intermediates for industrial polymer production.
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Affiliation(s)
- Ludwig Kirmair
- Munich Center for Integrated Protein Science (CiPSM) and Lehrstuhl für Biologische Chemie, Technische Universität München, 85350, Freising-Weihenstephan, Germany
| | - Daniel Leonard Seiler
- Munich Center for Integrated Protein Science (CiPSM) and Lehrstuhl für Biologische Chemie, Technische Universität München, 85350, Freising-Weihenstephan, Germany
| | - Arne Skerra
- Munich Center for Integrated Protein Science (CiPSM) and Lehrstuhl für Biologische Chemie, Technische Universität München, 85350, Freising-Weihenstephan, Germany.
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15
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Rydz J, Sikorska W, Kyulavska M, Christova D. Polyester-based (bio)degradable polymers as environmentally friendly materials for sustainable development. Int J Mol Sci 2014; 16:564-96. [PMID: 25551604 PMCID: PMC4307263 DOI: 10.3390/ijms16010564] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/11/2014] [Indexed: 11/16/2022] Open
Abstract
This review focuses on the polyesters such as polylactide and polyhydroxyalkonoates, as well as polyamides produced from renewable resources, which are currently among the most promising (bio)degradable polymers. Synthetic pathways, favourable properties and utilisation (most important applications) of these attractive polymer families are outlined. Environmental impact and in particular (bio)degradation of aliphatic polyesters, polyamides and related copolymer structures are described in view of the potential applications in various fields.
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Affiliation(s)
- Joanna Rydz
- Bulgarian Academy of Sciences, Institute of Polymers, Acad. Georgi Bonchev St., Bl. 103A, Sofia 1113, Bulgaria.
| | - Wanda Sikorska
- Polish Academy of Sciences, Centre of Polymer and Carbon Materials, 34 M. Curie-Sklodowska St., Zabrze 41-800, Poland.
| | - Mariya Kyulavska
- Bulgarian Academy of Sciences, Institute of Polymers, Acad. Georgi Bonchev St., Bl. 103A, Sofia 1113, Bulgaria.
| | - Darinka Christova
- Bulgarian Academy of Sciences, Institute of Polymers, Acad. Georgi Bonchev St., Bl. 103A, Sofia 1113, Bulgaria.
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16
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Nagai K, Yasuhira K, Tanaka Y, Kato DI, Takeo M, Higuchi Y, Negoro S, Shibata N. Crystallization and X-ray diffraction analysis of nylon hydrolase (NylC) from Arthrobacter sp. KI72. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1151-4. [PMID: 24100570 PMCID: PMC3792678 DOI: 10.1107/s1744309113024263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/30/2013] [Indexed: 11/10/2022]
Abstract
Nylon hydrolase (NylC) encoded by Arthrobacter plasmid pOAD2 (NylCp2) was expressed in Escherichia coli JM109 and purified by ammonium sulfate fractionation, anion-exchange column chromatography and gel-filtration chromatography. NylCp2 was crystallized by the sitting-drop vapour-diffusion method with ammonium sulfate as a precipitant in 0.1 M HEPES buffer pH 7.5 containing 0.2 M NaCl and 25% glycerol. Diffraction data were collected from the native crystal to a resolution of 1.60 Å. The obtained crystal was spindle shaped and belonged to the C-centred orthorhombic space group C2221, with unit-cell parameters a=70.84, b=144.90, c=129.05 Å. A rotation and translation search gave one clear solution containing two molecules per asymmetric unit.
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Affiliation(s)
- Keisuke Nagai
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Kengo Yasuhira
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Yusuke Tanaka
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Dai-ichiro Kato
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Masahiro Takeo
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Yoshiki Higuchi
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5248, Japan
| | - Seiji Negoro
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Naoki Shibata
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5248, Japan
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17
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Abstract
Biogenic polyamines are essential for cell growth and differentiation, while polyamine analogues exert antitumor activity in multiple experimental model systems, including breast and lung cancer. Dendrimers are widely used for drug delivery in vitro and in vivo. We report the bindings of biogenic polyamines, spermine (spm), and spermidine (spmd), and their synthetic analogues, 3,7,11,15-tetrazaheptadecane.4HCl (BE-333) and 3,7,11,15,19-pentazahenicosane.5HCl (BE-3333) to dendrimers of different compositions, mPEG-PAMAM (G3), mPEG-PAMAM (G4) and PAMAM (G4). FTIR and UV-visible spectroscopic methods as well as molecular modeling were used to analyze polyamine binding mode, the binding constant and the effects of polyamine complexation on dendrimer stability and conformation. Structural analysis showed that polyamines bound dendrimers through both hydrophobic and hydrophilic contacts with overall binding constants of K(spm-mPEG-G3) = 7.6 × 10(4) M(-1), K(spm-mPEG-PAMAM-G4) = 4.6 × 10(4) M(-1), K(spm-PAMAM-G4) = 6.6 × 10(4) M(-1), K(spmd-mPEG-G3) = 1.0 × 10(5) M(-1), K(spmd-mPEG-PAMAM-G4) = 5.5 × 10(4) M(-1), K(spmd-PAMAM-G4) = 9.2 × 10(4) M(-1), K(BE-333-mPEG-G3) = 4.2 × 10(4) M(-1), K(Be-333-mPEG-PAMAM-G4) = 3.2 × 10(4) M(-1), K(BE-333-PAMAM-G4) = 3.6 × 10(4) M(-1), K(BE-3333-mPEG-G3) = 2.2 × 10(4) M(-1), K(Be-3333-mPEG-PAMAM-G4) = 2.4 × 10(4) M(-1), K(BE-3333-PAMAM-G4) = 2.3 × 10(4) M(-1). Biogenic polyamines showed stronger affinity toward dendrimers than those of synthetic polyamines, while weaker interaction was observed as polyamine cationic charges increased. The free binding energies calculated from docking studies were: -3.2 (spermine), -3.5 (spermidine) and -3.03 (BE-3333) kcal/mol, with the following order of binding affinity: spermidine-PAMAM-G-4>spermine-PAMMAM-G4>BE-3333-PAMAM-G4 consistent with spectroscopic data. Our results suggest that dendrimers can act as carrier vehicles for delivering antitumor polyamine analogues to target tissues.
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Affiliation(s)
- Jean-Sebastian Mandeville
- Département de Chimie-Biologie, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Phillipe Bourassa
- Département de Chimie-Biologie, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Thekkumkattil John Thomas
- Department of Medicine, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
- The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Heidar-Ali Tajmir-Riahi
- Département de Chimie-Biologie, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
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18
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Raskatov JA, Meier JL, Puckett JW, Yang F, Ramakrishnan P, Dervan PB. Modulation of NF-κB-dependent gene transcription using programmable DNA minor groove binders. Proc Natl Acad Sci U S A 2012; 109:1023-8. [PMID: 22203967 PMCID: PMC3268328 DOI: 10.1073/pnas.1118506109] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Nuclear factor κB (NF-κB) is a transcription factor that regulates various aspects of immune response, cell death, and differentiation as well as cancer. In this study we introduce the Py-Im polyamide 1 that binds preferentially to the sequences 5'-WGGWWW-3' and 5'GGGWWW-3'. The compound is capable of binding to κB sites and reducing the expression of various NF-κB-driven genes including IL6 and IL8 by qRT-PCR. Chromatin immunoprecipitation experiments demonstrate a reduction of p65 occupancy within the proximal promoters of those genes. Genome-wide expression analysis by RNA-seq compares the DNA-binding polyamide with the well-characterized NF-κB inhibitor PS1145, identifies overlaps and differences in affected gene groups, and shows that both affect comparable numbers of TNF-α-inducible genes. Inhibition of NF-κB DNA binding via direct displacement of the transcription factor is a potential alternative to the existing antagonists.
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Affiliation(s)
| | | | | | - Fei Yang
- Division of Chemistry and Chemical Engineering and
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19
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Zhang Y, Sicot G, Cui X, Vogel M, Wuertzer CA, Lezon-Geyda K, Wheeler J, Harki DA, Muzikar KA, Stolper DA, Dervan PB, Perkins AS. Targeting a DNA binding motif of the EVI1 protein by a pyrrole-imidazole polyamide. Biochemistry 2011; 50:10431-41. [PMID: 22039883 PMCID: PMC3619939 DOI: 10.1021/bi200962u] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The zinc finger protein EVI1 is causally associated with acute myeloid leukemogenesis, and inhibition of its function with a small molecule therapeutic may provide effective therapy for EVI1-expressing leukemias. In this paper we describe the development of a pyrrole-imidazole polyamide to specifically block EVI1 binding to DNA. We first identify essential domains for leukemogenesis through structure-function studies on both EVI1 and the t(3;21)(q26;q22)-derived RUNX1-MDS1-EVI1 (RME) protein, which revealed that DNA binding to the cognate motif GACAAGATA via the first of two zinc finger domains (ZF1, encompassing fingers 1-7) is essential transforming activity. To inhibit DNA binding via ZF1, we synthesized a pyrrole-imidazole polyamide 1, designed to bind to a subsite within the GACAAGATA motif and thereby block EVI1 binding. DNase I footprinting and electromobility shift assays revealed a specific and high affinity interaction between polyamide 1 and the GACAAGATA motif. In an in vivo CAT reporter assay using NIH-3T3-derived cell line with a chromosome-embedded tet-inducible EVI1-VP16 as well as an EVI1-responsive reporter, polyamide 1 completely blocked EVI1-responsive reporter activity. Growth of a leukemic cell line bearing overexpressed EVI1 was also inhibited by treatment with polyamide 1, while a control cell line lacking EVI1 was not. Finally, colony formation by RME was attenuated by polyamide 1 in a serial replating assay. These studies provide evidence that a cell permeable small molecule may effectively block the activity of a leukemogenic transcription factor and provide a valuable tool to dissect critical functions of EVI1 in leukemogenesis.
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Affiliation(s)
- Yi Zhang
- Department of Pathology and Lab Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Géraldine Sicot
- Department of Pathology and Lab Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Xiaohui Cui
- Department of Pathology and Lab Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Marion Vogel
- Department of Pathology and Lab Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Charles A. Wuertzer
- Department of Pathology and Lab Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Kimberly Lezon-Geyda
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06510, United States
| | - John Wheeler
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06510, United States
| | - Daniel A. Harki
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Katy A. Muzikar
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | | | - Peter B. Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Archibald S. Perkins
- Department of Pathology and Lab Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
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20
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Sekowski S, Buczkowski A, Palecz B, Gabryelak T. Interaction of polyamidoamine (PAMAM) succinamic acid dendrimers generation 4 with human serum albumin. Spectrochim Acta A Mol Biomol Spectrosc 2011; 81:706-710. [PMID: 21788153 DOI: 10.1016/j.saa.2011.07.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 05/30/2011] [Accepted: 07/03/2011] [Indexed: 05/31/2023]
Abstract
Dendrimers, a relatively new group of highly branched three dimensional polymers, are intensively investigated to use them in biomedical and physicochemical sciences. Their specific architecture gives them the ability to interact with many different types of molecules. In our studies the interaction between PAMAM succinamic acid dendrimers generation 4 (PAMAM-SAH G4) and human serum albumin (HSA) was examined. Experiments showed that a single molecule of a HSA can bind approximately 6 particles of dendrimers. The fluorescence studies demonstrated that dendrimers lead to a decrease in protein fluorescence but changes in fluorescence anisotropy were not observed. Alterations in the spectrum of circular dichroism indicated changes in the secondary protein structure. The results clearly show that this generation of dendrimers possesses a strong ability to interact with human serum albumin.
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Affiliation(s)
- Szymon Sekowski
- Department of General Biophysics, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland.
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21
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Yasuhira K, Shibata N, Tanaka Y, Kumagai N, Tanaka Y, Nagai K, Kato DI, Takeo M, Negoro S, Higuchi Y. Crystallization and X-ray diffraction analysis of nylon-oligomer hydrolase (NylC) from Agromyces sp. KY5R. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:892-5. [PMID: 21821888 PMCID: PMC3151121 DOI: 10.1107/s1744309111022858] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 06/13/2011] [Indexed: 11/10/2022]
Abstract
6-Aminohexanoate-oligomer hydrolase (NylC) from Agromyces sp. KY5R was expressed in Escherichia coli JM109 and purified by ammonium sulfate fractionation, anion-exchange column chromatography and gel-filtration chromatography. NylC was crystallized by the sitting-drop vapour-diffusion method with sodium citrate as a precipitant in 0.1 M HEPES buffer pH 7.5 containing 0.2 M NaCl. Diffraction data were collected from native and K(2)PtCl(4)-derivative crystals to resolutions of 2.00 and 2.20 Å, respectively. The obtained crystal was plate-shaped, with an I-centred orthorhombic space group and unit-cell parameters a = 155.86, b = 214.45, c = 478.80 Å. The anomalous difference Patterson map of the K(2)PtCl(4)-derivative crystal suggested that the space group was I222 rather than I2(1)2(1)2(1).
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Affiliation(s)
- Kengo Yasuhira
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Naoki Shibata
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5248, Japan
| | - Yasuhito Tanaka
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Naoya Kumagai
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Yusuke Tanaka
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Keisuke Nagai
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Dai-ichiro Kato
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Masahiro Takeo
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Seiji Negoro
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Yoshiki Higuchi
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5248, Japan
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22
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He X, Li S, Xu M, Lin S, Zhou J, Yuan G. Investigation of non-covalent interaction of ANF promoter DNA and polyamides containing N-methylimidazole and N-methylpyrrole amino acids by electrospray ionization mass spectrometry. Rapid Commun Mass Spectrom 2011; 25:993-996. [PMID: 21416537 DOI: 10.1002/rcm.4953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 12/03/2010] [Accepted: 01/21/2011] [Indexed: 05/30/2023]
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23
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Dohm MT, Mowery BP, Czyzewski AM, Stahl SS, Gellman SH, Barron AE. Biophysical mimicry of lung surfactant protein B by random nylon-3 copolymers. J Am Chem Soc 2010; 132:7957-67. [PMID: 20481635 PMCID: PMC2981085 DOI: 10.1021/ja909734n] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Non-natural oligomers have recently shown promise as functional analogues of lung surfactant proteins B and C (SP-B and SP-C), two helical and amphiphilic proteins that are critical for normal respiration. The generation of non-natural mimics of SP-B and SP-C has previously been restricted to step-by-step, sequence-specific synthesis, which results in discrete oligomers that are intended to manifest specific structural attributes. Here we present an alternative approach to SP-B mimicry that is based on sequence-random copolymers containing cationic and lipophilic subunits. These materials, members of the nylon-3 family, are prepared by ring-opening polymerization of beta-lactams. The best of the nylon-3 polymers display promising in vitro surfactant activities in a mixed lipid film. Pulsating bubble surfactometry data indicate that films containing the most surface-active polymers attain adsorptive and dynamic-cycling properties that surpass those of discrete peptides intended to mimic SP-B. Attachment of an N-terminal octadecanoyl unit to the nylon-3 copolymers, inspired by the post-translational modifications found in SP-C, affords further improvements by reducing the percent surface area compression to reach low minimum surface tension. Cytotoxic effects of the copolymers are diminished relative to that of an SP-B-derived peptide and a peptoid-based mimic. The current study provides evidence that sequence-random copolymers can mimic the in vitro surface-active behavior of lung surfactant proteins in a mixed lipid film. These findings raise the possibility that random copolymers might be useful for developing a lung surfactant replacement, which is an attractive prospect given that such polymers are easier to prepare than are sequence-specific oligomers.
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Affiliation(s)
- Michelle T. Dohm
- Department of Chemistry, Northwestern University, 2145 N. Sheridan Rd., Evanston, Illinois 60208-3100
| | - Brendan P. Mowery
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin, 53706
| | - Ann M. Czyzewski
- Department of Chemical and Biological Engineering, Northwestern University, 2145 N. Sheridan Rd., Evanston, Illinois 60208-3100
| | - Shannon S. Stahl
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin, 53706
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin, 53706
| | - Annelise E. Barron
- Department of Chemical and Biological Engineering, Northwestern University, 2145 N. Sheridan Rd., Evanston, Illinois 60208-3100
- Department of Bioengineering, Stanford University, W300B James H. Clark Center, 318 Campus Drive, Stanford, California 94305-5440
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24
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Zhu SL, Gao PH, Li P, Jiang YY, Zhang DZ. [Advances in the chemical and biological studies of polyamides]. Yao Xue Xue Bao 2008; 43:1089-1093. [PMID: 19239025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Polyamides, containing N-methylpyrrole (Py) and N-methyl-imidazole (Im) amino acids, are synthetic oligomers programmed to read the DNA double helix in the minor groove with high affinities and sequence specificities resulting in modulation of gene expression. They are cell permeable, stable and have no cytotoxicity, which provide a promising tool of gene regulation. We describe here recent advances in the field of DNA binding polyamides, including pairing rules, specifities and affinities to DNA, synthesis methods, cellular and nuclear uptake properties, gene regulation and effectiveness in vivo. The potential problems and difficulties in future research are also discussed.
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Affiliation(s)
- Shao-Long Zhu
- Department of Pharmacology, College of Pharmacy, Second Military Medical University, Shanghai 200433, China
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25
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Abstract
The efficiency of various silver-based antimicrobial fillers (elementary silver and silver substituted materials) in polyamide (PA) toward their silver ion (Ag+) release characteristics in an aqueous medium was investigated and discussed. Anode stripping voltammetry (ASV) was used for the quantitative estimation of Ag+ release from these composites. The biocidal (Ag+) release from the composites was found to be dependent on the time of soaking in water and the nature of the filler. The long-term Ag+ release capability of the elementary silver-based PA/Ag composite is promising compared with the commercial counterparts. The silver ion release potential of polyamide composites where the silver filling was performed by using supercritical carbon dioxide (scCO2) is also discussed. The composites release Ag+ at a concentration level capable of rendering antimicrobial efficacy and proved to be active against the microbes. A good agreement exists between the Ag+ release experiments and antimicrobial test results. The observed results on the influence of the nature of the filler and crystallinity on the biocidal release and the varying long-term release properties could be helpful in the design of industrially relevant biomaterials.
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Affiliation(s)
- Radhesh Kumar
- Institute of Polymer Materials, Friedrich Alexander University, Erlangen-Nurenberg, Martensstrasse 7, 91058 Erlangen, Germany
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26
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Scherer RL, VanSaun MN, McIntyre O, Matrisian LM. Optical imaging of matrix metalloproteinase-7 activity in vivo using a proteolytic nanobeacon. Mol Imaging 2008; 7:118-131. [PMID: 19123982 PMCID: PMC2777890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Matrix metalloproteinases (MMPs) are extracellular proteolytic enzymes involved in tumor progression. We present the in vivo detection and quantitation of MMP7 activity using a specific near-infrared polymer-based proteolytic beacon, PB-M7NIR. PB-M7NIR is a pegylated polyamidoamine PAMAM-Generation 4 dendrimer core covalently coupled to a Cy5.5-labeled peptide representing a selective substrate that monitors MMP7 activity (sensor) and AF750 as an internal reference to monitor relative substrate concentration (reference). In vivo imaging of tumors expressing MMP7 had a median sensor to reference ratio 2.2-fold higher than a that of a bilateral control tumor. Ex vivo imaging of intestines of multiple intestinal neoplasia (APC Min) mice injected systemically with PB-M7NIR revealed a sixfold increase in the sensor to reference ratio in the adenomas of APC Min mice compared with control intestinal tissue or adenomas from MMP7-null Min mice. PB-M7NIR detected tumor sizes as small as 0.01 cm2, and the sensor to reference ratio was independent of tumor size. Histologic sectioning of xenograft tumors localized the proteolytic signal to the extracellular matrix; MMP7-overexpressing tumors displayed an approximately 300-fold enhancement in the sensor to reference ratio compared with nonexpressing tumor cells. In APC Min adenomas, the proteolytic signal colocalized with the endogenously expressed MMP7 protein, with sensor to reference ratios approximately sixfold greater than that of normal intestinal epithelium. PB-M7NIR provides a useful reagent for the in vivo and ex vivo quantitation and localization of MMP-selective proteolytic activity.
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Affiliation(s)
- Randy L. Scherer
- Department of Cancer Biology, Vanderbilt University, Nashville TN 37232-6840
- Department of Interdisciplinary Materials Science and Engineering, and Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville TN 37232-6840
| | - Michael N. VanSaun
- Department of Cancer Biology, Vanderbilt University, Nashville TN 37232-6840
| | - Oliver McIntyre
- Department of Cancer Biology, Vanderbilt University, Nashville TN 37232-6840
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville TN 37232-6840
| | - Lynn M. Matrisian
- Department of Cancer Biology, Vanderbilt University, Nashville TN 37232-6840
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville TN 37232-6840
- Department of Interdisciplinary Materials Science and Engineering, and Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville TN 37232-6840
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Chaubey B, Tripathi S, Désiré J, Baussanne I, Décout JL, Pandey VN. Mechanism of RNA cleavage catalyzed by sequence specific polyamide nucleic acid-neamine conjugate. Oligonucleotides 2007; 17:302-13. [PMID: 17854270 DOI: 10.1089/oli.2007.0085] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In earlier studies, we found that a conjugate of neamine-polyamide nucleic acid targeting transactivation response element of HIV-1 RNA genome (HIV-1 TAR) displayed anti-HIV-1 activity and sequence-specific cleavage of the target RNA in vitro. Here we show that both the position of conjugation of polyamide nucleic acid (PNA) on neamine and the length of the spacer are critical parameters for conferring cleavage activity to the conjugate. The conjugation of PNA via a spacer incorporating 11 atoms to the 5-position of ring I of the neamine core conferred sequence-specific RNA cleavage activity on the conjugate, while conjugation to the 4'-position of ring II abolished this activity. Similarly, 5-neamine PNA complementary to TAR sequence of HIV-1 genome (PNA(TAR)) conjugates having either a 23-atom spacer or a bulky dansyl group between PNA and the neamine core also resulted in complete loss of cleavage activity. Based on these observations, we propose a mechanism for the observed RNA cleavage catalyzed by the conjugate involving unprotonated and protonated amino groups at the 3-position of ring I and the 6'-position of ring II of the neamine core, respectively.
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Affiliation(s)
- Binay Chaubey
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, Newark, NJ 07103, USA
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28
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Yasuhira K, Tanaka Y, Shibata H, Kawashima Y, Ohara A, Kato DI, Takeo M, Negoro S. 6-Aminohexanoate oligomer hydrolases from the alkalophilic bacteria Agromyces sp. strain KY5R and Kocuria sp. strain KY2. Appl Environ Microbiol 2007; 73:7099-102. [PMID: 17827307 PMCID: PMC2074972 DOI: 10.1128/aem.00777-07] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alkalophilic, nylon oligomer-degrading strains, Agromyces sp. and Kocuria sp., were isolated from the wastewater of a nylon-6 factory and from activated sludge from a sewage disposal plant. The 6-aminohexanoate oligomer hydrolases (NylC) from the alkalophilic strains had 95.8 to 98.6% similarity to the enzyme in neutrophilic Arthrobacter sp. but had superior thermostability, activity under alkaline conditions, and affinity for nylon-related substrates, which would be advantageous for biotechnological applications.
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Affiliation(s)
- Kengo Yasuhira
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
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29
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Pintó-Marijuan M, de Agazio M, Zacchini M, Santos MA, Torné JM, Fleck I. Response of transglutaminase activity and bound putrescine to changes in light intensity under natural or controlled conditions in Quercus ilex leaves. Physiol Plant 2007; 131:159-69. [PMID: 18251934 DOI: 10.1111/j.1399-3054.2007.00939.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
In order to further study a previously observed relationship between polyamine (PA) content and changes in irradiation, we examined the level of free and bound PAs, the activity of transglutaminase (TGase, EC 2.3.2.13) and chlorophyll fluorescence in holm oak (Quercus ilex L.) leaves in response to different levels of light intensity and amount. A diurnal trend of free and bound putrescine (F-Put and B-Put, respectively) and TGase activity was observed in plants under natural conditions in the forest, with the highest value corresponding to the maximum light intensity and amount of light received by the leaves. In another set of experiments, potted Q. ilex plants in experimental fields were subjected to a range of periods of natural photosynthetic photon flux density (PPFD) by covering or not covering the whole trees. Under a natural photoperiod (uncovered leaves), B-Put content and TGase activity paralleled the diurnal PPFD pattern, reaching a maximum at the highest PPFD; prior to this maximum, free PAs showed a significant rise. Plants that were in darkness until midday and suddenly exposed to high light intensity showed enhanced TGase activity, resulting in the maximum accumulation of B-Put. The involvement of the accumulation of B-Put reflected in the changes of the B-Put/bound spermidine ratio during the photoprotective responses to high light stress in forest plants is discussed in relation to the chlorophyll fluorescence parameters observed.
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Affiliation(s)
- Marta Pintó-Marijuan
- Unitat Fisiologia Vegetal, Departament de Biologia Vegetal, Facultat Biologia, Universitat de Barcelona, Diagonal 645, E-08028 Barcelona, Spain
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30
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Abstract
Androgen receptor (AR) is essential for the growth and progression of prostate cancer in both hormone-sensitive and hormone-refractory disease. A DNA-binding polyamide that targets the consensus androgen response element binds the prostate-specific antigen (PSA) promoter androgen response element, inhibits androgen-induced expression of PSA and several other AR-regulated genes in cultured prostate cancer cells, and reduces AR occupancy at the PSA promoter and enhancer. Down-regulation of PSA by this polyamide was comparable to that produced by the synthetic antiandrogen bicalutamide (Casodex) at the same concentration. Genome-wide expression analysis reveals that a similar number of transcripts are affected by treatment with the polyamide and with bicalutamide. Direct inhibition of the AR-DNA interface by sequence-specific DNA binding small molecules could offer an alternative approach to antagonizing AR activity.
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Affiliation(s)
- Nicholas G. Nickols
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Peter B. Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
- *To whom correspondence should be addressed at:
Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Mail Code 164-30, Pasadena, CA 91125. E-mail:
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31
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Romberg B, Metselaar JM, Baranyi L, Snel CJ, Bünger R, Hennink WE, Szebeni J, Storm G. Poly(amino acid)s: Promising enzymatically degradable stealth coatings for liposomes. Int J Pharm 2007; 331:186-9. [PMID: 17145145 DOI: 10.1016/j.ijpharm.2006.11.018] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Revised: 11/03/2006] [Accepted: 11/06/2006] [Indexed: 11/29/2022]
Abstract
Poly(amino acid)s (PAAs) were evaluated as coating polymers for long-circulating liposomes. The pharmacokinetics of PAA-coated liposomes were assessed in rats. Prolonged circulation times were obtained, comparable to those reported for poly(ethylene glycol) (PEG)-liposomes. Besides, the enzymatic degradability of PAAs was studied. PAAs - in free as well as liposome-associated form - are degradable by proteases, which is beneficial for reducing the risks of accumulation in vivo. Furthermore, complement activation by PAA-liposomes was evaluated in vitro and in vivo. Like other liposome types, they appear to activate the complement system. However, a role of endotoxin contamination of the PAA-liposome formulations used cannot be excluded in our complement activation studies.
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Affiliation(s)
- Birgit Romberg
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, PO Box 80082, 3508 TB Utrecht, The Netherlands.
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32
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Heumann S, Eberl A, Pobeheim H, Liebminger S, Fischer-Colbrie G, Almansa E, Cavaco-Paulo A, Gübitz GM. New model substrates for enzymes hydrolysing polyethyleneterephthalate and polyamide fibres. ACTA ACUST UNITED AC 2006; 69:89-99. [PMID: 16624419 DOI: 10.1016/j.jbbm.2006.02.005] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 02/08/2006] [Accepted: 02/09/2006] [Indexed: 11/28/2022]
Abstract
Recently the potential of enzymes for surface hydrophilisation and/or functionalisation of polyethyleneterephthalate (PET) and polyamide (PA) has been discovered. However, there was no correlation between enzyme class/activity (e.g. esterase, lipase, cutinase) and surface hydrolysis of these polymers and consequently no simple assay to estimate this capability. Enzymes active on the model substrates bis (benzoyloxyethyl) terephthalate and adipic acid bishexyl-amide, were also capable of increasing the hydrophilicity of PET and PA. When dosed at the identical activity on 4-nitrophenyl butyrate, only enzymes from Thermobifida fusca, Aspergillus sp., Beauveria sp. and commercial enzymes (TEXAZYME PES sp5 and Lipase PS) increased the hydrophilicity of PET fibres while other esterases and lipases did not show any effect. Activity on PET correlated with the activity on the model substrate. Hydrophilicity of fibres was greatly improved based on increases in rising height of up to 4.3 cm and the relative decrease of water absorption time between control and sample of the water was up to 76%. Similarly, enzymes increasing the hydrophilicity of PA fibres such as from Nocardia sp., Beauveria sp. and F. solani hydrolysed the model substrate; however, there was no common enzyme activity (e.g. protease, esterase, amidase) which could be attributed to all these enzymes.
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Affiliation(s)
- Sonja Heumann
- Research Centre Applied Biocatalysis, Petersgasse 14, A-8010 Graz, Austria
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33
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Lin C, Zhong Z, Lok MC, Jiang X, Hennink WE, Feijen J, Engbersen JFJ. Linear poly(amido amine)s with secondary and tertiary amino groups and variable amounts of disulfide linkages: Synthesis and in vitro gene transfer properties. J Control Release 2006; 116:130-7. [PMID: 17079046 DOI: 10.1016/j.jconrel.2006.09.009] [Citation(s) in RCA: 148] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2006] [Accepted: 08/24/2006] [Indexed: 11/15/2022]
Abstract
A group of novel poly(amido amine) homo- and copolymers (PAAs) containing secondary and tertiary amine groups in their main chain and different structures in the bisacrylamide segments were synthesized and evaluated as non-viral gene delivery vectors. Among these, also the disulfide-containing cystaminebisacrylamide was employed as a (co)monomer, yielding PAAs with variable amounts of bioreducible disulfide linkages in the main chain. Michael addition the trifunctional 1-(2-aminoethyl) piperazine to equimolar amounts of the appropriate bis(acrylamide) yielded linear polymers as was elucidated by their (13)C NMR spectra. The polymers possess buffering capacities between pH 5.1 and pH 7.4 higher than branched polyethylenimine (pEI) and are able to efficiently condense DNA into nanosized (<150 nm) and positively charged complexes. Transfection experiments with COS-7 cells showed that polyplexes from PAAs with disulfide linkages give significant higher transfections than those from PAAs lacking the disulfide linkage, and XTT assays showed that these polymers are essentially non-toxic. Variation of the disulfide content revealed that polyplexes of PAA copolymers with appropriate disulfide content have largely improved biophysical properties, yielding enhanced levels of gene expression along with low toxicity. The results demonstrate that bioreducible poly(amido amine)s are a very promising class of polymers for safe and efficient gene delivery.
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Affiliation(s)
- Chao Lin
- Department of Biomedical Chemistry, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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34
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Sasek V, Vitásek J, Chromcová D, Prokopová I, Brozek J, Náhlík J. Biodegradation of synthetic polymers by composting and fungal treatment. Folia Microbiol (Praha) 2006; 51:425-30. [PMID: 17176762 DOI: 10.1007/bf02931586] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two types of copolymers--poly(ester-amide)s--by the anionic copolymerization of epsilon-caprolactam and epsilon-caprolactone, and aromatic-aliphatic copolyesters based on glycolyzed polyethylene terephthalate from used beverage bottles and epsilon-caprolactone were prepared. Biodegradation tests of these copolymers were performed by two methods, viz. composting under controlled conditions and treatment with ligninolytic fungi. Both methods resulted in degradation of the copolymers, composting being more robust. Out of fungal strains tested Inonotus hispidus degraded aromatic-aliphatic copolyesters most intensively.
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Affiliation(s)
- V Sasek
- Institute of Microbiology, Academy of Sciences of the Czech Republic, 142 20 Prague, Czechia.
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35
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Font X, Caminal G, Gabarrell X, Vicent T. Treatment of toxic industrial wastewater in fluidized and fixed-bed batch reactors with Trametes versicolor: influence of immobilisation. Environ Technol 2006; 27:845-54. [PMID: 16972380 DOI: 10.1080/09593332708618702] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
This work presents the results obtained in the treatment of industrial pulp mill wastewater (black liquor) with the white-rot fungus Trametes versicolor immobilised in nylon and polyurethane foam cubes. Reductions in colour (36%), aromatic compounds (54%) and toxicity (3.15 times reduction of the initial value) were obtained when the fungus was immobilised in nylon and good toxicity reduction (5.7-fold reduction of the initial value) when polyurethane foam was used. These results were compared with those obtained with Trametes versicolor in the form of pellets for colour and aromatic compounds (84.8% and 70.2% respectively). Correlations among different parameters have been studied. Relationships between colour and changes in the molecular weight distribution profiles, as well as a correlation between laccase production and toxicity reduction have been found. For laccase production vs. toxicity reduction a different behaviour has been observed depending on the bioreactor configuration (fixed-bed reactor with immobilised Trametes versicolor or fluidised bed reactor with pellets of Trametes versicolor).
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Affiliation(s)
- X Font
- Departament d'Enginyeria Química, Escola Tècnica Superior d'Enginyeria, Universitat Autònoma de Barcelona, 08193 - Bellaterra, Spain
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Burnett R, Melander C, Puckett JW, Son LS, Wells RD, Dervan PB, Gottesfeld JM. DNA sequence-specific polyamides alleviate transcription inhibition associated with long GAA.TTC repeats in Friedreich's ataxia. Proc Natl Acad Sci U S A 2006; 103:11497-502. [PMID: 16857735 PMCID: PMC1544198 DOI: 10.1073/pnas.0604939103] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The DNA abnormality found in 98% of Friedreich's ataxia (FRDA) patients is the unstable hyperexpansion of a GAA.TTC triplet repeat in the first intron of the frataxin gene. Expanded GAA.TTC repeats result in decreased transcription and reduced levels of frataxin protein in affected individuals. Beta-alanine-linked pyrrole-imidazole polyamides bind GAA.TTC tracts with high affinity and disrupt the intramolecular DNA.DNA-associated region of the sticky-DNA conformation formed by long GAA.TTC repeats. Fluorescent polyamide-Bodipy conjugates localize in the nucleus of a lymphoid cell line derived from a FRDA patient. The synthetic ligands increase transcription of the frataxin gene in cell culture, resulting in increased levels of frataxin protein. DNA microarray analyses indicate that a limited number of genes are significantly affected in FRDA cells. Polyamides may increase transcription by altering the DNA conformation of genes harboring long GAA.TTC repeats or by chromatin opening.
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Affiliation(s)
- Ryan Burnett
- *Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Christian Melander
- *Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - James W. Puckett
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
| | - Leslie S. Son
- Center for Genome Research, Institute for Biosciences and Technology, Texas A&M University System Health Science Center, 2121 West Holcombe Boulevard, Houston, TX 77030
| | - Robert D. Wells
- Center for Genome Research, Institute for Biosciences and Technology, Texas A&M University System Health Science Center, 2121 West Holcombe Boulevard, Houston, TX 77030
| | - Peter B. Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
| | - Joel M. Gottesfeld
- *Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
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37
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Liu Y, Deng Y, Zheng R, Zhang P, Zhai H, Zhu C. Synthesis and cellular effect of a novel conjugate of polyamide and phospholipid. Chem Pharm Bull (Tokyo) 2006; 54:832-5. [PMID: 16755053 DOI: 10.1248/cpb.54.832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In order to improve the cell penetration of polyamide and its movement toward nucleic DNA we synthesized a conjugate of polyamide and phospholipid, which showed a significantly reduced cytotoxicity and effective apoptosis when comparing with the native polyamide.
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Affiliation(s)
- Yi Liu
- Department of Applied Chemistry, Beijing Institute of Technology, 100081 Beijing, China
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38
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Blattes R, Monod C, Susbielle G, Cuvier O, Wu JH, Hsieh TS, Laemmli UK, Käs E. Displacement of D1, HP1 and topoisomerase II from satellite heterochromatin by a specific polyamide. EMBO J 2006; 25:2397-408. [PMID: 16675949 PMCID: PMC1478169 DOI: 10.1038/sj.emboj.7601125] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Accepted: 04/11/2006] [Indexed: 11/09/2022] Open
Abstract
The functions of DNA satellites of centric heterochromatin are difficult to assess with classical molecular biology tools. Using a chemical approach, we demonstrate that synthetic polyamides that specifically target AT-rich satellite repeats of Drosophila melanogaster can be used to study the function of these sequences. The P9 polyamide, which binds the X-chromosome 1.688 g/cm3 satellite III (SAT III), displaces the D1 protein. This displacement in turn results in a selective loss of HP1 and topoisomerase II from SAT III, while these proteins remain bound to the adjacent rDNA repeats and to other regions not targeted by P9. Conversely, targeting of (AAGAG)n satellite V repeats by the P31 polyamide results in the displacement of HP1 from these sequences, indicating that HP1 interactions with chromatin are sensitive to DNA-binding ligands. P9 fed to larvae suppresses the position-effect variegation phenotype of white-mottled adult flies. We propose that this effect is due to displacement of the heterochromatin proteins D1, HP1 and topoisomerase II from SAT III, hence resulting in stochastic chromatin opening and desilencing of the nearby white gene.
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Affiliation(s)
- Roxane Blattes
- Laboratoire de Biologie Moléculaire Eucaryote, UMR 5099 CNRS-Université Paul Sabatier, Toulouse Cedex, France
| | - Caroline Monod
- Laboratoire de Biologie Moléculaire Eucaryote, UMR 5099 CNRS-Université Paul Sabatier, Toulouse Cedex, France
| | - Guillaume Susbielle
- Laboratoire de Biologie Moléculaire Eucaryote, UMR 5099 CNRS-Université Paul Sabatier, Toulouse Cedex, France
| | - Olivier Cuvier
- Institut de Génétique Humaine, CNRS UPR 1142, Montpellier Cedex, France
| | - Jian-hong Wu
- Department of Biochemistry, Nanaline H Duke Building, Duke University Medical Center, Durham, NC, USA
| | - Tao-shih Hsieh
- Department of Biochemistry, Nanaline H Duke Building, Duke University Medical Center, Durham, NC, USA
| | - Ulrich K Laemmli
- Département de Biologie Moléculaire, Université de Genève, Sciences II, Geneva, Switzerland
| | - Emmanuel Käs
- Laboratoire de Biologie Moléculaire Eucaryote, UMR 5099 CNRS-Université Paul Sabatier, Toulouse Cedex, France
- LBME, UMR5099, IBCG, 118 route de Narbonne, 31062 Toulouse Cedex 9, France. Tel.: +33 561 335959; Fax: +33 561 335886; E-mail:
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39
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Mukhopadhyay R. E. coli stick to the right. Anal Chem 2005; 77:428A. [PMID: 16285142 DOI: 10.1021/ac053500p] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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40
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Abstract
Mapping and sequencing the genetic blueprint in human, mice, yeast and other model organisms has created challenges and opportunities for chemistry, biology and human medicine. An understanding of the function of each of the approximately 25,000 genes in humans, and the biological circuitry that controls these genes will be driven in part by new technologies from the world of chemistry. Many cellular events that lead to cancer and the progression of human disease represent aberrant gene expression. Small molecules that can be programmed to mimic transcription factors and bind a large repertoire of DNA sequences in the human genome would be useful tools in biology and potentially in human medicine. Polyamides are synthetic oligomers programmed to read the DNA double helix. They are cell permeable, bind chromatin and have been shown to downregulate endogenous genes in cell culture.
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Affiliation(s)
- Peter B Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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41
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Halby L, Ryabinin VA, Sinyakov AN, Boutorine AS. Functionalized head-to-head hairpin polyamides: Synthesis, double-stranded DNA-binding activity and affinity. Bioorg Med Chem Lett 2005; 15:3720-4. [PMID: 16005219 DOI: 10.1016/j.bmcl.2005.05.106] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2005] [Revised: 05/17/2005] [Accepted: 05/18/2005] [Indexed: 11/23/2022]
Abstract
A series of 4 functionalized head-to-head-linked hairpin oligo(N-methylpyrrole) carboxamides with different linkers have been synthesized. Their ability to bind double-stranded DNA and sequence specificity were compared and the apparent Kd values of their DNA complexes were determined. These compounds, particularly those with iminodiacetic linkers, revealed a high affinity for DNA (Kd = 4.5-4.8 x 10(-9) M) and sequence specific recognition of 9-10 base pairs.
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Affiliation(s)
- Ludovic Halby
- USM 0503-Régulation et Dynamique des Génomes, Muséum National d'Histoire Naturelle, Paris, France
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42
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Abstract
Biodegradable and biocompatible amphoteric poly(amido-amine) (PAA)-based hydrogels, containing carboxyl groups along with amino groups in their repeating unit, were considered as scaffolds for tissue engineering applications. These hydrogels were obtained by co-polymerising 2,2-bisacrylamidoacetic acid with 2-methylpiperazine with or without the addition of different mono-acrylamides as modifiers, and in the presence of primary bis-amines as crosslinking agents. Hybrid PAA/albumin hydrogels were also prepared. The polymerisation reaction was a Michael-type polyaddition carried out in aqueous media. The PAA hydrogels were soft and swellable materials. Cytotoxicity tests were carried out by the direct contact method with fibroblast cell lines on the hydrogels both in their native state (that is, as free bases) and as salts with acids of different strength, namely hydrochloric, sulfuric, acetic and lactic acid. This was done in order to ascertain whether counterion-specific differences in cytotoxicity existed. It was found that all the amphoteric PAA hydrogels considered were cytobiocompatible both as free bases and salts. Selected hydrogels samples underwent degradation tests under controlled conditions simulating biological environments, i.e. Dulbecco medium at pH 7.4 and 37 degrees C. All samples degraded completely and dissolved within 10 d, with the exception of hybrid PAA/albumin hydrogels that did not dissolve even after eight months. The degradation products of all samples turned to be non-cytotoxic. All these results led us to conclude that PAA-based hydrogels have a definite potential as degradable matrices for biomedical applications.
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Affiliation(s)
- Paolo Ferruti
- Dipartimento di Chimica Organica e Industriale, Università di Milano, via Venezian 21, 20133 Milano, Italy.
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43
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Affiliation(s)
- Jenifer K Lum
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, MI 48109-1055, USA
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van der Aa MAEM, Koning GA, d'Oliveira C, Oosting RS, Wilschut KJ, Hennink WE, Crommelin DJA. An NLS peptide covalently linked to linear DNA does not enhance transfection efficiency of cationic polymer based gene delivery systems. J Gene Med 2005; 7:208-17. [PMID: 15508141 DOI: 10.1002/jgm.643] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Transfection with non-viral gene delivery vectors, such as cationic polymers, generally results in low transgene expression in vivo. This is likely due to poor cytoplasmic transport and intra-nuclear DNA delivery. METHODS In this study two strategies to improve nuclear import were investigated. Linear DNA constructs with or without an NLS peptide were prepared by PCR. Alternatively, linear DNA obtained by enzymatic cleavage followed by capping of both ends with DNA-hairpins was used. An NLS peptide was attached to one of the capped ends of the linear DNA. Both biodegradable (pDMAEAppz) and non-degradable polymers (PEI or pDMAEMA) were used to complex the DNA. Several cell types, dividing and non-dividing, were transfected with the linear DNA constructs containing a SV40-derived NLS peptide. Nuclear import of the DNA constructs was studied using digitonin-permeabilized cells. RESULTS Linear DNA prepared by PCR proved not useful as it was degraded from the 3'end. Linear DNA capped with hairpins was more successful with regard to stability. However, Cells transfected with linear DNA constructs by electroporation or by using cationic polymers with linear DNA containing a NLS peptide, failed to show significantly higher luciferase expression levels when compared to cells transfected with plasmid DNA or linear DNA without an NLS peptide attached. No nuclear localization was observed in digitonin-permeabilized cells. CONCLUSION Taken together, these data demonstrate that this nuclear localisation signal when attached to DNA is neither able to improve transfection efficiency of cationic polymers nor the nuclear import of the DNA constructs.
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Affiliation(s)
- M A E M van der Aa
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, P.O. Box 80082, 3508 TB Utrecht, the Netherlands
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45
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Buchmueller KL, Staples AM, Howard CM, Horick SM, Uthe PB, Le NM, Cox KK, Nguyen B, Pacheco KAO, Wilson WD, Lee M. Extending the language of DNA molecular recognition by polyamides: unexpected influence of imidazole and pyrrole arrangement on binding affinity and specificity. J Am Chem Soc 2005; 127:742-50. [PMID: 15643900 DOI: 10.1021/ja044359p] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pyrrole (Py) and imidazole (Im) polyamides can be designed to target specific DNA sequences. The effect that the pyrrole and imidazole arrangement, plus DNA sequence, have on sequence specificity and binding affinity has been investigated using DNA melting (DeltaT(M)), circular dichroism (CD), and surface plasmon resonance (SPR) studies. SPR results obtained from a complete set of triheterocyclic polyamides show a dramatic difference in the affinity of f-ImPyIm for its cognate DNA (K(eq) = 1.9 x 10(8) M(-1)) and f-PyPyIm for its cognate DNA (K(eq) = 5.9 x 10(5) M(-1)), which could not have been anticipated prior to characterization of these compounds. Moreover, f-ImPyIm has a 10-fold greater affinity for CGCG than distamycin A has for its cognate, AATT. To understand this difference, the triamide dimers are divided into two structural groupings: central and terminal pairings. The four possible central pairings show decreasing selectivity and affinity for their respective cognate sequences: -ImPy > -PyPy- >> -PyIm- approximately -ImIm-. These results extend the language of current design motifs for polyamide sequence recognition to include the use of "words" for recognizing two adjacent base pairs, rather than "letters" for binding to single base pairs. Thus, polyamides designed to target Watson-Crick base pairs should utilize the strength of -ImPy- and -PyPy- central pairings. The f/Im and f/Py terminal groups yielded no advantage for their respective C/G or T/A base pairs. The exception is with the -ImPy- central pairing, for which f/Im has a 10-fold greater affinity for C/G than f/Py has for T/A.
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Affiliation(s)
- Karen L Buchmueller
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA
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46
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Abstract
Regulation of gene expression by transcription factors touches many aspects of eukaryotic biology, and its systematic, external control by organic molecules represents a challenge in chemistry. Here we report the design of a completely organic, nonpeptidic compound that mimics a transcription factor. The design takes advantage of the specific DNA-binding affinity of a hairpin polyamide molecule and the ability of wrenchnolol to bind to the Sur-2 subunit of human mediator complex. The hybrid compound of these two molecules activates transcription of a reporter gene in vitro in a promoter-dependent manner through simultaneous contacts with DNA and Sur-2. Our results indicate that it is possible to generate a transcription factor out of nonpeptidic components.
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Affiliation(s)
- Youngjoo Kwon
- The Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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Edayathumangalam RS, Weyermann P, Dervan PB, Gottesfeld JM, Luger K. Nucleosomes in solution exist as a mixture of twist-defect states. J Mol Biol 2005; 345:103-14. [PMID: 15567414 DOI: 10.1016/j.jmb.2004.10.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2004] [Revised: 09/29/2004] [Accepted: 10/08/2004] [Indexed: 11/19/2022]
Abstract
The 2.0 A crystal structure of a nucleosome core particle in complex with a bivalent pyrrole-imidazole polyamide reveals that this "clamp" effectively crossbraces the two gyres of the DNA superhelix, thereby stabilizing the nucleosome against dissociation. Using X-ray crystallography and footprinting techniques, we show that the clamp preferentially binds nucleosomes over free DNA, and that nucleosomal DNA exists as a mixture of multiple twist-defect intermediates in solution. The nucleosomes exist in one of two different conformations in various crystal structures that trap twist-defect intermediates, even on a strong positioning sequence. Evidence has been obtained supporting the existence of twist-defect states in nucleosomal DNA in solution that are similar to those obtained in crystal structures. Our results also substantiate the idea that twist diffusion may represent an important means of altering the accessibility of nucleosomal DNA both in the presence and in the absence of ATP-dependent chromatin-remodelling enzymes.
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48
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Pang YP. Nonbonded bivalence approach to cell-permeable molecules that target DNA sequences. Bioorg Med Chem 2005; 12:3063-8. [PMID: 15142565 DOI: 10.1016/j.bmc.2004.02.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2003] [Revised: 01/17/2004] [Accepted: 02/26/2004] [Indexed: 11/18/2022]
Abstract
Polyamides such as the natural antibiotic distamycin A can form binary or ternary complexes with B-DNA. The driving forces and advantages for forming the ternary complexes are not fully understood. The computational studies reported herein suggest that three- and four-ring polyamides have a propensity for forming the same dimer conformations in water as those in their ternary complexes. The pre-dimerization of a polyamide in water facilitates the formation of the ternary complex, making the polyamide more selective, and tighter binding to the minor groove whose minimal width is predetermined by the B-DNA sequence. Relative to the dimer tethered with covalent bonds, the smaller, monomeric polyamide available from reversible dimerization in water makes the molecule inherently more cell permeable. A nonbonded bivalence approach that dimerizes molecules by intermolecular interactions is proposed for improving affinity, selectivity, and cell permeability.
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Affiliation(s)
- Yuan-Ping Pang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA.
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Mizuta M, Terada T, Seio K, Sekine M. Properties of ferrocene-polyamide compounds as redox active DNA binding molecules toward the SNPs detection. ACTA ACUST UNITED AC 2004:237-8. [PMID: 17150566 DOI: 10.1093/nass/48.1.237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Ferrocene-polyamides having not only sequence discrimination ability but also a redox mediator were synthesized. The affinity and selectivity of these compounds for a DNA duplex having a cognate GCG sequence were investigated by CD spectroscopy. Furthermore, the binding of the ferrocene-polyamides to DNA duplexes immobilized to a gold electrode was detected by cyclic voltammetry (CV) experiments. The electrochemical studies revealed that the fully matched DNA duplex having a GCG sequence showed the largest electric current, and the introduction of a mismatch site decreased the current significantly. These results suggested the potential of the ferrocene-polyamide compounds as new electrochemical ligands for electrochemical SNPs detection.
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Affiliation(s)
- Masahiro Mizuta
- Department of Life Science, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Japan
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50
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Caldarelli S, Depecker G, Patino N, Di Giorgio A, Barouillet T, Doglio A, Condom R. Synthesis and cellular uptake of a fluorescently labeled cyclic PNA-based compound. Bioorg Med Chem Lett 2004; 14:4435-8. [PMID: 15357967 DOI: 10.1016/j.bmcl.2004.06.055] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2004] [Revised: 06/01/2004] [Accepted: 06/17/2004] [Indexed: 11/17/2022]
Abstract
A cyclic hexameric PNA-based compound labeled with fluorescein has been prepared following the liquid phase FPB strategy. Its cellular uptake, without and with electroporation, has been investigated by fluorescence microscopy.
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Affiliation(s)
- Sergio Caldarelli
- Laboratoire de Chimie Bioorganique UMR-CNRS 6001, Université de Nice-Sophia Antipolis, Parc Valrose, 06108 Cédex 2, France
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