1
|
Jang YH, Raspaud E, Lansac Y. DNA-protamine condensates under low salt conditions: molecular dynamics simulation with a simple coarse-grained model focusing on electrostatic interactions. NANOSCALE ADVANCES 2023; 5:4798-4808. [PMID: 37705794 PMCID: PMC10496769 DOI: 10.1039/d2na00847e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 08/14/2023] [Indexed: 09/15/2023]
Abstract
Protamine, a small, strongly positively-charged protein, plays a key role in achieving chromatin condensation inside sperm cells and is also involved in the formulation of nanoparticles for gene therapy and packaging of mRNA-based vaccines against viral infection and cancer. The detailed mechanisms of such condensations are still poorly understood especially under low salt conditions where electrostatic interaction predominates. Our previous study, with a refined coarse-grained model in full consideration of the long-range electrostatic interactions, has demonstrated the crucial role of electrostatic interaction in protamine-controlled reversible DNA condensation. Therefore, we herein pay our attention only to the electrostatic interaction and devise a coarser-grained bead-spring model representing the right linear charge density on protamine and DNA chains but treating other short-range interactions as simply as possible, which would be suitable for real-scale simulations. Effective pair potential calculations and large-scale molecular dynamics simulations using this extremely simple model reproduce the phase behaviour of DNA in a wide range of protamine concentrations under low salt conditions, again revealing the importance of the electrostatic interaction in this process and providing a detailed nanoscale picture of bundle formation mediated by a charge disproportionation mechanism. Our simulations also show that protamine length alters DNA overcharging and in turn redissolution thresholds of DNA condensates, revealing the important role played by entropies and correlated fluctuations of condensing agents and thus offering an additional opportunity to design tailored nanoparticles for gene therapy. The control mechanism of DNA-protamine condensates will also provide a better microscopic picture of biomolecular condensates, i.e., membraneless organelles arising from liquid-liquid phase separation, that are emerging as key principles of intracellular organization. Such condensates controlled by post-translational modification of protamine, in particular phosphorylation, or by variations in protamine length from species to species may also be responsible for the chromatin-nucleoplasm patterning observed during spermatogenesis in several vertebrate and invertebrate species.
Collapse
Affiliation(s)
- Yun Hee Jang
- GREMAN UMR 7347, Université de Tours, CNRS, INSA CVL 37200 Tours France
- Department of Energy Science and Engineering, DGIST Daegu 42988 Korea
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Saclay 91405 Orsay France
| | - Eric Raspaud
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Saclay 91405 Orsay France
| | - Yves Lansac
- GREMAN UMR 7347, Université de Tours, CNRS, INSA CVL 37200 Tours France
- Department of Energy Science and Engineering, DGIST Daegu 42988 Korea
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Saclay 91405 Orsay France
| |
Collapse
|
2
|
Halder S, Paul M, Dyagala S, Aggrawal R, Aswal VK, Biswas S, Saha SK. Role of Gemini Surfactants with Variable Spacers and SiO 2 Nanoparticles in ct-DNA Compaction and Applications toward In Vitro/ In Vivo Gene Delivery. ACS APPLIED BIO MATERIALS 2023. [PMID: 37277159 DOI: 10.1021/acsabm.3c00256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Compaction of calf thymus DNA (ct-DNA) by two cationic gemini surfactants, 12-4-12 and 12-8-12, in the absence and presence of negatively charged SiO2 nanoparticles (NPs) (∼100 nm) has been explored using various techniques. 12-8-12 having a longer hydrophobic spacer induces a greater extent of ct-DNA compaction than 12-4-12, which becomes more efficient with SiO2 NPs. While 50% ct-DNA compaction in the presence of SiO2 NPs occurs at ∼77 nM of 12-8-12 and ∼130 nM of 12-4-12, but a conventional counterpart surfactant, DTAB, does it at its concentration as high as ∼7 μM. Time-resolved fluorescence anisotropy measurements show changes in the rotational dynamics of a fluorescent probe, DAPI, and helix segments in the condensed DNA. Fluorescence lifetime data and ethidium bromide exclusion assays reveal the binding sites of surfactants to ct-DNA. 12-8-12 with SiO2 NPs has shown the highest cell viability (≥90%) and least cell death in the human embryonic kidney (HEK) 293 cell lines in contrast to the cell viability of ≤80% for DTAB. These results show that 12-8-12 with SiO2 NPs has the highest time and dose-dependent cytotoxicity compared to 12-8-12 and 12-4-12 in the murine breast cancer 4T1 cell line. Fluorescence microscopy and flow cytometry are performed for in vitro cellular uptake of YOYO-1-labeled ct-DNA with surfactants and SiO2 NPs using 4T1 cells after 3 and 6 h incubations. The in vivo tumor accumulation studies are carried out using a real-time in vivo imaging system after intravenous injection of the samples into 4T1 tumor-bearing mice. 12-8-12 with SiO2 has delivered the highest amount of ct-DNA in cells and tumors in a time-dependent manner. Thus, the application of a gemini surfactant with a hydrophobic spacer and SiO2 NPs in compacting and delivering ct-DNA to the tumor is proven, warranting its further exploration in nucleic acid therapy for cancer treatment.
Collapse
Affiliation(s)
- Sayantan Halder
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Milan Paul
- Department of Pharmacy, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Shalini Dyagala
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Rishika Aggrawal
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Vinod K Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre (BARC), Trombay, Mumbai, Maharashtra 400085, India
| | - Swati Biswas
- Department of Pharmacy, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Subit K Saha
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| |
Collapse
|
3
|
Li N, Huang X, Chen J, Shao H. Investigating the conversion from coordination bond to electrostatic interaction on self-assembled monolayer by SECM. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.140569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
4
|
Thagun C, Horii Y, Mori M, Fujita S, Ohtani M, Tsuchiya K, Kodama Y, Odahara M, Numata K. Non-transgenic Gene Modulation via Spray Delivery of Nucleic Acid/Peptide Complexes into Plant Nuclei and Chloroplasts. ACS NANO 2022; 16:3506-3521. [PMID: 35195009 PMCID: PMC8945396 DOI: 10.1021/acsnano.1c07723] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Genetic engineering of economically important traits in plants is an effective way to improve global welfare. However, introducing foreign DNA molecules into plant genomes to create genetically engineered plants not only requires a lengthy testing period and high developmental costs but also is not well-accepted by the public due to safety concerns about its effects on human and animal health and the environment. Here, we present a high-throughput nucleic acids delivery platform for plants using peptide nanocarriers applied to the leaf surface by spraying. The translocation of sub-micrometer-scale nucleic acid/peptide complexes upon spraying varied depending on the physicochemical characteristics of the peptides and was controlled by a stomata-dependent-uptake mechanism in plant cells. We observed efficient delivery of DNA molecules into plants using cell-penetrating peptide (CPP)-based foliar spraying. Moreover, using foliar spraying, we successfully performed gene silencing by introducing small interfering RNA molecules in plant nuclei via siRNA-CPP complexes and, more importantly, in chloroplasts via our CPP/chloroplast-targeting peptide-mediated delivery system. This technology enables effective nontransgenic engineering of economically important plant traits in agricultural systems.
Collapse
Affiliation(s)
- Chonprakun Thagun
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yoko Horii
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Maai Mori
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Seiya Fujita
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Misato Ohtani
- Department
of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Kousuke Tsuchiya
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Yutaka Kodama
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- Center
for Bioscience Research and Education, Utsunomiya
University, Tochigi 321-8505, Japan
| | - Masaki Odahara
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- (Ma.O.)
| | - Keiji Numata
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- (K.N.)
| |
Collapse
|
5
|
Chaya H, Naito M, Cho M, Toh K, Hayashi K, Fukushima S, Yamasaki Y, Kataoka K, Miyata K. Dynamic Stabilization of Unit Polyion Complexes Incorporating Small Interfering RNA by Fine-Tuning of Cationic Block Length in Two-Branched Poly(ethylene glycol)- b-poly(l-lysine). Biomacromolecules 2021; 23:388-397. [PMID: 34935361 DOI: 10.1021/acs.biomac.1c01344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To stabilize small interfering RNA (siRNA) in the bloodstream for systemic RNAi therapeutics, we previously fabricated ultrasmall siRNA nanocarriers that were sub-20 nm in hydrodynamic diameter, named as unit polyion complexes (uPICs), using two-branched poly(ethylene glycol)-b-poly(l-lysine) (bPEG-PLys). The blood retention time of uPICs is dramatically increased in the presence of free bPEG-PLys, suggesting dynamic stabilization of uPICs by free bPEG-PLys based on their equilibrium. Herein, we examined how the degree of polymerization of PLys (DPPLys) affected the dynamic stability of uPICs in the bloodstream during prolonged circulation. We prepared a series of bPEG-PLys with DPPLys values of 10, 13, 20, 40, and 80 for the uPIC formation and siRNA with 40 negative charges. These bPEG-PLys were then evaluated in physicochemical characterization and pharmacokinetic analyses. Structural analyses revealed that the uPIC size and association numbers were mainly determined by the molecular weights of PEG and DPPLys, respectively. Under bPEG-PLys-rich conditions, the hydrodynamic diameters of uPICs were 15-20 nm, which were comparable to that of the bPEG block (i.e., ∼18 nm). Importantly, DPPLys significantly affected the association constant of bPEG-PLys to siRNA (Ka) and blood retention of free bPEG-PLys. A smaller DPPLys resulted in a lower Ka and a longer blood retention time of free bPEG-PLys. Thus, DPPLys can control the dynamic stability of uPICs, i.e., the balance between Ka and blood concentration of free bPEG-PLys. Ultimately, the bPEG-PLys with DPPLys values of 14 and 19 prolonged the blood circulation of siRNA-loaded uPICs with relatively small amounts of free bPEG-PLys. This study revealed that the uPIC formation between siRNA and bPEG-PLys can be controlled by their charges, which may be helpful for designing PIC-based delivery systems.
Collapse
Affiliation(s)
- Hiroyuki Chaya
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Mitsuru Naito
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masaru Cho
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kazuko Toh
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Kotaro Hayashi
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Shigeto Fukushima
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Yuichi Yamasaki
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kazunori Kataoka
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Kanjiro Miyata
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| |
Collapse
|
6
|
Zhu Y, Liu L, Mustafi M, Rank LA, Gellman SH, Weisshaar JC. Local rigidification and possible coacervation of the Escherichia coli DNA by cationic nylon-3 polymers. Biophys J 2021; 120:5243-5254. [PMID: 34757079 DOI: 10.1016/j.bpj.2021.10.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/06/2021] [Accepted: 10/26/2021] [Indexed: 12/17/2022] Open
Abstract
Synthetic, cationic random nylon-3 polymers (β-peptides) show promise as inexpensive antimicrobial agents less susceptible to proteolysis than normal peptides. We have used superresolution, single-cell, time-lapse fluorescence microscopy to compare the effects on live Escherichia coli cells of four such polymers and the natural antimicrobial peptides LL-37 and cecropin A. The longer, densely charged monomethyl-cyclohexyl (MM-CH) copolymer and MM homopolymer rapidly traverse the outer membrane and the cytoplasmic membrane. Over the next ∼5 min, they locally rigidify the chromosomal DNA and slow the diffusive motion of ribosomal species to a degree comparable to LL-37. The shorter dimethyl-dimethylcyclopentyl (DM-DMCP) and dimethyl-dimethylcyclohexyl (DM-DMCH) copolymers, and cecropin A are significantly less effective at rigidifying DNA. Diffusion of the DNA-binding protein HU and of ribosomal species is hindered as well. The results suggest that charge density and contour length are important parameters governing these antimicrobial effects. The data corroborate a model in which agents having sufficient cationic charge distributed across molecular contour lengths comparable to local DNA-DNA interstrand spacings (∼6 nm) form a dense network of multivalent, electrostatic "pseudo-cross-links" that cause the local rigidification. In addition, at times longer than ∼30 min, we observe that the MM-CH copolymer and the MM homopolymer (but not the other four agents) cause gradual coalescence of the two nucleoid lobes into a single dense lobe localized at one end of the cell. We speculate that this process involves coacervation of the DNA by the cationic polymer, and may be related to the liquid droplet coacervates observed in eukaryotic cells.
Collapse
Affiliation(s)
- Yanyu Zhu
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin
| | - Lei Liu
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin
| | - Mainak Mustafi
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin
| | - Leslie A Rank
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin
| | - James C Weisshaar
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin.
| |
Collapse
|
7
|
McErlean EM, Ziminska M, McCrudden CM, McBride JW, Loughran SP, Cole G, Mulholland EJ, Kett V, Buckley NE, Robson T, Dunne NJ, McCarthy HO. Rational design and characterisation of a linear cell penetrating peptide for non-viral gene delivery. J Control Release 2020; 330:1288-1299. [PMID: 33227336 DOI: 10.1016/j.jconrel.2020.11.037] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 01/19/2023]
Abstract
The design of a non-viral gene delivery system that can release a functional nucleic acid at the intracellular destination site is an exciting but also challenging proposition. The ideal gene delivery vector must be non-toxic, non-immunogenic, overcome extra- and intra-cellular barriers, protect the nucleic acid cargo from degradation with stability over a range of temperatures. A new 15 amino acid linear peptide termed CHAT was designed in this study with the goal of delivering DNA with high efficiency into cells in vitro and tissues in vivo. Rational design involved incorporation of key amino acids including arginine for nucleic acid complexation and cellular uptake, tryptophan to enhance hydrophobic interaction with cell membranes, histidine to facilitate endosomal escape and cysteine for stability and controlled cargo release. Six linear peptides were synthesised with strategic sequences and amino acid substitutions. Data demonstrated that all six peptides complexed pDNA to produce cationic nanoparticles less than 200 nm in diameter, but not all peptides resulted in successful transfection; indicating the influence of peptide design for endosomal escape. Peptide 4, now termed CHAT, was non-cytotoxic, traversed the plasma membrane of breast and prostate cancer cell lines, and elicited reporter-gene expression following intra-tumoural and intravenous delivery in vivo. CHAT presents an exciting new peptide for the delivery of nucleic acid therapeutics.
Collapse
Affiliation(s)
- Emma M McErlean
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Monika Ziminska
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Cian M McCrudden
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - John W McBride
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Stephen P Loughran
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Grace Cole
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Eoghan J Mulholland
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Vicky Kett
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Niamh E Buckley
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Tracy Robson
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons Ireland, 111 St Stephen's Green, Dublin 2, Ireland
| | - Nicholas J Dunne
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; School of Mechanical and Manufacturing Engineering, Dublin City University, Dublin 9, Ireland; Centre for Medical Engineering Research, School of Mechanical and Manufacturing Engineering, Dublin City University, Dublin 9, Ireland; Department of Mechanical and Manufacturing Engineering, School of Engineering, Trinity College Dublin, Dublin 2, Ireland; Advanced Manufacturing Research Centre (I-Form), School of Mechanical and Manufacturing Engineering, Dublin City University, Glasnevin, Dublin 9, Ireland; Advanced Materials and Bioengineering Research Centre (AMBER), Royal College of Surgeons in Ireland and Trinity College Dublin, Dublin, Ireland; Advanced Materials and Bioengineering Research Centre (AMBER), Royal College of Surgeons in Ireland and Trinity College Dublin, Dublin 2, Ireland; Trinity Centre for Biomedical Engineering, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Helen O McCarthy
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; School of Chemical Sciences, Dublin City University, Dublin 9, Ireland.
| |
Collapse
|
8
|
Osada K. Structural Polymorphism of Single pDNA Condensates Elicited by Cationic Block Polyelectrolytes. Polymers (Basel) 2020; 12:polym12071603. [PMID: 32707655 PMCID: PMC7408586 DOI: 10.3390/polym12071603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 12/17/2022] Open
Abstract
DNA folding is a core phenomenon in genome packaging within a nucleus. Such a phenomenon is induced by polyelectrolyte complexation between anionic DNA and cationic proteins of histones. In this regard, complexes formed between DNA and cationic polyelectrolytes have been investigated as models to gain insight into genome packaging. Upon complexation, DNA undergoes folding to reduce its occupied volume, which often results in multi-complex associated aggregates. However, when cationic copolymers comprising a polycation block and a neutral hydrophilic polymer block are used instead, DNA undergoes folding as a single molecule within a spontaneously formed polyplex micelle (PM), thereby allowing the observation of the higher-order structures that DNA forms. The DNA complex forms polymorphic structures, including globular, rod-shaped, and ring-shaped (toroidal) structures. This review focuses on the polymorphism of DNA, particularly, to elucidate when, how, and why DNA organizes into these structures with cationic copolymers. The interactions between DNA and the copolymers, and the specific nature of DNA in rigidity; i.e., rigid but foldable, play significant roles in the observed polymorphism. Moreover, PMs serve as potential gene vectors for systemic application. The significance of the controlled DNA folding for such an application is addressed briefly in the last part.
Collapse
Affiliation(s)
- Kensuke Osada
- Quantum Medical Science Directorate, National Institutes for Quantum and Radiological Science and Technology (QST), Anagawa, Inage-ku, Chiba-shi, Chiba 263-8555, Japan
| |
Collapse
|
9
|
Ueno M, Yamauchi S, Kumekawa D, Yamasaki Y. Peptide Sequence-Dependent Gene Expression of PEGylated Peptide/DNA Complexes. Mol Pharm 2019; 16:3072-3082. [PMID: 31173498 DOI: 10.1021/acs.molpharmaceut.9b00295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Oligolysine-based PEG-peptides with 15 or 20 amino acid residues including two cysteines were synthesized to formulate cross-linked polyplex micelles (PMs) incorporating luciferase-coding plasmid DNA (pDNA). Two cysteine residues were separately allocated at the C-terminal, center, or N-terminal of peptide moieties. Although TEM observation showed that all PEG-peptides condensed pDNA into rod-like or toroidal morphologies, the rod length distribution of PMs was affected by both the amino acid sequence and the peptide length of PEG-peptides. In comparison to the cysteine-uninstalled PEG-peptides, the cysteine-installed PEG-peptides exhibited a reductive environment-responsive pDNA release, which was observed in a gel retardation assay. From physicochemical characterizations, a relationship between the amino acid sequence and the in vitro gene expression efficacy of PMs in a cell-free protein synthesis system has been clearly demonstrated. Finally, the cell-based assay using HeLa cells has been tested, and the differences between both results of cell-free and cell-based systems are discussed.
Collapse
Affiliation(s)
- Mikiko Ueno
- Department of Materials Engineering, Graduate School of Engineering , The University of Tokyo , Hongo 7-3-1 , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Satoshi Yamauchi
- Department of Materials Engineering, Graduate School of Engineering , The University of Tokyo , Hongo 7-3-1 , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Daiki Kumekawa
- Department of Materials Engineering, Graduate School of Engineering , The University of Tokyo , Hongo 7-3-1 , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Yuichi Yamasaki
- Department of Materials Engineering, Graduate School of Engineering , The University of Tokyo , Hongo 7-3-1 , Bunkyo-ku, Tokyo 113-8656 , Japan
| |
Collapse
|
10
|
Zinchenko A, Hiramatsu H, Yamaguchi H, Kubo K, Murata S, Kanbe T, Hazemoto N, Yoshikawa K, Akitaya T. Amino Acid Sequence of Oligopeptide Causes Marked Difference in DNA Compaction and Transcription. Biophys J 2019; 116:1836-1844. [PMID: 31076102 PMCID: PMC6531782 DOI: 10.1016/j.bpj.2019.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/04/2019] [Accepted: 04/12/2019] [Indexed: 02/04/2023] Open
Abstract
Compaction of T4 phage DNA (166 kbp) by short oligopeptide octamers composed of two types of amino acids, four cationic lysine (K), and four polar nonionic serine (S) having different sequence order was studied by single-molecule fluorescent microscopy. We found that efficient DNA compaction by oligopeptide octamers depends on the geometrical match between phosphate groups of DNA and cationic amines. The amino acid sequence order in octamers dramatically affects the mechanism of DNA compaction, which changes from a discrete all-or-nothing coil-globule transition induced by a less efficient (K4S4) octamer to a continuous compaction transition induced by a (KS)4 octamer with a stronger DNA-binding character. This difference in the DNA compaction mechanism dramatically changes the packaging density, and the morphology of T4 DNA condensates: DNA is folded into ordered toroidal or rod morphologies during all-or-nothing compaction, whereas disordered DNA condensates are formed as a result of the continuous DNA compaction. Furthermore, the difference in DNA compaction mechanism has a certain effect on the inhibition scenario of the DNA transcription activity, which is gradual for the continuous DNA compaction and abrupt for the all-or-nothing DNA collapse.
Collapse
Affiliation(s)
- Anatoly Zinchenko
- Graduate School of Environmental Studies, Nagoya University, Furocho, Chikusa-ku, Nagoya, Japan.
| | - Hiroyuki Hiramatsu
- Faculty of Pharmaceutical Science, Nagoya City University, Mizuho-ku, Nagoya, Japan
| | | | - Koji Kubo
- Graduate School of Environmental Studies, Nagoya University, Furocho, Chikusa-ku, Nagoya, Japan
| | - Shizuaki Murata
- Graduate School of Environmental Studies, Nagoya University, Furocho, Chikusa-ku, Nagoya, Japan
| | - Toshio Kanbe
- Laboratory of Medical Mycology, Research Institute for Disease Mechanism and Control, School of Medicine, Nagoya University, Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Norio Hazemoto
- Faculty of Pharmaceutical Science, Nagoya City University, Mizuho-ku, Nagoya, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Tatsuo Akitaya
- Department of Chemistry, Asahikawa Medical University, Asahikawa, Hokkaido, Japan.
| |
Collapse
|
11
|
Gao T, Zhang W, Wang Y, Yang G. DNA Compaction and Charge Neutralization Regulated by Divalent Ions in very Low pH Solution. Polymers (Basel) 2019; 11:E337. [PMID: 30960321 PMCID: PMC6419228 DOI: 10.3390/polym11020337] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/02/2019] [Accepted: 02/06/2019] [Indexed: 12/11/2022] Open
Abstract
DNA conformation is strongly dependent on the valence of counterions in solution, and a valence of at least three is needed for DNA compaction. Recently, we directly demonstrated DNA compaction and its regulation, mediated by divalent cations, by lowering the pH of a solution. In the present study, we found that the critical electrophoretic mobility of DNA is promoted to around -1.0 × 10-4 cm² V-1 s-1 to incur DNA compaction or condensation in a tri- and tetravalent counterions solution, corresponding to an about 89% neutralized charge fraction of DNA. This is also valid for DNA compaction by divalent counterions in a low pH solution. It is notable that the critical charge neutralization of DNA for compaction is only about 1% higher than the saturated charge fraction of DNA in a mild divalent ion solution. We also found that DNA compaction by divalent cations at low pH is weakened and even decondensed with an increasing concentration of counterions.
Collapse
Affiliation(s)
- Tianyong Gao
- College of Mathematical, Physics and Electronic Information Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Wei Zhang
- College of Mathematical, Physics and Electronic Information Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Yanwei Wang
- College of Mathematical, Physics and Electronic Information Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Guangcan Yang
- College of Mathematical, Physics and Electronic Information Engineering, Wenzhou University, Wenzhou 325035, China.
| |
Collapse
|
12
|
Vu T, Davidson SL, Shim J. Investigation of compacted DNA structures induced by Na + and K + monovalent cations using biological nanopores. Analyst 2019; 143:906-913. [PMID: 29362734 DOI: 10.1039/c7an01857f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In aqueous solutions, an elongated, negatively charged DNA chain can quickly change its conformation into a compacted globule in the presence of positively charged molecules, or cations. This well-known process, called DNA compaction, is a method with great potential for gene therapy and delivery. Experimental conditions to induce these compacted DNA structures are often limited to the use of common compacting agents, such as cationic surfactants, polymers, and multivalent cations. In this study, we show that in highly concentrated buffers of 1 M monovalent cation solutions at pH 7.2 and 10, biological nanopores allow real-time sensing of individual compacted structures induced by K+ and Na+, the most abundant monovalent cations in human bodies. Herein, we studied the ratio between compacted and linear structures for 15-mer single-stranded DNA molecules containing only cytosine nucleotides, optimizing the probability of linear DNA chains being compacted. Since the binding affinity of each nucleotide to cation is different, the ability of the DNA strand to fold into a compacted structure greatly depends on the type of cations and nucleotides present. Our experimental results compare favorably with findings from previous molecular dynamics simulations for the DNA compacting potential of K+ and Na+ monovalent cations. We estimate that the majority of single-stranded DNA molecules in our experiment are compacted. From the current traces of nanopores, the ratio of compacted DNA to linear DNA molecules is approximately 30 : 1 and 15 : 1, at a pH of 7.2 and 10, respectively. Our comparative studies reveal that Na+ monovalent cations have a greater potential of compacting the 15C-ssDNA than K+ cations.
Collapse
Affiliation(s)
- Trang Vu
- Department of Biomedical Engineering, Rowan University, Glassboro, New Jersey 08028, USA.
| | | | | |
Collapse
|
13
|
Rigidification of the Escherichia coli cytoplasm by the human antimicrobial peptide LL-37 revealed by superresolution fluorescence microscopy. Proc Natl Acad Sci U S A 2018; 116:1017-1026. [PMID: 30598442 PMCID: PMC6338858 DOI: 10.1073/pnas.1814924116] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Natural antimicrobial peptides (AMPs) that exhibit broad-spectrum antibacterial activity are often highly positively charged. Fluorescence microscopy shows that after permeabilization of Escherichia coli membranes by the cationic AMP LL-37 a massive influx of peptide freezes the diffusive motion of the chromosomal DNA and a subset of ribosomes. Both are highly negatively charged. Cells cannot recover growth. We suggest that LL-37 forms noncovalent, electrostatic linkages between DNA strands and among polyribosomes, rigidifying the entire cytoplasm. While the preponderance of polyanionic biopolymers in the cytoplasm facilitates diffusion in normal growth, this same characteristic renders the bacterium highly susceptible to attack by polycationic AMPs. The results help explain why bacteria develop resistance to AMPs very slowly and may inform the design of new antibacterial agents. Superresolution, single-particle tracking reveals effects of the cationic antimicrobial peptide LL-37 on the Escherichia coli cytoplasm. Seconds after LL-37 penetrates the cytoplasmic membrane, the chromosomal DNA becomes rigidified on a length scale of ∼30 nm, evidenced by the loss of jiggling motion of specific DNA markers. The diffusive motion of a subset of ribosomes is also frozen. The mean diffusion coefficients of the DNA-binding protein HU and the nonendogenous protein Kaede decrease twofold. Roughly 108 LL-37 copies flood the cell (mean concentration ∼90 mM). Much of the LL-37 remains bound within the cell after extensive rinsing with fresh growth medium. Growth never recovers. The results suggest that the high concentration of adsorbed polycationic peptides forms a dense network of noncovalent, electrostatic linkages within the chromosomal DNA and among 70S-polysomes. The bacterial cytoplasm comprises a concentrated collection of biopolymers that are predominantly polyanionic (e.g., DNA, ribosomes, RNA, and most globular proteins). In normal cells, this provides a kind of electrostatic lubrication, enabling facile diffusion despite high biopolymer volume fraction. However, this same polyanionic nature renders the cytoplasm susceptible to massive adsorption of polycationic agents once penetration of the membranes occurs. If this phenomenon proves widespread across cationic agents and bacterial species, it will help explain why resistance to antimicrobial peptides develops only slowly. The results suggest two design criteria for polycationic peptides that efficiently kill gram-negative bacteria: facile penetration of the outer membrane and the ability to alter the cytoplasm by electrostatically linking double-stranded DNA and 70S-polysomes.
Collapse
|
14
|
Joyeux M. A segregative phase separation scenario of the formation of the bacterial nucleoid. SOFT MATTER 2018; 14:7368-7381. [PMID: 30204212 DOI: 10.1039/c8sm01205a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The mechanism responsible for the compaction of the genomic DNA of bacteria inside a structure called the nucleoid is a longstanding but still lively debated question. Most puzzling is the fact that the nucleoid occupies only a small fraction of the cell, although it is not separated from the rest of the cytoplasm by any membrane and would occupy a volume about a thousand times larger outside the cell. Here, by performing numerical simulations using coarse-grained models, we elaborate on the conjecture that the formation of the nucleoid may result from a segregative phase separation mechanism driven by the demixing of the DNA coil and non-binding globular macromolecules present in the cytoplasm, presumably functional ribosomes. Simulations performed with crowders having a spherical, dumbbell or octahedral geometry highlight the sensitive dependence of the level of DNA compaction on the dissymmetry of DNA/DNA, DNA/crowder, and crowder/crowder repulsive interactions, thereby supporting the segregative phase separation scenario. Simulations also consistently predict a much stronger DNA compaction close to the jamming threshold. Moreover, simulations performed with crowders of different sizes suggest that the final density distribution of each species results from the competition between thermodynamic forces and steric hindrance, so that bigger crowders are expelled selectively from the nucleoid only at moderate total crowder concentrations. This work leads to several predictions, which may eventually be tested experimentally.
Collapse
Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes, Grenoble, France.
| |
Collapse
|
15
|
Muramatsu A, Shimizu Y, Yoshikawa Y, Fukuda W, Umezawa N, Horai Y, Higuchi T, Fujiwara S, Imanaka T, Yoshikawa K. Naturally occurring branched-chain polyamines induce a crosslinked meshwork structure in a giant DNA. J Chem Phys 2017; 145:235103. [PMID: 28010109 DOI: 10.1063/1.4972066] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We studied the effect of branched-chain polyamines on the folding transition of genome-sized DNA molecules in aqueous solution by the use of single-molecule observation with fluorescence microcopy. Detailed morphological features of polyamine/DNA complexes were characterized by atomic force microscopy (AFM). The AFM observations indicated that branched-chain polyamines tend to induce a characteristic change in the higher-order structure of DNA by forming bridges or crosslinks between the segments of a DNA molecule. In contrast, natural linear-chain polyamines cause a parallel alignment between DNA segments. Circular dichroism measurements revealed that branched-chain polyamines induce the A-form in the secondary structure of DNA, while linear-chain polyamines have only a minimum effect. This large difference in the effects of branched- and linear-chain polyamines is discussed in relation to the difference in the manner of binding of these polyamines to negatively charged double-stranded DNA.
Collapse
Affiliation(s)
- Akira Muramatsu
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan
| | - Yuta Shimizu
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan
| | - Wakao Fukuda
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Yuhei Horai
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Shinsuke Fujiwara
- School of Science and Technology, Kwansei-Gakuin University, Sanda 669-1337, Japan
| | - Tadayuki Imanaka
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan
| |
Collapse
|
16
|
Joyeux M. Coarse-Grained Model of the Demixing of DNA and Non-Binding Globular Macromolecules. J Phys Chem B 2017; 121:6351-6358. [PMID: 28599107 DOI: 10.1021/acs.jpcb.7b03011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The volume occupied by the unconstrained genomic DNA of prokaryotes in saline solutions is thousand times larger than the cell. Moreover, it is not separated from the rest of the cell by a membrane. Nevertheless, it occupies only a small fraction of the cell called the nucleoid. The mechanisms leading to such compaction are the matter of ongoing debates. The present work aims at exploring a newly proposed mechanism, according to which the formation of the nucleoid would result from the demixing of the DNA and nonbinding globular macromolecules of the cytoplasm, like ribosomes. To this end, a coarse-grained model of prokaryotic cells was developed, and demixing was analyzed as a function of the size and number of crowders. The model suggests that compaction of the DNA is actually governed by the volume occupancy ratio of the crowders and remains weak almost up to the jamming critical density. Strong compaction is however observed just before jamming, suggesting that crowding and electrostatic repulsion work synergetically in this limit. Finally, simulations performed with crowders with different sizes indicate that the DNA and the largest crowders demix preferentially. Together with the recent observation of the gradual compaction of long DNA molecules upon increase of the concentration of bovine serum albumin proteins and silica nanoparticles, this work supports the demixing mechanism as a key player for the formation of the nucleoid.
Collapse
Affiliation(s)
- Marc Joyeux
- LIPHY, Université Grenoble Alpes and CNRS , Grenoble, France
| |
Collapse
|
17
|
Krzemien KM, Beckers M, Quack S, Michaelis J. Atomic force microscopy of chromatin arrays reveal non-monotonic salt dependence of array compaction in solution. PLoS One 2017; 12:e0173459. [PMID: 28296908 PMCID: PMC5351988 DOI: 10.1371/journal.pone.0173459] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/22/2017] [Indexed: 12/03/2022] Open
Abstract
Compaction of DNA in chromatin is a hallmark of the eukaryotic cell and unravelling its structure is required for an understanding of DNA involving processes. Despite strong experimental efforts, many questions concerning the DNA packing are open. In particular, it is heavily debated whether an ordered structure referred to as the “30 nm fibre” exist in vivo. Scanning probe microscopy has become a cutting edge technology for the high-resolution imaging of DNA- protein complexes. Here, we perform high-resolution atomic force microscopy of non-cross-linked chromatin arrays in liquid, under different salt conditions. A statistical analysis of the data reveals that array compaction is salt dependent in a non-monotonic fashion. A simple physical model can qualitatively explain the observed findings due to the opposing effects of salt dependent stiffening of DNA, nucleosome stability and histone-histone interactions. While for different salt concentrations different compaction states are observed, our data do not provide support for the existence of regular chromatin fibres. Our studies add new insights into chromatin structure, and with that contribute to a further understanding of the DNA condensation.
Collapse
Affiliation(s)
| | | | - Salina Quack
- Institute of Biophysics, Ulm University, Ulm, Germany
| | - Jens Michaelis
- Institute of Biophysics, Ulm University, Ulm, Germany
- * E-mail:
| |
Collapse
|
18
|
Joyeux M. In vivo compaction dynamics of bacterial DNA: A fingerprint of DNA/RNA demixing? Curr Opin Colloid Interface Sci 2016. [DOI: 10.1016/j.cocis.2016.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
19
|
Zinchenko A. DNA conformational behavior and compaction in biomimetic systems: Toward better understanding of DNA packaging in cell. Adv Colloid Interface Sci 2016; 232:70-79. [PMID: 26976700 DOI: 10.1016/j.cis.2016.02.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 02/05/2016] [Accepted: 02/11/2016] [Indexed: 10/22/2022]
Abstract
In a living cell, long genomic DNA is strongly compacted and exists in the environment characterized by a dense macromolecular crowding, high concentrations of mono- and divalent cations, and confinement of ca. 10μm size surrounded by a phospholipid membrane. Experimental modelling of such complex biological system is challenging but important to understand spatiotemporal dynamics and functions of the DNA in cell. The accumulated knowledge about DNA condensation/compaction in conditions resembling those in the real cell can be eventually used to design and construct partly functional "artificial cells" having potential applications in drug delivery systems, gene therapy, and production of synthetic cells. In this review, I would like to overview the past progress in our understanding of the DNA conformational behavior and, in particular, DNA condensation/compaction phenomenon and its relation to the DNA biological activity. This understanding was gained by designing relevant experimental models mimicking DNA behavior in the environment of living cell. Starting with a brief summary of classic experimental systems to study DNA condensation/compaction, in later parts, I highlight recent experimental methodologies to address the effects of macromolecular crowding and nanoscale and microscale confinements on DNA conformation dynamics. All the studies are discussed in the light of their relevance to DNA behavior in living cells, and future prospects of the field are outlined.
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Joyeux M. Compaction of bacterial genomic DNA: clarifying the concepts. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:383001. [PMID: 26345139 DOI: 10.1088/0953-8984/27/38/383001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The unconstrained genomic DNA of bacteria forms a coil, whose volume exceeds 1000 times the volume of the cell. Since prokaryotes lack a membrane-bound nucleus, in sharp contrast with eukaryotes, the DNA may consequently be expected to occupy the whole available volume when constrained to fit in the cell. Still, it has been known for more than half a century that the DNA is localized in a well-defined region of the cell, called the nucleoid, which occupies only 15% to 25% of the total volume. Although this problem has focused the attention of many scientists in recent decades, there is still no certainty concerning the mechanism that enables such a dramatic compaction. The goal of this Topical Review is to take stock of our knowledge on this question by listing all possible compaction mechanisms with the proclaimed desire to clarify the physical principles they are based upon and discuss them in the light of experimental results and the results of simulations based on coarse-grained models. In particular, the fundamental differences between ψ-condensation and segregative phase separation and between the condensation by small and long polycations are highlighted. This review suggests that the importance of certain mechanisms, like supercoiling and the architectural properties of DNA-bridging and DNA-bending nucleoid proteins, may have been overestimated, whereas other mechanisms, like segregative phase separation and the self-association of nucleoid proteins, as well as the possible role of the synergy of two or more mechanisms, may conversely deserve more attention.
Collapse
Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique (CNRS UMR5588), Université Joseph Fourier Grenoble 1, BP 87, 38402 St Martin d'Hères, France
| |
Collapse
|
22
|
Moriyama R, Iwasaki Y, Miyoshi D. Stabilization of DNA Structures with Poly(ethylene sodium phosphate). J Phys Chem B 2015; 119:11969-77. [PMID: 26173001 DOI: 10.1021/acs.jpcb.5b03787] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structure and stability of biomolecules under molecular crowding conditions are of interest because such information clarifies how biomolecules behave under cell-mimicking conditions. The anionic surfaces of chromatin, which is composed of DNA strands and histone complexes, are concentrated in cell nuclei and thus generate a polyanionic crowding environment. In this study, we designed and synthesized an anionic polymer, poly(ethylene sodium phosphate) (PEP·Na), which has a nucleic acid phosphate backbone and created a cell nucleus-like environment. The effects of molecular crowding with PEP·Na on the thermodynamics of DNA duplexes, triplexes, and G-quadruplexes were systematically studied. Thermodynamic analysis demonstrated that PEP·Na significantly stabilized the DNA structures; e.g., a free energy change at 25 °C for duplex formation decreased from -6.6 to -12.8 kcal/mol with 20 wt % PEP·Na. Thermodynamic parameters further indicated that the factors for the stabilization of the DNA structures were dependent on sodium ion concentration. At lower polymer concentrations, the stabilization was attributed to a shielding of the electrostatic repulsion between DNA strands by the sodium ions of PEP·Na. In contrast, at higher polymer concentrations, the DNA structures were entropically stabilized by volume exclusion, which could be enhanced by electrostatic repulsion between phosphate groups in DNA strands and in PEP·Na. Additionally, increasing PEP·Na concentration resulted in increasing enthalpy of the DNA duplex but decreasing enthalpy of DNA G-quadruplex, indicating that the polymers also promoted dehydration of the DNA strands. Thus, polyanionic crowding affects the thermodynamics of DNA structures via the sodium ions, volume exclusion, and hydration. The stabilization of DNA by the cell nucleus-like polyanionic crowding provides new information regarding DNA structures and allows for modeling reactions in cell nuclei.
Collapse
Affiliation(s)
- Rui Moriyama
- Organization for Research and Development of Innovative Science and Technology, Kansai University , 3-3-35, Yamate-cho, Suita-shi, Osaka 564-8680, Japan
| | - Yasuhiko Iwasaki
- Organization for Research and Development of Innovative Science and Technology, Kansai University , 3-3-35, Yamate-cho, Suita-shi, Osaka 564-8680, Japan.,Department of Chemistry and Materials Engineering, Faculty of Chemistry, Materials and Bioengineering, Kansai University , 3-3-35, Yamate-cho, Suita-shi, Osaka 564-8680, Japan
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology, Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe-shi, Hyogo 650-0047, Japan
| |
Collapse
|
23
|
Yu S, Larson RG. Monte-Carlo simulations of PAMAM dendrimer-DNA interactions. SOFT MATTER 2014; 10:5325-5336. [PMID: 24924736 DOI: 10.1039/c4sm00452c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We use Monte Carlo simulations to determine the influence of poly(amido amine) (PAMAM) dendrimer size and charge on its interactions with double-stranded DNA conformation and interaction strength. To achieve a compromise between simulation speed and molecular detail, we combine the coarse-grained DNA model of de Pablo et al. which resolves each DNA base using three beads - and thereby retains the double-helix structure - with a dendrimer model with resolution similar to that of the DNA. The resulting predictions of the effects of dendrimer generation, dendrimer surface charge density, and salt concentration on dendrimer-DNA complexes are in agreement with both experiments and all-atom MD simulations. The model predicts that DNA wraps a fully charged G5 or G6 dendrimer at low salt concentration (10 mM) similarly to a histone octamer, and for the G5 dendrimer, DNA super helices with both handednesses occur. At salt concentrations above 50 mM, or when a high fraction of dendrimer surface charges are neutralized by acetylation, DNA adheres but does not compactly wrap the dendrimer, in agreement with experimental findings. We are also able to simulate pairs of dendrimers binding to the same DNA strand. Thus, our mesoscale simulation not only elucidates dendrimer-DNA interactions, but also provides a methodology for efficiently simulating chromatin formation and other cationic macroion-DNA complexes.
Collapse
Affiliation(s)
- Shi Yu
- Chemical Engineering Department, University of Michigan, Ann Arbor 48109, USA.
| | | |
Collapse
|
24
|
Tsuchiya M, Hashimoto M, Takenaka Y, Motoike IN, Yoshikawa K. Global genetic response in a cancer cell: self-organized coherent expression dynamics. PLoS One 2014; 9:e97411. [PMID: 24831017 PMCID: PMC4022610 DOI: 10.1371/journal.pone.0097411] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 04/18/2014] [Indexed: 12/19/2022] Open
Abstract
Understanding the basic mechanism of the spatio-temporal self-control of genome-wide gene expression engaged with the complex epigenetic molecular assembly is one of major challenges in current biological science. In this study, the genome-wide dynamical profile of gene expression was analyzed for MCF-7 breast cancer cells induced by two distinct ErbB receptor ligands: epidermal growth factor (EGF) and heregulin (HRG), which drive cell proliferation and differentiation, respectively. We focused our attention to elucidate how global genetic responses emerge and to decipher what is an underlying principle for dynamic self-control of genome-wide gene expression. The whole mRNA expression was classified into about a hundred groups according to the root mean square fluctuation (rmsf). These expression groups showed characteristic time-dependent correlations, indicating the existence of collective behaviors on the ensemble of genes with respect to mRNA expression and also to temporal changes in expression. All-or-none responses were observed for HRG and EGF (biphasic statistics) at around 10–20 min. The emergence of time-dependent collective behaviors of expression occurred through bifurcation of a coherent expression state (CES). In the ensemble of mRNA expression, the self-organized CESs reveals distinct characteristic expression domains for biphasic statistics, which exhibits notably the presence of criticality in the expression profile as a route for genomic transition. In time-dependent changes in the expression domains, the dynamics of CES reveals that the temporal development of the characteristic domains is characterized as autonomous bistable switch, which exhibits dynamic criticality (the temporal development of criticality) in the genome-wide coherent expression dynamics. It is expected that elucidation of the biophysical origin for such critical behavior sheds light on the underlying mechanism of the control of whole genome.
Collapse
Affiliation(s)
- Masa Tsuchiya
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, School of Media and Governance, Keio University, Fujisawa, Japan
- * E-mail: (MT); (KY)
| | - Midori Hashimoto
- Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Japan
| | - Yoshiko Takenaka
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Ikuko N. Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
- * E-mail: (MT); (KY)
| |
Collapse
|
25
|
Zinchenko A, Tsumoto K, Murata S, Yoshikawa K. Crowding by Anionic Nanoparticles Causes DNA Double-Strand Instability and Compaction. J Phys Chem B 2014; 118:1256-62. [DOI: 10.1021/jp4107712] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Anatoly Zinchenko
- Graduate
School of Environmental Studies, Nagoya University, Nagoya, 464-8601, Japan
| | - Kanta Tsumoto
- Graduate
School of Engineering, Mie University, Mie, 514-8507, Japan
| | - Shizuaki Murata
- Graduate
School of Environmental Studies, Nagoya University, Nagoya, 464-8601, Japan
| | - Kenichi Yoshikawa
- Faculty
of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394, Japan
| |
Collapse
|
26
|
Yu S, Li MH, Choi SK, Baker JR, Larson RG. DNA condensation by partially acetylated poly(amido amine) dendrimers: effects of dendrimer charge density on complex formation. Molecules 2013; 18:10707-20. [PMID: 24005965 PMCID: PMC6271276 DOI: 10.3390/molecules180910707] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 08/29/2013] [Accepted: 08/30/2013] [Indexed: 12/05/2022] Open
Abstract
The ability of poly(amido amine) (or PAMAM) dendrimers to condense semiflexible dsDNA and penetrate cell membranes gives them great potential in gene therapy and drug delivery but their high positive surface charge makes them cytotoxic. Here, we describe the effects of partial neutralization by acetylation on DNA condensation using light scattering, circular dichroism, and single molecule imaging of dendrimer-DNA complexes combed onto surfaces and tethered to those surfaces under flow. We find that DNA can be condensed by generation-five (G5) dendrimers even when the surface charges are more than 65% neutralized, but that such dendrimers bind negligibly when an end-tethered DNA is stretched in flow. We also find that when fully charged dendrimers are introduced by flow to end-tethered DNA, all DNA molecules become equally highly coated with dendrimers at a rate that becomes very fast at high dendrimer concentration, and that dendrimers remain bound during subsequent flow of dendrimer-free buffer. These results suggest that the presence of dendrimer-free DNA coexisting with dendrimer-bound DNA after bulk mixing of the two in solution may result from diffusion-limited irreversible dendrimer-DNA binding, rather than, or in addition to, the previously proposed cooperative binding mechanism of dendrimers to DNA.
Collapse
Affiliation(s)
- Shi Yu
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ming-Hsin Li
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seok Ki Choi
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - James R. Baker
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ronald G. Larson
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-734-936-0772; Fax: +1-734-763-0459
| |
Collapse
|
27
|
Krotova MK, Vasilevskaya VV, Khokhlov AR. Compaction of DNA in solutions of highly charged proteins carrying the same charge as DNA. POLYMER SCIENCE SERIES C 2012. [DOI: 10.1134/s1811238212020014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
28
|
Railsback JG, Singh A, Pearce RC, McKnight TE, Collazo R, Sitar Z, Yingling YG, Melechko AV. Weakly charged cationic nanoparticles induce DNA bending and strand separation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2012; 24:4261-4265. [PMID: 22711427 DOI: 10.1002/adma.201104891] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 04/17/2012] [Indexed: 06/01/2023]
Abstract
Weakly charged cationic nanoparticles cause structural changes including local denaturing and compaction to DNA under mild conditions. The charged ligands bind to the phosphate backbone of DNA and the uncharged ligands penetrate the helix and disrupt base pairing. Mobility shifts in electrophoresis, molecular dynamics, and UV-vis spectrophotometry give clues to the details of the interactions.
Collapse
Affiliation(s)
- Justin G Railsback
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | | | | | | | | | | | | | | |
Collapse
|
29
|
Prediction of chemical-protein interactions network with weighted network-based inference method. PLoS One 2012; 7:e41064. [PMID: 22815915 PMCID: PMC3397956 DOI: 10.1371/journal.pone.0041064] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 06/16/2012] [Indexed: 12/11/2022] Open
Abstract
Chemical-protein interaction (CPI) is the central topic of target identification and drug discovery. However, large scale determination of CPI is a big challenge for in vitro or in vivo experiments, while in silico prediction shows great advantages due to low cost and high accuracy. On the basis of our previous drug-target interaction prediction via network-based inference (NBI) method, we further developed node- and edge-weighted NBI methods for CPI prediction here. Two comprehensive CPI bipartite networks extracted from ChEMBL database were used to evaluate the methods, one containing 17,111 CPI pairs between 4,741 compounds and 97 G protein-coupled receptors, the other including 13,648 CPI pairs between 2,827 compounds and 206 kinases. The range of the area under receiver operating characteristic curves was 0.73 to 0.83 for the external validation sets, which confirmed the reliability of the prediction. The weak-interaction hypothesis in CPI network was identified by the edge-weighted NBI method. Moreover, to validate the methods, several candidate targets were predicted for five approved drugs, namely imatinib, dasatinib, sertindole, olanzapine and ziprasidone. The molecular hypotheses and experimental evidence for these predictions were further provided. These results confirmed that our methods have potential values in understanding molecular basis of drug polypharmacology and would be helpful for drug repositioning.
Collapse
|
30
|
Uda RM, Ohshita M. Phototriggered DNA Complexation and Compaction Using Poly(vinyl alcohol) Carrying a Malachite Green Moiety. Biomacromolecules 2012; 13:1510-4. [DOI: 10.1021/bm3001952] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ryoko M. Uda
- Department of Chemical Engineering, Nara National College of Technology, Yata 22, Yamato-koriyama,
Nara 639-1080, Japan
| | - Minami Ohshita
- Department of Chemical Engineering, Nara National College of Technology, Yata 22, Yamato-koriyama,
Nara 639-1080, Japan
| |
Collapse
|
31
|
Creating a unique environment for selecting reactive enzymes with DNA: ‘Sticky’ binding of oligocation-grafted polymers to DNA. Bioorg Med Chem 2012; 20:1346-53. [DOI: 10.1016/j.bmc.2011.12.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 12/05/2011] [Accepted: 12/07/2011] [Indexed: 11/20/2022]
|
32
|
Rudiuk S, Yoshikawa K, Baigl D. Enhancement of DNA compaction by negatively charged nanoparticles: effect of nanoparticle size and surfactant chain length. J Colloid Interface Sci 2011; 368:372-7. [PMID: 22071517 DOI: 10.1016/j.jcis.2011.10.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 10/12/2011] [Accepted: 10/13/2011] [Indexed: 11/29/2022]
Abstract
We study the compaction of genomic DNA by a series of alkyltrimethylammonium bromide surfactants having different hydrocarbon chain lengths n: dodecyl-(DTAB, n=12), tetradecyl-(TTAB, n=14) and hexadecyl-(CTAB, n=16), in the absence and in the presence of negatively charged silica nanoparticles (NPs) with a diameter in the range 15-100 nm. We show that NPs greatly enhance the ability of all cationic surfactants to induce DNA compaction and that this enhancement increases with an increase in NP diameter. In the absence of NP, the ability of cationic surfactants to induce DNA compaction increases with an increase in n. Conversely, in the presence of NPs, the enhancement of DNA compaction increases with a decrease in n. Therefore, although CTAB is the most efficient surfactant to compact DNA, maximal enhancement by NPs is obtained for the largest NP diameter (here, 100 nm) and the smallest surfactant chain length (here, DTAB). We suggest a mechanism where the preaggregation of surfactants on NP surface mediated by electrostatic interactions promotes cooperative binding to DNA and thus enhances the ability of surfactants to compact DNA. We show that the amplitude of enhancement is correlated with the difference between the surfactant concentration corresponding to aggregation on DNA alone and that corresponding to the onset of adsorption on nanoparticles.
Collapse
Affiliation(s)
- Sergii Rudiuk
- Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | | | | |
Collapse
|
33
|
Xie L, Xie L, Kinnings SL, Bourne PE. Novel computational approaches to polypharmacology as a means to define responses to individual drugs. Annu Rev Pharmacol Toxicol 2011; 52:361-79. [PMID: 22017683 DOI: 10.1146/annurev-pharmtox-010611-134630] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polypharmacology, which focuses on designing therapeutics to target multiple receptors, has emerged as a new paradigm in drug discovery. Polypharmacological effects are an attribute of most, if not all, drug molecules. The efficacy and toxicity of drugs, whether designed as single- or multitarget therapeutics, result from complex interactions between pharmacodynamic, pharmacokinetic, genetic, epigenetic, and environmental factors. Ultimately, to predict a drug response phenotype, it is necessary to understand the change in information flow through cellular networks resulting from dynamic drug-target interactions and the impact that this has on the complete biological system. Although such is a future objective, we review recent progress and challenges in computational techniques that enable the prediction and analysis of in vitro and in vivo drug-response phenotypes.
Collapse
Affiliation(s)
- Lei Xie
- Department of Computer Science, Hunter College, The City University of New York, New York, New York 10065, USA.
| | | | | | | |
Collapse
|
34
|
Shiosaki S, Kuramoto M, Toita R, Mori T, Niidome T, Katayama Y. A hydrophilic polymer grafted with a histone tail peptide as an artificial gene regulator. Bioorg Med Chem 2011; 19:4101-5. [PMID: 21636282 DOI: 10.1016/j.bmc.2011.05.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 05/06/2011] [Accepted: 05/07/2011] [Indexed: 11/27/2022]
Abstract
In chromatin, gene transcription is regulated through posttranslational modifications on the histone N-terminal tail sequences, typically an acetyl group modification on lysine residues. To realize a simple model of the gene regulation of chromatin, we designed a hydrophilic polymer grafted with histone H3 tail peptides. The polyplex formed from the polymer and DNA suppressed the gene expression effectively although the polyplex was weaker than the polyplex of poly-L-lysine and DNA. This weaker polyplex afforded the acetylation of the lysine residue of the grafted peptides by histone acetyltransferase. Subsequently, the gene expression was activated due to the relaxation of the polyplex which was brought by a cationic charge decrease in the grafted peptides. This molecular system is the first functional model of the gene regulation of the chromatin.
Collapse
Affiliation(s)
- Shujiro Shiosaki
- Graduate School of Systems Life Sciences, Kyushu University, Nishi-ku, Fukuoka, Japan
| | | | | | | | | | | |
Collapse
|
35
|
Zhou PP, Qiu WY, Liu S, Jin NZ. Halogen as halogen-bonding donor and hydrogen-bonding acceptor simultaneously in ring-shaped H3N·X(Y)·HF (X = Cl, Br and Y = F, Cl, Br) complexes. Phys Chem Chem Phys 2011; 13:7408-18. [PMID: 21423995 DOI: 10.1039/c1cp00025j] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of ring-shaped molecular complexes formed by H(3)N, HF and XY (X = Cl, Br and Y = F, Cl, Br) have been investigated at the MP2/aug-cc-pVTZ level of theory. Their optimized geometry, stretching mode, and interaction energy have been obtained. We found that each complex possesses two red-shifted hydrogen bonds and one red-shifted halogen bond, and the two hydrogen bonds exhibit strong cooperative effects on the halogen bond. The cooperativity among the NH(3)···FH, FH···XY and H(3)N···XY interactions leads to the formations of these complexes. The AIM analysis has been performed at the CCSD(T)/aug-cc-pVQZ level of theory to examine the topological characteristics at the bond critical point and at the ring critical point, confirming the coexistence of the two hydrogen bonds and one halogen bond for each complex. The NBO analysis carried out at the B3LYP/aug-cc-pVTZ level of theory demonstrates the effects of hyperconjugation, hybridization, and polarization coming into play during the hydrogen and halogen bonding formations processes, based on which a clockwise loop of charge transfer was discovered. The molecular electrostatic potential has been employed to explore the formation mechanisms of these molecular complexes.
Collapse
Affiliation(s)
- Pan-Pan Zhou
- Department of Chemistry, State Key Laboratory of Applied Organic Chemistry, Lanzhou University, 222 South Tianshui Road, Lanzhou 730000, PR China
| | | | | | | |
Collapse
|
36
|
Takenaka T, Zinchenko AA, Yoshikawa K, Murata S. Roles of Mono- and Divalent Cations in DNA Compaction Induced by Histone-Mimic Nanoparticles. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2010. [DOI: 10.1246/bcsj.20090324] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
37
|
Sato YT, Kawamura K, Niidome T, Katayama Y. Characterization of gene expression regulation using D-RECS polymer by enzymatic reaction for an effective design of enzyme-responsive gene regulator. J Control Release 2010; 143:344-9. [DOI: 10.1016/j.jconrel.2010.01.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 12/23/2009] [Accepted: 01/08/2010] [Indexed: 10/19/2022]
|
38
|
Wan L, You Y, Zou Y, Oupický D, Mao G. DNA release dynamics from bioreducible poly(amido amine) polyplexes. J Phys Chem B 2010; 113:13735-41. [PMID: 19522487 DOI: 10.1021/jp901835u] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The DNA release dynamics of bioreducible poly(amido amine) polyplexes were studied in real time by atomic force microscopy (AFM). DNA release is triggered by a depolymerization of high-molecular-weight polycations into low-molecular-weight oligocations that occurs by means of the thiol and disulfide exchange reaction mechanism. AFM images were captured in a simulated physiological reducing environment that used dithiothreitol. Distinctive stages of disassembly are common among various polyplexes that have different disulfide content, molecular weight, and polymer architecture, while the DNA release rate depends upon the disulfide content. In the first stage, polyplexes evolve from metastable structures into the more stable toroid structure upon the depolymerization. In the second stage, toroids either aggregate or fuse into larger toroids. In the last stage, DNA wormlike chains and loops are held by a central compact core. The results confirm the prospect of bioreducible poly(amido amine)s as controlled DNA delivery vectors. The study offers new physical insights into the DNA release pathway including intermediate structures that have a high degree of structural heterogeneity and disassembly induced particle growth. The study identifies disassembly induced colloidal and morphological instability as an important issue to be addressed.
Collapse
Affiliation(s)
- Lei Wan
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, USA
| | | | | | | | | |
Collapse
|
39
|
Toma AC, de Frutos M, Livolant F, Raspaud E. DNA Condensed by Protamine: A “Short” or “Long” Polycation Behavior. Biomacromolecules 2009; 10:2129-34. [DOI: 10.1021/bm900275s] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Adriana C. Toma
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Sud, 91405 Orsay Cedex, France
| | - Marta de Frutos
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Sud, 91405 Orsay Cedex, France
| | - Françoise Livolant
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Sud, 91405 Orsay Cedex, France
| | - Eric Raspaud
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Sud, 91405 Orsay Cedex, France
| |
Collapse
|
40
|
Wan L, Manickam DS, Oupický D, Mao G. DNA release dynamics from reducible polyplexes by atomic force microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:12474-82. [PMID: 18839970 PMCID: PMC2825055 DOI: 10.1021/la802088y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Controlled intracellular disassembly of polyelectrolyte complexes of polycations and DNA (polyplexes) is a crucial step for the success of nonviral gene delivery. Motivated by our previous observation of different gene delivery performances among multiblock reducible copolypeptide vectors ( Manickam, D. S. ; Oupicky, D. Bioconjugate Chem. 2006, 17, 1395- 1403 ), atomic force microscopy is used to visualize plasmid DNA in various decondensed states from reducible polypeptide polyplexes under simulated physiological reducing conditions. DNA decondensation is triggered by reductive degradation of disulfide-containing cationic polypeptides. Striking differences in DNA release dynamics between polyplexes based on polypeptides of histidine-rich peptide (HRP, CKHHHKHHHKC) and nuclear localization signal (NLS, CGAGPKKKRKVC) peptide are presented. The HRP and NLS polyplexes are similar to each other in their initial morphology with a majority of them containing only one DNA plasmid. Upon reductive degradation by dithiothreitol, DNA is released from NLS abruptly regardless of the initial polyplex morphology, while DNA release from HRP polyplexes displays a gradual decondensation that is dependent on the size of polyplexes. The release rate is higher for larger HRP polyplexes. The smaller HRP polyplexes become unstable when they are in contact with expanding chains nearby. The results reveal potentially rich DNA release dynamics that can be controlled by subtle variation in multivalent counterion binding to DNA as well as the cellular matrix.
Collapse
Affiliation(s)
- Lei Wan
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202
| | - Devika S. Manickam
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48202
| | - David Oupický
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48202
| | - Guangzhao Mao
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202
- Corresponding author:
| |
Collapse
|
41
|
Mann A, Richa R, Ganguli M. DNA condensation by poly-l-lysine at the single molecule level: Role of DNA concentration and polymer length. J Control Release 2008; 125:252-62. [DOI: 10.1016/j.jconrel.2007.10.019] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Revised: 10/09/2007] [Accepted: 10/23/2007] [Indexed: 11/25/2022]
|