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Samokhvalov AV, Mironova AA, Eremin SA, Zherdev AV, Dzantiev BB. Polycations as Aptamer-Binding Modulators for Sensitive Fluorescence Anisotropy Assay of Aflatoxin B1. SENSORS (BASEL, SWITZERLAND) 2024; 24:3230. [PMID: 38794084 PMCID: PMC11125339 DOI: 10.3390/s24103230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/01/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024]
Abstract
Fluorescence induced by the excitation of a fluorophore with plane-polarized light has a different polarization depending on the size of the fluorophore-containing reagent and the rate of its rotation. Based on this effect, many analytical systems have been implemented in which an analyte contained in a sample and labeled with a fluorophore (usually fluorescein) competes to bind to antibodies. Replacing antibodies in such assays with aptamers, low-cost and stable oligonucleotide receptors, is complicated because binding a fluorophore to them causes a less significant change in the polarization of emissions. This work proposes and characterizes the compounds of the reaction medium that improve analyte binding and reduce the mobility of the aptamer-fluorophore complex, providing a higher analytical signal and a lower detection limit. This study was conducted on aflatoxin B1 (AFB1), a ubiquitous toxicant contaminating foods of plant origins. Eight aptamers specific to AFB1 with the same binding site and different regions stabilizing their structures were compared for affinity, based on which the aptamer with 38 nucleotides in length was selected. The polymers that interact reversibly with oligonucleotides, such as poly-L-lysine and polyethylene glycol, were tested. It was found that they provide the desired reduction in the depolarization of emitted light as well as high concentrations of magnesium cations. In the selected optimal medium, AFB1 detection reached a limit of 1 ng/mL, which was 12 times lower than in the tris buffer commonly used for anti-AFB1 aptamers. The assay time was 30 min. This method is suitable for controlling almond samples according to the maximum permissible levels of their contamination by AFB1. The proposed approach could be applied to improve other aptamer-based analytical systems.
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Affiliation(s)
- Alexey V. Samokhvalov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (A.V.S.); (A.A.M.); (A.V.Z.)
| | - Alena A. Mironova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (A.V.S.); (A.A.M.); (A.V.Z.)
| | - Sergei A. Eremin
- Faculty of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Anatoly V. Zherdev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (A.V.S.); (A.A.M.); (A.V.Z.)
| | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (A.V.S.); (A.A.M.); (A.V.Z.)
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2
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Collette D, Dunlap D, Finzi L. Macromolecular Crowding and DNA: Bridging the Gap between In Vitro and In Vivo. Int J Mol Sci 2023; 24:17502. [PMID: 38139331 PMCID: PMC10744201 DOI: 10.3390/ijms242417502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
The cellular environment is highly crowded, with up to 40% of the volume fraction of the cell occupied by various macromolecules. Most laboratory experiments take place in dilute buffer solutions; by adding various synthetic or organic macromolecules, researchers have begun to bridge the gap between in vitro and in vivo measurements. This is a review of the reported effects of macromolecular crowding on the compaction and extension of DNA, the effect of macromolecular crowding on DNA kinetics, and protein-DNA interactions. Theoretical models related to macromolecular crowding and DNA are briefly reviewed. Gaps in the literature, including the use of biologically relevant crowders, simultaneous use of multi-sized crowders, empirical connections between macromolecular crowding and liquid-liquid phase separation of nucleic materials are discussed.
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Affiliation(s)
| | | | - Laura Finzi
- Department of Physics, College of Arts & Sciences, Emory University, Atlanta, GA 30322, USA; (D.C.); (D.D.)
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3
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Liu D, Li Q, Luo J, Huang Q, Zhang Y. An SPRI beads-based DNA purification strategy for flexibility and cost-effectiveness. BMC Genomics 2023; 24:125. [PMID: 36927488 PMCID: PMC10022144 DOI: 10.1186/s12864-023-09211-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Current solid-phase reversible immobilization (SPRI) beads technology is widely used in molecular biology due to its convenience for DNA manipulation. However, the high performance commercial SPRI beads have no price advantage over our method. Furthermore, the use of commercially available SPRI beads standards does not provide the flexibility required for a number of specific nucleic acid handling scenarios. RESULTS We report an efficient DNA purification strategy by combining home-made beads-suspension buffer with SPRI beads. The method tests the critical concentrations of polyethylene glycol (PEG) 8000 and beads to maximise recovery. And the composition of the SPRI beads DNA purification system (SDPS) was determined at 20% PEG 8000, 2 M NaCl and 16.3 mM MgCl2, and 1.25 mg/ml beads (1/8th original concentration). Then, we tested the DNA recovery of the SDPS, and the result showed that it was comparable to the control (AMPure XP beads). In the study, we have also developed an adjustment SPRI beads DNA purification system (ASDPS), the volume of ASDPS per reaction is 0.6× reaction volume (beads/samples). The performance of ASDPS is similar to SDPS and the control. But the cost of our methods is only about 1/24th of the control. To further assess its performance, we prepare the DNA-seq libraries to evaluate the yield, library quality, capture efficiency and consistency. We have compared all these results with the performance of the control and confirmed its efficiency. CONCLUSION We have proposed an alternative DNA purification approach with great flexibility, allowing researchers to manipulate DNA in different conditions. And ultimately, its application will benefit molecular biology research in the future.
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Affiliation(s)
- Danli Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng, Shenzhen, 518120, China
| | - Qiujia Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jing Luo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng, Shenzhen, 518120, China
| | - Qitong Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng, Shenzhen, 518120, China
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, 6708PB, Netherlands
| | - Yubo Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng, Shenzhen, 518120, China.
- College of Life Science and Engineering, Foshan University, Foshan, China.
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4
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Kim S, Lee ES, Cha BS, Park KS. High Fructose Concentration Increases the Fluorescence Stability of DNA-Templated Copper Nanoclusters by Several Thousand Times. NANO LETTERS 2022; 22:6121-6127. [PMID: 35895973 DOI: 10.1021/acs.nanolett.2c01287] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
DNA-templated copper nanoclusters (CuNCs) have limited applications because of their low fluorescence stability (several tens of minutes). In this study, we prepared CuNCs with improved temporal fluorescence stability by introducing fructose into the CuNC synthesis process and optimizing the reaction conditions. The inclusion of fructose increased the operating lifetime of CuNCs by approximately 5200-fold from 30 min to 108 days and improved their stability against heat, acids, and bases compared to CuNCs synthesized under original conditions. In addition, the fluorescence signal of CuNCs was maintained for a significantly longer time when stored at refrigeration (4 °C) and freezing (-20 °C) temperatures. Importantly, this method did not require the addition of substances other than fructose or any additional physicochemical treatment to maintain the fluorescence of DNA-templated CuNCs for more than several tens of days. As such, this study could serve as a basis to improve the stability of CuNCs for various applications.
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Affiliation(s)
- Seokjoon Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Eun Sung Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Byung Seok Cha
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
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5
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Oh YS, Park JH, Han SW, Kim SK, Lee YA. Retained binding mode of various DNA-binding molecules under molecular crowding condition. J Biomol Struct Dyn 2017; 36:3035-3046. [DOI: 10.1080/07391102.2017.1375992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Ye Sol Oh
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
| | - Jin Ha Park
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
| | - Sung Wook Han
- Department of Health & Biotechnology, Kyungwoon University, Kumi City, Gyeong-buk 39253, Republic of Korea
| | - Seog K. Kim
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
| | - Young-Ae Lee
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
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6
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Deiana M, Mettra B, Matczyszyn K, Pitrat D, Olesiak-Banska J, Monnereau C, Andraud C, Samoc M. Unravelling the Binding Mechanism of a Poly(cationic) Anthracenyl Fluorescent Probe with High Affinity toward Double-Stranded DNA. Biomacromolecules 2016; 17:3609-3618. [DOI: 10.1021/acs.biomac.6b01113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Marco Deiana
- Advanced
Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Bastien Mettra
- Laboratoire
de Chimie, CNRS UMR 5182, Ecole Normale Supérieure de Lyon, Université Lyon 1, 69007 Lyon, France
| | - Katarzyna Matczyszyn
- Advanced
Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Delphine Pitrat
- Laboratoire
de Chimie, CNRS UMR 5182, Ecole Normale Supérieure de Lyon, Université Lyon 1, 69007 Lyon, France
| | - Joanna Olesiak-Banska
- Advanced
Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Cyrille Monnereau
- Laboratoire
de Chimie, CNRS UMR 5182, Ecole Normale Supérieure de Lyon, Université Lyon 1, 69007 Lyon, France
| | - Chantal Andraud
- Laboratoire
de Chimie, CNRS UMR 5182, Ecole Normale Supérieure de Lyon, Université Lyon 1, 69007 Lyon, France
| | - Marek Samoc
- Advanced
Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
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7
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Deiana M, Mettra B, Matczyszyn K, Piela K, Pitrat D, Olesiak-Banska J, Monnereau C, Andraud C, Samoc M. Interactions of a biocompatible water-soluble anthracenyl polymer derivative with double-stranded DNA. Phys Chem Chem Phys 2016; 17:30318-27. [PMID: 26506886 DOI: 10.1039/c5cp05381a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We have studied the interaction of a polymeric water soluble anthracenyl derivative () with salmon testes DNA. The results from UV-Vis, fluorescence, Fourier transform infrared (FT-IR) and circular dichroism spectroscopies indicate that the groove binding process regulates the interaction between and DNA. The binding constants, calculated by absorption spectroscopy at 298, 304 and 310 K, were equal to 3.2 × 10(5) M(-1), 4.7 × 10(5) M(-1), and 6.6 × 10(5) M(-1) respectively, proving a relatively high affinity of for salmon testes DNA. Results of Hoechst 33258 displacement assays strongly support the groove binding mode of to DNA. The association stoichiometry of the :DNA adduct was found to be 1 for every 5 base pairs. FT-IR spectra, recorded at different /DNA molar ratios, indicate the involvement of the phosphate groups and adenine and thymine DNA bases in the association process. Thermodynamic results suggest that hydrophobic forces regulate the binding of with DNA without excluding some extent of involvement of van der Waals forces and hydrogen bonding arising due to surface binding between the hydrophilic polymeric arms of the ligand and the functional groups positioned on the edge of the groove. The resulting composite biomaterial could constitute a valuable candidate for future biological and/or photonic applications.
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Affiliation(s)
- Marco Deiana
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
| | - Bastien Mettra
- Laboratoire de Chimie, CNRS UMR 5182, Ecole Normale Supérieure de Lyon, Université, Lyon 1, Lyon, France
| | - Katarzyna Matczyszyn
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
| | - Katarzyna Piela
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Delphine Pitrat
- Laboratoire de Chimie, CNRS UMR 5182, Ecole Normale Supérieure de Lyon, Université, Lyon 1, Lyon, France
| | - Joanna Olesiak-Banska
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
| | - Cyrille Monnereau
- Laboratoire de Chimie, CNRS UMR 5182, Ecole Normale Supérieure de Lyon, Université, Lyon 1, Lyon, France
| | - Chantal Andraud
- Laboratoire de Chimie, CNRS UMR 5182, Ecole Normale Supérieure de Lyon, Université, Lyon 1, Lyon, France
| | - Marek Samoc
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
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8
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Junquera E, Aicart E. Recent progress in gene therapy to deliver nucleic acids with multivalent cationic vectors. Adv Colloid Interface Sci 2016; 233:161-175. [PMID: 26265376 DOI: 10.1016/j.cis.2015.07.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 07/10/2015] [Accepted: 07/12/2015] [Indexed: 12/16/2022]
Abstract
Due to the potential use as transfecting agents of nucleic acids (DNA or RNA), multivalent cationic non-viral vectors have received special attention in the last decade. Much effort has been addressed to synthesize more efficient and biocompatible gene vectors able to transport nucleic acids into the cells without provoking an immune response. Among them, the mostly explored to compact and transfect nucleic acids are: (a) gemini and multivalent cationic lipids, mixed with a helper lipid, by forming lipoplexes; and (b) cationic polymers, polycations, and polyrotaxanes, by forming polyplexes. This review is focused on the progress and recent advances experimented in this area, mainly during the present decade, devoting special attention to the lipoplexes and polyplexes, as follows: (a) to its biophysical characterization (mainly electrostatics, structure, size and morphology) using a wide variety of experimental methods; and (b) to its biological activity (transfection efficacy and cytotoxicity) addressed to confirm the optimum formulations and viability of these complexes as very promising gene vectors of nucleic acids in nanomedicine.
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Affiliation(s)
- Elena Junquera
- Grupo de Química Coloidal y Supramolecular, Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
| | - Emilio Aicart
- Grupo de Química Coloidal y Supramolecular, Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain.
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9
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Uda RM, Matsui T. Photoinduced conformational changes in DNA by poly(vinyl alcohol) carrying a malachite green moiety for protecting DNA against attack by nuclease. SOFT MATTER 2015; 11:8246-8252. [PMID: 26339777 DOI: 10.1039/c5sm01874a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Light is a highly advantageous means of specific cell targeting. Though targeted gene delivery is an important characteristic of an ideal delivery vehicle, there has been little effort to develop a photoresponsive vector. Among nonviral vectors, cationic substances interact effectively with negatively charged DNA. With this property in mind, we designed copolymers of poly(vinyl alcohol) carrying a malachite green moiety (PVAMG) with different molecular weights. Though PVAMG has no affinity for DNA in the absence of light, it undergoes photoionization in the presence of light to afford cationic DNA binding sites. The DNA-PVAMG complex was investigated with respect to DNA conformational changes and its protective nature, which are important properties for nonviral vectors. PVAMG irradiation promoted DNA conformational transitions from coils to partial globules to compacted globules. The complex had a protective effect against DNase I after PVAMG irradiation, while DNA was degraded under dark conditions. The effect on DNA transition and the protective nature were sensitive to the molecular weight of PVAMG. The data regarding binding constants and binding mode provided insight into the structure of the DNA-PVAMG complex. To withstand DNase I attacks, complexation results in the compaction of DNA, which is further covered with PVAMG.
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Affiliation(s)
- Ryoko M Uda
- Department of Chemical Engineering, Nara National College of Technology, Yata 22, Yamato-koriyama, Nara 639-1080, Japan.
| | - Takashi Matsui
- Department of Chemical Engineering, Nara National College of Technology, Yata 22, Yamato-koriyama, Nara 639-1080, Japan.
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10
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Cheng C, Jia JL, Ran SY. Polyethylene glycol and divalent salt-induced DNA reentrant condensation revealed by single molecule measurements. SOFT MATTER 2015; 11:3927-35. [PMID: 25871460 DOI: 10.1039/c5sm00619h] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In this study, we investigated the DNA condensation induced by polyethylene glycol (PEG) with different molecular weights (PEG 600 and PEG 6000) in the presence of NaCl or MgCl2 by using magnetic tweezers (MT) and atomic force microscopy (AFM). The MT measurements show that with increasing NaCl concentration, the critical condensation force in the PEG 600-DNA or PEG 6000-DNA system increased approximately linearly. PEG 6000 solution has a larger critical force than PEG 600 solution at a given NaCl concentration. In comparison, a parabolic trend of the critical condensation force was observed with increasing MgCl2 concentration, indicating that DNA undergoes a reentrant condensation. The AFM results show that the morphologies of the compacted DNA-PEG complexes depended on the salt concentration and were consistent with the MT results.
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Affiliation(s)
- Chao Cheng
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
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11
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Dey D, Maiti C, Maiti S, Dhara D. Interaction between calf thymus DNA and cationic bottle-brush copolymers: equilibrium and stopped-flow kinetic studies. Phys Chem Chem Phys 2015; 17:2366-77. [DOI: 10.1039/c4cp03309d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polyplex formation betweenctDNA and PEGylated cationic bottle-brush copolymers: PEG influences the DNA compaction behavior and the kinetics of polyplex formation.
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Affiliation(s)
- Debabrata Dey
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- India
| | - Chiranjit Maiti
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- India
| | - Souvik Maiti
- Proteomics and Structural Biology Unit
- Institute of Genomics and Integrative Biology
- CSIR
- Delhi 110007
- India
| | - Dibakar Dhara
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- India
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12
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Dey D, Kumar S, Banerjee R, Maiti S, Dhara D. Polyplex Formation between PEGylated Linear Cationic Block Copolymers and DNA: Equilibrium and Kinetic Studies. J Phys Chem B 2014; 118:7012-25. [DOI: 10.1021/jp501234p] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Debabrata Dey
- Department
of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Santosh Kumar
- Proteomics
and Structural Biology Unit, Institute of Genomics and Integrative
Biology, CSIR, Mall Road, Delhi 110007, India
| | - Rakesh Banerjee
- Department
of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Souvik Maiti
- Proteomics
and Structural Biology Unit, Institute of Genomics and Integrative
Biology, CSIR, Mall Road, Delhi 110007, India
| | - Dibakar Dhara
- Department
of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
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13
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Tajmir-Riahi HA, Nafisi S, Sanyakamdhorn S, Agudelo D, Chanphai P. Applications of chitosan nanoparticles in drug delivery. Methods Mol Biol 2014; 1141:165-84. [PMID: 24567139 DOI: 10.1007/978-1-4939-0363-4_11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We have reviewed the binding affinities of several antitumor drugs doxorubicin (Dox), N-(trifluoroacetyl) doxorubicin (FDox), tamoxifen (Tam), 4-hydroxytamoxifen (4-Hydroxytam), and endoxifen (Endox) with chitosan nanoparticles of different sizes (chitosan-15, chitosan-100, and chitosan-200 KD) in order to evaluate the efficacy of chitosan nanocarriers in drug delivery systems. Spectroscopic and molecular modeling studies showed the binding sites and the stability of drug-polymer complexes. Drug-chitosan complexation occurred via hydrophobic and hydrophilic contacts as well as H-bonding network. Chitosan-100 KD was the more effective drug carrier than the chitosan-15 and chitosan-200 KD.
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Affiliation(s)
- H A Tajmir-Riahi
- Department of Chemistry-Physics, University of Québec at Trois-Rivières, Trois-Rivières, QC, Canada
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14
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Encapsulation of biogenic and synthetic polyamines by nanoparticles PEG and mPEG-anthracene. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 130:30-9. [DOI: 10.1016/j.jphotobiol.2013.10.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 10/20/2013] [Accepted: 10/22/2013] [Indexed: 11/19/2022]
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15
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PEG–calf thymus DNA interactions: Conformational, morphological and spectroscopic thermal studies. Int J Biol Macromol 2013; 61:373-8. [DOI: 10.1016/j.ijbiomac.2013.07.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/29/2013] [Accepted: 07/30/2013] [Indexed: 12/11/2022]
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16
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Li C, Ma C, Xu P, Gao Y, Zhang J, Qiao R, Zhao Y. Effective and reversible DNA condensation induced by a simple cyclic/rigid polyamine containing carbonyl moiety. J Phys Chem B 2013; 117:7857-67. [PMID: 23734659 DOI: 10.1021/jp312766u] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The transfection of DNA in gene therapy largely depends on the possibility of obtaining its condensation. The details of nanoparticle formation are essential for functioning, as mediated by the diverse elements containing molecular structure, ionic strength in mediums, and condensing motivator. Here, we report two kinds of DNA condensing agents based on simple cyclic/rigid polyamine molecules, having evaluated their structural effect on nanoparticle formation. The reversible condensation-dissociation process was achieved by ion-switching, attributing to a possible condensing mechanism-competitive building of external hydrogen bonds. Using poly[(dA-dT)2] and poly[(dG-dC)2] as substrates, respectively, circular dichroism (CD) signals clearly presented dissimilar interactions between polyamines and both rich sequences, implying potential preference for G-C sequence. The presence of divalent ion Zn(2+) as an efficient motivator accelerated the achievement of DNA condensation, and an accessible schematic model was depicted to explain the promotion in detail. In addition, by comparison with the behaviors of linear polyamines, differences between condensation and aggregation were explicitly elucidated in aspects of morphology and surface charges, as well as induced condition. The present work may have the potential to reveal the precise mechanism of DNA nanoparticle formation and, in particular, be applied to gene delivery as an efficient nonviral vector.
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Affiliation(s)
- Chao Li
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, PR China
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17
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Novo L, van Gaal EVB, Mastrobattista E, van Nostrum CF, Hennink WE. Decationized crosslinked polyplexes for redox-triggered gene delivery. J Control Release 2013; 169:246-56. [PMID: 23583705 DOI: 10.1016/j.jconrel.2013.03.035] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 03/25/2013] [Accepted: 03/29/2013] [Indexed: 11/16/2022]
Abstract
The clinical applicability of polymers as gene delivery systems depends not only on their efficiency, but also on their safety. The cytotoxicity of these systems remains a major issue, mainly due to their cationic nature. Therefore, it is highly preferable to have a system based on biocompatible neutral polymers, lacking polycations, without compromising the DNA condensing and protecting capacities. Here, we introduce a concept to obtain a neutral polymeric gene delivery system, through a 3-step process (charge-driven condensation; stabilization through disulfide crosslinking; polyplex decationization) to generate polyplexes with a core of disulfide crosslinked poly(hydroxypropyl methacrylamide) (pHPMA) in which plasmid DNA (pDNA) is entrapped and a shell of poly(ethylene glycol) (PEG). The resulting polyplexes combine beneficial features of high and stable DNA loading capacity, stealth behavior and reduced toxicity. The nanoparticles are designed to release the pDNA after cellular uptake through cleavage of disulfide crosslinks within the intracellular reducing environment. This was shown by forced introduction of the polyplexes into the cytosol of HeLa cells by electroporation, which resulted in a high level of expression of the reporter gene. Additionally, the decationized polyplexes showed no interference on the cellular cell viability or metabolic activity (even at high dose) and no complex-induced membrane destabilization. Furthermore, decationized polyplexes showed a low degree of non-specific uptake, which is a highly favorable property for targeted therapy. Summarizing, the stabilized, decationized polyplexes presented here contribute to solve the high toxicity, low stability and lack of cellular/tissue specificity of cationic polymer based gene delivery systems.
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Affiliation(s)
- Luís Novo
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
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Charak S, Shandilya M, Tyagi G, Mehrotra R. Spectroscopic and molecular docking studies on chlorambucil interaction with DNA. Int J Biol Macromol 2012; 51:406-11. [DOI: 10.1016/j.ijbiomac.2012.06.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/07/2012] [Accepted: 06/10/2012] [Indexed: 11/26/2022]
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Suga K, Tomita H, Tanaka S, Umakoshi H. Hydrophobic properties of tRNA with varied conformations evaluated by an aqueous two-phase system. Int J Biol Sci 2012; 8:1188-96. [PMID: 23091416 PMCID: PMC3477688 DOI: 10.7150/ijbs.5059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 09/25/2012] [Indexed: 11/05/2022] Open
Abstract
The surface properties of transfer RNA (tRNA) were analyzed using a poly(ethylene glycol)/dextran aqueous two-phase system (ATPS), where the surface net hydrophobicity (HFS) and the local hydrophobicity (LH) were evaluated based on the partition coefficient of tRNA in the ATPS. According to the evaluated HFS values, the surface of the tRNA molecule was hydrophilic at 20° -40 °C, and it became hydrophobic at 50° -80 °C because of the exposure of the intrinsic nucleobases of tRNA. In contrast, the LH values were found to be maximal at 20° -40 °C. The conformation of tRNA was investigated by Raman and circular dichroism (CD) spectroscopies, corroborating the results with the calculated prediction of its secondary structure (Mfold). It was shown that 66% of A-form structure existed at room temperature; the base stacking (θ(265)) was gradually decreased, and the A-form structure (θ(208)) was denatured along with a sigmoid curve against the temperature increase; the denatured secondary structures were observed above 50° C by Mfold prediction. The HFS value of the DNA duplex was found to be hydrophilic, compared to that of the single-stranded DNA, indicating that the exposure of nucleobases is a key factor of the hydrophobic properties of nucleotides. We conclude that the hydrophobic property of the tRNA surface was directly affected by its conformational transition.
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Affiliation(s)
- Keishi Suga
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Osaka, Japan
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Froehlich E, Mandeville JS, Arnold D, Kreplak L, Tajmir-Riahi HA. Effect of PEG and mPEG-Anthracene on tRNA Aggregation and Particle Formation. Biomacromolecules 2011; 13:282-7. [DOI: 10.1021/bm2016515] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E. Froehlich
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières (Québec), Canada G9A 5H7
| | - J. S. Mandeville
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières (Québec), Canada G9A 5H7
| | - D. Arnold
- Department of Physics, Sir James
Dunn Building, Dalhousie University, Lord
Dalhousie Drive, Halifax, Canada NS B3H 3J5
| | - L. Kreplak
- Department of Physics, Sir James
Dunn Building, Dalhousie University, Lord
Dalhousie Drive, Halifax, Canada NS B3H 3J5
| | - H. A. Tajmir-Riahi
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières (Québec), Canada G9A 5H7
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