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Kolesnikov ES, Gushchin IY, Zhilyaev PA, Onufriev AV. Why Na+ has higher propensity than K+ to condense DNA in a crowded environment. J Chem Phys 2023; 159:145103. [PMID: 37815107 DOI: 10.1063/5.0159341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/22/2023] [Indexed: 10/11/2023] Open
Abstract
Experimentally, in the presence of the crowding agent polyethylene glycol (PEG), sodium ions compact double-stranded DNA more readily than potassium ions. Here, we have used molecular dynamics simulations and the "ion binding shells model" of DNA condensation to provide an explanation for the observed variations in condensation of short DNA duplexes in solutions containing different monovalent cations and PEG; several predictions are made. According to the model we use, externally bound ions contribute the most to the ion-induced aggregation of DNA duplexes. The simulations reveal that for two adjacent DNA duplexes, the number of externally bound Na+ ions is larger than the number of K+ ions over a wide range of chloride concentrations in the presence of PEG, providing a qualitative explanation for the higher propensity of sodium ions to compact DNA under crowded conditions. The qualitative picture is confirmed by an estimate of the corresponding free energy of DNA aggregation that is at least 0.2kBT per base pair more favorable in solution with NaCl than with KCl at the same ion concentration. The estimated attraction free energy of DNA duplexes in the presence of Na+ depends noticeably on the DNA sequence; we predict that AT-rich DNA duplexes are more readily condensed than GC-rich ones in the presence of Na+. Counter-intuitively, the addition of a small amount of a crowding agent with high affinity for the specific condensing ion may lead to the weakening of the ion-mediated DNA-DNA attraction, shifting the equilibrium away from the DNA condensed phase.
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Affiliation(s)
- Egor S Kolesnikov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Department of Physics, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Ivan Yu Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Petr A Zhilyaev
- The Center for Materials Technologies, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow 121205, Russia
| | - Alexey V Onufriev
- Department of Physics, Virginia Tech, Blacksburg, Virginia 24061, USA
- Department of Computer Science, Virginia Tech, 2160C Torgersen Hall, Blacksburg, Virginia 24061, USA
- Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, USA
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2
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Forte J, Hanieh PN, Poerio N, Olimpieri T, Ammendolia MG, Fraziano M, Fabiano MG, Marianecci C, Carafa M, Bordi F, Sennato S, Rinaldi F. Mucoadhesive Rifampicin-Liposomes for the Treatment of Pulmonary Infection by Mycobacterium abscessus: Chitosan or ε-Poly-L-Lysine Decoration. Biomolecules 2023; 13:924. [PMID: 37371504 DOI: 10.3390/biom13060924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Mycobacterium abscessus (Mabs) is a dangerous non-tubercular mycobacterium responsible for severe pulmonary infections in immunologically vulnerable patients, due to its wide resistance to many different antibiotics which make its therapeutic management extremely difficult. Drug nanocarriers as liposomes may represent a promising delivery strategy against pulmonary Mabs infection, due to the possibility to be aerosolically administrated and to tune their properties in order to increase nebulization resistance and retainment of encapsulated drug. In fact, liposome surface can be modified by decoration with mucoadhesive polymers to enhance its stability, mucus penetration and prolong its residence time in the lung. The aim of this work is to employ Chitosan or ε-poly-L-lysine decoration for improving the properties of a novel liposomes composed by hydrogenated phosphatidyl-choline from soybean (HSPC) and anionic 1,2-Dipalmitoyl-sn-glycero-3-phosphorylglycerol sodium salt (DPPG) able to entrap Rifampicin. A deep physicochemical characterization of polymer-decorated liposomes shows that both polymers improve mucoadhesion without affecting liposome features and Rifampicin entrapment efficiency. Therapeutic activity on Mabs-infected macrophages demonstrates an effective antibacterial effect of ε-poly-L-lysine liposomes with respect to chitosan-decorated ones. Altogether, these results suggest a possible use of ε-PLL liposomes to improve antibiotic delivery in the lung.
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Affiliation(s)
- Jacopo Forte
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Patrizia Nadia Hanieh
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Noemi Poerio
- Dipartimento di Biologia Università di Roma "Tor Vergata", Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Tommaso Olimpieri
- Dipartimento di Biologia Università di Roma "Tor Vergata", Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Maria Grazia Ammendolia
- Centro Nazionale Tecnologie Innovative in Sanità Pubblica, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy
| | - Maurizio Fraziano
- Dipartimento di Biologia Università di Roma "Tor Vergata", Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Maria Gioia Fabiano
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Carlotta Marianecci
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Maria Carafa
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Federico Bordi
- Istituto dei Sistemi Complessi (ISC)-CNR, sede "Sapienza" and Dipartimento di Fisica, Sapienza Università di Roma, 00185 Rome, Italy
| | - Simona Sennato
- Istituto dei Sistemi Complessi (ISC)-CNR, sede "Sapienza" and Dipartimento di Fisica, Sapienza Università di Roma, 00185 Rome, Italy
| | - Federica Rinaldi
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
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3
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Dillion Lima Cavalcanti I, Humberto Xavier Junior F, Stela Santos Magalhães N, Cajubá de Britto Lira Nogueira M. ISOTHERMAL TITRATION CALORIMETRY (ITC) AS A PROMISING TOOL IN PHARMACEUTICAL NANOTECHNOLOGY. Int J Pharm 2023; 641:123063. [PMID: 37209790 DOI: 10.1016/j.ijpharm.2023.123063] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/10/2023] [Accepted: 05/13/2023] [Indexed: 05/22/2023]
Abstract
Isothermal titration calorimetry (ITC) is a technique for evaluating the thermodynamic profiles of connection between two molecules, allowing the experimental design of nanoparticles systems with drugs and/or biological molecules. Taking into account the relevance of ITC, we conducted, therefore, an integrative revision of the literature, from 2000 to 2023, on the main purposes of using this technique in pharmaceutical nanotechnology. The search were carried out in the Pubmed, Sciencedirect, Web of Science, and Scifinder databases using the descriptors "Nanoparticles", "Isothermal Titration Calorimetry", and "ITC". We have observed that the ITC technique has been increasingly used in pharmaceutical nanotechnology, seeking to understand the interaction mechanisms in the formation of nanoparticles. Additionally, to understand the behavior of nanoparticles with biological materials (proteins, DNA, cell membranes, among others), thereby helping to understand the behavior of nanocarriers in vivo studies. As a contribution, we intended to reveal the importance of ITC in the laboratory routine, which is itself a quick and easy technique to obtain relevant results that help to optimize the nanosystems formulation process.
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Affiliation(s)
- Iago Dillion Lima Cavalcanti
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego - Cidade Universitária, Recife - PE, Brazil
| | - Francisco Humberto Xavier Junior
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego - Cidade Universitária, Recife - PE, Brazil; Department of Pharmacy, Pharmaceutical Biotechnology Laboratory (BioTecFarm), Federal University of Paraíba (UFPB), Campus I Lot. Cidade Universitaria, PB, 58051-900, Brazil
| | - Nereide Stela Santos Magalhães
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego - Cidade Universitária, Recife - PE, Brazil
| | - Mariane Cajubá de Britto Lira Nogueira
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego - Cidade Universitária, Recife - PE, Brazil; Laboratory of Nanotechnology, Biotechnology and Cell Culture (NanoBioCel), Academic Center of Vitória, Federal University of Pernambuco (CAV/UFPE), R. Alto do Reservatório - Alto José Leal, Vitória de Santo Antão - PE, 55608-680, Brazil.
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Härk HH, Porosk L, de Mello LR, Arukuusk P, da Silva ER, Kurrikoff K. Modification of the Linker Amino Acid in the Cell-Penetrating Peptide NickFect55 Leads to Enhanced pDNA Transfection for In Vivo Applications. Pharmaceutics 2023; 15:pharmaceutics15030883. [PMID: 36986744 PMCID: PMC10051810 DOI: 10.3390/pharmaceutics15030883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/11/2023] Open
Abstract
Despite numerous efforts over the last three decades, nucleic acid-based therapeutics still lack delivery platforms in the clinical stage. Cell-penetrating peptides (CPPs) may offer solutions as potential delivery vectors. We have previously shown that designing a “kinked” structure in the peptide backbone resulted in a CPP with efficient in vitro transfection properties. Further optimization of the charge distribution in the C-terminal part of the peptide led to potent in vivo activity with the resultant CPP NickFect55 (NF55). Currently, the impact of the linker amino acid was further investigated in the CPP NF55, with the aim to discover potential transfection reagents for in vivo application. Taking into account the expression of the delivered reporter in the lung tissue of mice, and the cell transfection in the human lung adenocarcinoma cell line, the new peptides NF55-Dap and NF55-Dab* have a high potential for delivering nucleic acid-based therapeutics to treat lung associated diseases, such as adenocarcinoma.
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Affiliation(s)
- Heleri H. Härk
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia; (L.P.); (P.A.); (K.K.)
- Correspondence:
| | - Ly Porosk
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia; (L.P.); (P.A.); (K.K.)
| | - Lucas R. de Mello
- Departamento de Biofisica, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil; (L.R.d.M.); (E.R.d.S.)
| | - Piret Arukuusk
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia; (L.P.); (P.A.); (K.K.)
| | - Emerson R. da Silva
- Departamento de Biofisica, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil; (L.R.d.M.); (E.R.d.S.)
| | - Kaido Kurrikoff
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia; (L.P.); (P.A.); (K.K.)
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Giona RM, Vitorazi L, Loh W. Assessing the Contribution of the Neutral Blocks in DNA/Block-Copolymer Polyplexes: Poly(acrylamide) vs. Poly(ethylene Oxide). Molecules 2023; 28:molecules28010398. [PMID: 36615592 PMCID: PMC9824764 DOI: 10.3390/molecules28010398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/24/2022] [Accepted: 12/26/2022] [Indexed: 01/04/2023] Open
Abstract
The interaction of DNA with different block copolymers, namely poly (trimethylammonium chloride methacryloyoxy)ethyl)-block-poly(acrylamide), i.e., (PTEA)-b-(PAm), and poly (trimethylammonium chloride methacryloyoxy)ethyl)-block-poly(ethylene oxide), i.e., (PTEA)-b-(PEO), was studied. The nature of the cationic block was maintained fixed (PTEA), whereas the neutral blocks contained varying amounts of acrylamide or (ethylene oxide) units. According to results from isothermal titration microcalorimetry measurements, the copolymers interaction with DNA is endothermic with an enthalpy around 4.0 kJ mol−1 of charges for (PTEA)-b-(PAm) and 5.5 kJ mol−1 of charges for (PTEA)-b-(PEO). The hydrodynamic diameters of (PTEA)-b-(PEO)/DNA and (PTEA)-b-(PAm)/DNA polyplexes prepared by titration were around 200 nm at charge ratio (Z+/−) < 1. At Z+/− close and above 1, the (PTEA)50-b-(PAm)50/DNA and (PTEA)50-b-(PAm)200/DNA polyplexes precipitated. Interestingly, (PTEA)50-b-(PAm)1000/DNA polyplexes remained with a size of around 300 nm even after charge neutralization, probably due to the size of the neutral block. Conversely, for (PTEA)96-b-(PEO)100/DNA polyplexes, the size distribution was broad, indicating a more heterogeneous system. Polyplexes were also prepared by direct mixture at Z+/− of 2.0, and they displayed diameters around 120−150 nm, remaining stable for more than 10 days. Direct and reverse titration experiments showed that the order of addition affects both the size and charge of the resulting polyplexes.
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Affiliation(s)
- Renata Mello Giona
- LaMaFI—Laboratório de Materiais e Fenômenos de Interface, Chemistry Department, Universidade Tecnológica Federal do Paraná (UTFPR), Medianeira, Curitiba 85884-000, Paraná (PR), Brazil
- Institute of Chemistry, Universidade Estadual de Campinas (UNICAMP), Caixa Postal 6154, Campinas 13083-970, São Paulo State (SP), Brazil
| | - Letícia Vitorazi
- Institute of Chemistry, Universidade Estadual de Campinas (UNICAMP), Caixa Postal 6154, Campinas 13083-970, São Paulo State (SP), Brazil
- Laboratório de Materiais Poliméricos, EEIMVR, Universidade Federal Fluminense, Volta Redonda 27255-125, Rio de Janeiro (RJ), Brazil
| | - Watson Loh
- Institute of Chemistry, Universidade Estadual de Campinas (UNICAMP), Caixa Postal 6154, Campinas 13083-970, São Paulo State (SP), Brazil
- Correspondence:
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6
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First direct evidence for direct cell-membrane penetrations of polycationic homopoly(amino acid)s produced by bacteria. Commun Biol 2022; 5:1132. [PMID: 36289442 PMCID: PMC9606270 DOI: 10.1038/s42003-022-04110-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/13/2022] [Indexed: 11/08/2022] Open
Abstract
Bacteria produce polycationic homopoly(amino acid)s, which are characterized by isopeptide backbones. Although the biological significance of polycationic homopoly(amino acid)s remains unclear, increasing attention has recently been focused on their potential use to achieve cellular internalization. Here, for the first time, we provide direct evidence that two representative bacterial polycationic isopeptides, ε-poly-L-α-lysine (ε-PαL) and ε-oligo-L-β-lysine (ε-OβL), were internalized into mammalian cells by direct cell-membrane penetration and then diffused throughout the cytosol. In this study, we used clickable ε-PαL and ε-OβL derivatives carrying a C-terminal azide group, which were enzymatically produced and then conjugated with a fluorescent dye to analyze subcellular localization. Interestingly, fluorescent proteins conjugated with the clickable ε-PαL or ε-OβL were also internalized into cells and diffused throughout the cytosol. Notably, a Cre recombinase conjugate with ε-PαL entered cells and mediated the Cre/loxP recombination, and ε-PαL was found to deliver a full-length IgG antibody to the cytosol and nucleus.
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7
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Park HS, Kang YK. Exploring Helical Folding in Oligomers of Cyclopentane-Based ϵ-Amino Acids: A Computational Study. Chemistry 2022; 11:e202100253. [PMID: 35083888 PMCID: PMC8886640 DOI: 10.1002/open.202100253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/21/2021] [Indexed: 11/28/2022]
Abstract
The conformational preferences of oligopeptides of an ϵ‐amino acid (2‐((1R,3S)‐3‐(aminomethyl)cyclopentyl)acetic acid, Amc5a) with a cyclopentane substituent in the Cβ−Cγ−Cδ sequence of the backbone were investigated using DFT methods in chloroform and water. The most preferred conformation of Amc5a oligomers (dimer to hexamer) was the H16 helical structure both in chloroform and water. Four residues were found to be sufficient to induce a substantial H16 helix population in solution. The Amc5a hexamer adopted a stable left‐handed (M)‐2.316 helical conformation with a rise of 4.8 Å per turn. The hexamer of Ampa (an analogue of Amc5a with replacing cyclopentane by pyrrolidine) adopted the right‐handed mixed (P)‐2.918/16 helical conformation in chloroform and the (M)‐2.416 helical conformation in water. Therefore, hexamers of ϵ‐amino acid residues exhibited different preferences of helical structures depending on the substituents in peptide backbone and the solvent polarity as well as the chain length.
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Affiliation(s)
- Hae Sook Park
- Department of Nursing, Cheju Halla University, Cheju, 63092, Republic of Korea
| | - Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
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8
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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.
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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.
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Tolokh IS, Drozdetski AV, Pollack L, Baker NA, Onufriev AV. Multi-shell model of ion-induced nucleic acid condensation. J Chem Phys 2016; 144:155101. [PMID: 27389241 PMCID: PMC4841795 DOI: 10.1063/1.4945382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 03/17/2016] [Indexed: 11/15/2022] Open
Abstract
We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes induced by trivalent cobalt(iii) hexammine (CoHex) ions. The model is based on partitioning of bound counterion distribution around single NA duplex into "external" and "internal" ion binding shells distinguished by the proximity to duplex helical axis. In the aggregated phase the shells overlap, which leads to significantly increased attraction of CoHex ions in these overlaps with the neighboring duplexes. The duplex aggregationfree energy is decomposed into attractive and repulsive components in such a way that they can be represented by simple analytical expressions with parameters derived from molecular dynamic simulations and numerical solutions of Poisson equation. The attractive term depends on the fractions of bound ions in the overlapping shells and affinity of CoHex to the "external" shell of nearly neutralized duplex. The repulsive components of the free energy are duplex configurational entropy loss upon the aggregation and the electrostatic repulsion of the duplexes that remains after neutralization by bound CoHex ions. The estimates of the aggregationfree energy are consistent with the experimental range of NA duplex condensation propensities, including the unusually poor condensation of RNA structures and subtle sequence effects upon DNAcondensation. The model predicts that, in contrast to DNA, RNA duplexes may condense into tighter packed aggregates with a higher degree of duplex neutralization. An appreciable CoHex mediated RNA-RNA attraction requires closer inter-duplex separation to engage CoHex ions (bound mostly in the "internal" shell of RNA) into short-range attractive interactions. The model also predicts that longer NA fragments will condense more readily than shorter ones. The ability of this model to explain experimentally observed trends in NAcondensation lends support to proposed NAcondensation picture based on the multivalent "ion binding shells."
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Affiliation(s)
- Igor S Tolokh
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, USA
| | | | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853-3501, USA
| | - Nathan A Baker
- Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Alexey V Onufriev
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, USA
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10
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Vvedenskii AV, Sizova SV, Kuzmich AI. The physicochemical properties of histone H2A and modified histone H2A-TAT complexes with plasmid DNA. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915050231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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11
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Markedly lowering the viscosity of aqueous solutions of DNA by additives. Int J Pharm 2015; 494:66-72. [PMID: 26260229 DOI: 10.1016/j.ijpharm.2015.08.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/22/2015] [Accepted: 08/05/2015] [Indexed: 01/15/2023]
Abstract
Aqueous solutions of DNAs, while relevant in drug delivery and as a target of therapies, are often very viscous making them difficult to use. Since less viscous solutions could enable targeted drug delivery and/or therapies, the purpose of the present work was to explore compounds capable of "thinning" such DNA solutions under pharmaceutically relevant conditions. To this end, viscosities of aqueous solutions of DNAs and model polyanions were examined at 25 °C in the absence and presence of a number of bulky organic salts (and related compounds) previously found to substantially lower the viscosities of concentrated protein solutions. Out of two dozen compounds tested, only three were found to be effective; the FDA-approved local anesthetics lidocaine, mepivacaine, and prilocaine at near-isotonic concentrations and pH 6.4 lowered solution viscosity of three different DNAs up to about 20 fold. The observed multi-fold viscosity reductions appear to be due to these bulky organic salts' structure-specific non-covalent binding to nucleotide bases resulting in denaturation (unwinding) to, and stabilization of, single-stranded DNA.
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12
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Smith RJ, Beck RW, Prevette LE. Impact of molecular weight and degree of conjugation on the thermodynamics of DNA complexation and stability of polyethylenimine-graft-poly(ethylene glycol) copolymers. Biophys Chem 2015; 203-204:12-21. [DOI: 10.1016/j.bpc.2015.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 04/27/2015] [Accepted: 04/28/2015] [Indexed: 12/13/2022]
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13
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Roviello GN, Musumeci D, Roviello V. Cationic peptides as RNA compaction agents: a study on the polyA compaction activity of a linear alpha,epsilon-oligo-L-lysine. Int J Pharm 2015; 485:244-8. [PMID: 25772417 DOI: 10.1016/j.ijpharm.2015.03.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/05/2015] [Accepted: 03/09/2015] [Indexed: 11/16/2022]
Abstract
In this work, we investigate the compaction activity of a sequential alpha,epsilon-peptide composed of l-lysines towards two RNA targets, in view of its possible pharmaceutical application in RNA-targeting and RNA delivery. The basic oligolysine, object of the present study, proved not only to be efficient in compacting the single-stranded polyA RNA, but also to strongly interact with the polyA·polyU complex, as evidenced by CD-binding and UV-melting experiments. In particular, the marked differences in the CD spectra of the RNA targets upon addition of the peptide, as well as the different UV melting behaviour for the polyA·polyU complex in the presence and absence of the peptide, sustain the hypothesis of a strong RNA compaction capacity of the alpha,epsilon-oligolysine. Finally, by using HPLC analysis, we found a good resistance of the peptide against the lytic action of human serum, an important requirement in view of in vitro/in vivo biological assays.
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Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini - CNR, via Mezzocannone 16, 80134 Napoli, Italy.
| | - Domenica Musumeci
- Istituto di Biostrutture e Bioimmagini - CNR, via Mezzocannone 16, 80134 Napoli, Italy; Dipartimento di Scienze Chimiche, Università di Napoli "Federico II", 80126 Napoli, Italy
| | - Valentina Roviello
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale(DICMaPI), Università di Napoli "Federico II", 80125 Napoli, Italy
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Vasconcelos L, Madani F, Arukuusk P, Pärnaste L, Gräslund A, Langel U. Effects of cargo molecules on membrane perturbation caused by transportan10 based cell-penetrating peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:3118-29. [PMID: 25135660 DOI: 10.1016/j.bbamem.2014.08.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 07/30/2014] [Accepted: 08/08/2014] [Indexed: 11/25/2022]
Abstract
Cell-penetrating peptides with the ability to escape endosomes and reach the target are of great value as delivery vectors for different bioactive cargoes and future treatment of human diseases. We have studied two such peptides, NickFect1 and NickFect51, both originated from stearylated transportan10 (PF3). To obtain more insight into the mechanism(s) of peptide delivery and the biophysical properties of an efficient vector system, we investigated the effect of different bioactive oligonucleotide cargoes on peptide-membrane perturbation and peptide structural induction. We studied the membrane interactions of the peptides with large unilamellar vesicles and compared their effects with parent peptides transportan10 and PF3. In addition, cellular uptake and peptide-mediated oligonucleotide delivery were analyzed. Calcein leakage experiments showed that similar to transportan10, NickFect51 caused a significant degree of membrane leakage, whereas NickFect1, similar to PF3, was less membrane perturbing. The results are in agreement with previously published results indicating that NickFect51 is a more efficient endosomal escaper. However, the presence of a large cargo like plasmid DNA inhibited NickFect's membrane perturbation and cellular uptake efficiency of the peptide was reduced. We conclude that the pathway for cellular uptake of peptide complexes is cargo dependent, whereas the endosomal escape efficacy depends on peptide hydrophobicity and chemical structure. For small interfering RNA delivery, NickFect51 appears to be optimal. The biophysical signature shows that the peptide alone causes membrane perturbation, but the cargo complex does not. These two biophysical characteristics of the peptide and its cargo complex may be the signature of an efficient delivery vector system.
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Affiliation(s)
- Luís Vasconcelos
- Department of Neurochemistry, Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden.
| | - Fatemeh Madani
- Department of Neurochemistry, Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden
| | - Piret Arukuusk
- Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu, Estonia
| | - Ly Pärnaste
- Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu, Estonia
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden
| | - Ulo Langel
- Department of Neurochemistry, Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden; Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu, Estonia
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15
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Tolokh IS, Pabit SA, Katz AM, Chen Y, Drozdetski A, Baker N, Pollack L, Onufriev AV. Why double-stranded RNA resists condensation. Nucleic Acids Res 2014; 42:10823-31. [PMID: 25123663 PMCID: PMC4176364 DOI: 10.1093/nar/gku756] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The addition of small amounts of multivalent cations to solutions containing double-stranded DNA leads to inter-DNA attraction and eventual condensation. Surprisingly, the condensation is suppressed in double-stranded RNA, which carries the same negative charge as DNA, but assumes a different double helical form. Here, we combine experiment and atomistic simulations to propose a mechanism that explains the variations in condensation of short (25 base-pairs) nucleic acid (NA) duplexes, from B-like form of homopolymeric DNA, to mixed sequence DNA, to DNA:RNA hybrid, to A-like RNA. Circular dichroism measurements suggest that duplex helical geometry is not the fundamental property that ultimately determines the observed differences in condensation. Instead, these differences are governed by the spatial variation of cobalt hexammine (CoHex) binding to NA. There are two major NA-CoHex binding modes--internal and external--distinguished by the proximity of bound CoHex to the helical axis. We find a significant difference, up to 5-fold, in the fraction of ions bound to the external surfaces of the different NA constructs studied. NA condensation propensity is determined by the fraction of CoHex ions in the external binding mode.
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Affiliation(s)
- Igor S Tolokh
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853-3501, USA
| | - Andrea M Katz
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853-3501, USA
| | - Yujie Chen
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853-3501, USA
| | | | - Nathan Baker
- Applied Statistics and Computational Modeling Group, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853-3501, USA
| | - Alexey V Onufriev
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA Department of Physics, Virginia Tech, Blacksburg, VA 24061, USA
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16
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Zeng Z, Peng Z, Chen L, Chen Y. Facile fabrication of thermally responsive Pluronic F127-based nanocapsules for controlled release of doxorubicin hydrochloride. Colloid Polym Sci 2014. [DOI: 10.1007/s00396-014-3183-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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17
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Arukuusk P, Pärnaste L, Oskolkov N, Copolovici DM, Margus H, Padari K, Möll K, Maslovskaja J, Tegova R, Kivi G, Tover A, Pooga M, Ustav M, Langel U. New generation of efficient peptide-based vectors, NickFects, for the delivery of nucleic acids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:1365-73. [PMID: 23357356 DOI: 10.1016/j.bbamem.2013.01.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 01/11/2013] [Accepted: 01/16/2013] [Indexed: 12/20/2022]
Abstract
Harnessing of a branched structure is a novel approach in the design of cell-penetrating peptides and it has provided highly efficient transfection reagents for intracellular delivery of nucleic acids. The new stearylated TP10 analogs, NickFects, condense plasmid DNA, splice correcting oligonucleotides and short interfering RNAs into stable nanoparticles with a size of 62-160nm. Such nanoparticles have a negative surface charge (-11 to -18mV) in serum containing medium and enable highly efficient gene expression, splice correction and gene silencing. One of the novel peptides, NickFect51 is capable of transfecting plasmid DNA into a large variety of cell lines, including refractory suspension and primary cells and in several cases exceeds the transfection level of commercially available reagent Lipofectamine™ 2000 without any cytotoxic side effects. Additionally we demonstrate the advantages of NickFect51 in a protein production system, QMCF technology, for expression and production of recombinant proteins in hardly transfectable suspension cells.
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Affiliation(s)
- Piret Arukuusk
- Institute of Technology, University of Tartu, Tartu, Estonia.
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18
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Yan J, Berezhnoy NV, Korolev N, Su CJ, Nordenskiöld L. Structure and internal organization of overcharged cationic-lipid/peptide/DNA self-assembly complexes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:1794-800. [DOI: 10.1016/j.bbamem.2012.03.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 03/15/2012] [Accepted: 03/30/2012] [Indexed: 10/28/2022]
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19
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Korolev N, Berezhnoy NV, Eom KD, Tam JP, Nordenskiöld L. A universal description for the experimental behavior of salt-(in)dependent oligocation-induced DNA condensation. Nucleic Acids Res 2012; 40:2808-21. [PMID: 22563605 PMCID: PMC3729243 DOI: 10.1093/nar/gks214] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We report a systematic study of the condensation of plasmid DNA by oligocations with variation of the charge, Z, from +3 to +31. The oligocations include a series of synthetic linear ε-oligo(L-lysines), (denoted εKn, n = 3–10, 31; n is the number of lysines with the ligand charge Z = n+1) and branched α-substituted homologues of εK10: εYK10, εLK10 (Z = +11); εRK10, εYRK10 and εLYRK10 (Z = +21). Data were obtained by light scattering, UV absorption monitored precipitation assay and isothermal titration calorimetry in a wide range concentrations of DNA and monovalent salt (KCl, CKCl). The dependence of EC50 (ligand concentration at the midpoint of DNA condensation) on C(KCl) shows the existence of a salt-independent regime at low C(KCl) and a salt-dependent regime with a steep rise of EC50 with increase of C(KCl). Increase of the ligand charge shifts the transition from the salt-independent to salt-dependent regime to higher C(KCl). A novel and simple relationship describing the EC50 dependence on DNA concentration, charge of the ligand and the salt-dependent dissociation constant of the ligand–DNA complex is derived. For the ε-oligolysines εK6–εK10, the experimental dependencies of EC50 on C(KCl) and Z are well-described by an equation with a common set of parameters. Implications from our findings for understanding DNA condensation in chromatin are discussed.
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Affiliation(s)
- Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.
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20
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Korolev N, Zhao Y, Allahverdi A, Eom KD, Tam JP, Nordenskiöld L. The effect of salt on oligocation-induced chromatin condensation. Biochem Biophys Res Commun 2012; 418:205-10. [DOI: 10.1016/j.bbrc.2011.12.112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Accepted: 12/21/2011] [Indexed: 11/24/2022]
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21
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Yan J, Korolev N, Eom KD, Tam JP, Nordenskiöld L. Biophysical Properties and Supramolecular Structure of Self-Assembled Liposome/ε-Peptide/DNA Nanoparticles: Correlation with Gene Delivery. Biomacromolecules 2011; 13:124-31. [DOI: 10.1021/bm201359r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiang Yan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore,
637551
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore,
637551
| | - Khee Dong Eom
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore,
637551
| | - James P. Tam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore,
637551
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore,
637551
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22
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Liu Y, Lu C, Yang Y, Fan Y, Yang R, Liu CF, Korolev N, Nordenskiöld L. Influence of histone tails and H4 tail acetylations on nucleosome-nucleosome interactions. J Mol Biol 2011; 414:749-64. [PMID: 22051513 DOI: 10.1016/j.jmb.2011.10.031] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 10/18/2011] [Accepted: 10/19/2011] [Indexed: 10/16/2022]
Abstract
Nucleosome-nucleosome interaction plays a fundamental role in chromatin folding and self-association. The cation-induced condensation of nucleosome core particles (NCPs) displays properties similar to those of chromatin fibers, with important contributions from the N-terminal histone tails. We study the self-association induced by addition of cations [Mg(2+), Ca(2+), cobalt(III)hexammine(3+), spermidine(3+) and spermine(4)(+)] for NCPs reconstituted with wild-type unmodified histones and with globular tailless histones and for NCPs with the H4 histone tail having lysine (K) acetylations or lysine-to-glutamine mutations at positions K5, K8, K12 and K16. In addition, the histone construct with the single H4K16 acetylation was investigated. Acetylated histones were prepared by a semisynthetic native chemical ligation method. The aggregation behavior of NCPs shows a general cation-dependent behavior similar to that of the self-association of nucleosome arrays. Unlike nucleosome array self-association, NCP aggregation is sensitive to position and nature of the H4 tail modification. The tetra-acetylation in the H4 tail significantly weakens the nucleosome-nucleosome interaction, while the H4 K→Q tetra-mutation displays a more modest effect. The single H4K16 acetylation also weakens the self-association of NCPs, which reflects the specific role of H4K16 in the nucleosome-nucleosome stacking. Tailless NCPs can aggregate in the presence of oligocations, which indicates that attraction also occurs by tail-independent nucleosome-nucleosome stacking and DNA-DNA attraction in the presence of cations. The experimental data were compared with the results of coarse-grained computer modeling for NCP solutions with explicit presence of mobile ions.
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Affiliation(s)
- Ying Liu
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore, Singapore
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23
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Roviello GN, Di Gaetano S, Capasso D, Franco S, Crescenzo C, Bucci EM, Pedone C. RNA-binding and viral reverse transcriptase inhibitory activity of a novel cationic diamino acid-based peptide. J Med Chem 2011; 54:2095-101. [PMID: 21391685 DOI: 10.1021/jm1012769] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel cationic peptide based on L-lysine and L-diaminobutyric acid was prepared for the first time by solid phase synthesis. After HPLC purification and ESI MS characterization, we studied by CD and IR spectroscopy the structural features of the novel basic peptide, which is able to form a β-turn-like structure. Furthermore, its interaction with DNA and RNA was investigated by CD and UV spectroscopy, which revealed a preferential RNA-binding ability of the sequential peptide, whereas its inhibitory activity toward HIV and Moloney murine leukemia virus (MMLV) reverse transcriptase action was evaluated by semiquantitative PCR. The cationic sequential peptide was able to inhibit the reverse transcriptase activity in both cases, even if our PCR data suggested a major activity in the case of HIV-RT, probably due to the stronger cationic peptide-protein interaction evidenced by UV spectroscopy.
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Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, I-80134 Napoli, Italy.
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24
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Moccia M, Roviello GN, Bucci EM, Pedone C, Saviano M. Synthesis of a l-lysine-based alternate alpha,epsilon-peptide: A novel linear polycation with nucleic acids-binding ability. Int J Pharm 2010; 397:179-83. [DOI: 10.1016/j.ijpharm.2010.06.044] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 06/24/2010] [Accepted: 06/24/2010] [Indexed: 10/19/2022]
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25
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Alatorre-Meda M, Taboada P, Krajewska B, Willemeit M, Deml A, Klösel R, Rodríguez JR. DNA−Poly(diallyldimethylammonium chloride) Complexation and Transfection Efficiency. J Phys Chem B 2010; 114:9356-66. [DOI: 10.1021/jp1016856] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Manuel Alatorre-Meda
- Grupo de Nanomateriales y Materia Blanda, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Grupo de Física de Coloides y Polímeros, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Faculty of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland; and Biontex Laboratories GmbH, D-82152
| | - Pablo Taboada
- Grupo de Nanomateriales y Materia Blanda, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Grupo de Física de Coloides y Polímeros, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Faculty of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland; and Biontex Laboratories GmbH, D-82152
| | - Barbara Krajewska
- Grupo de Nanomateriales y Materia Blanda, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Grupo de Física de Coloides y Polímeros, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Faculty of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland; and Biontex Laboratories GmbH, D-82152
| | - Markus Willemeit
- Grupo de Nanomateriales y Materia Blanda, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Grupo de Física de Coloides y Polímeros, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Faculty of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland; and Biontex Laboratories GmbH, D-82152
| | - Alexander Deml
- Grupo de Nanomateriales y Materia Blanda, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Grupo de Física de Coloides y Polímeros, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Faculty of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland; and Biontex Laboratories GmbH, D-82152
| | - Roland Klösel
- Grupo de Nanomateriales y Materia Blanda, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Grupo de Física de Coloides y Polímeros, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Faculty of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland; and Biontex Laboratories GmbH, D-82152
| | - Julio R. Rodríguez
- Grupo de Nanomateriales y Materia Blanda, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Grupo de Física de Coloides y Polímeros, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Faculty of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland; and Biontex Laboratories GmbH, D-82152
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26
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Kim W, Yamasaki Y, Jang WD, Kataoka K. Thermodynamics of DNA Condensation Induced by Poly(ethylene glycol)-block-polylysine through Polyion Complex Micelle Formation. Biomacromolecules 2010; 11:1180-6. [DOI: 10.1021/bm901305p] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Wankee Kim
- Department of Materials Science and Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, 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, Center for NanoBio Integration, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Core Research Program for Evolutional Science and Technology (CREST), Japan Science and
| | - Yuichi Yamasaki
- Department of Materials Science and Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, 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, Center for NanoBio Integration, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Core Research Program for Evolutional Science and Technology (CREST), Japan Science and
| | - Woo-Dong Jang
- Department of Materials Science and Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, 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, Center for NanoBio Integration, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Core Research Program for Evolutional Science and Technology (CREST), Japan Science and
| | - Kazunori Kataoka
- Department of Materials Science and Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, 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, Center for NanoBio Integration, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Core Research Program for Evolutional Science and Technology (CREST), Japan Science and
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27
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Survey of the year 2008: applications of isothermal titration calorimetry. J Mol Recognit 2010; 23:395-413. [DOI: 10.1002/jmr.1025] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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28
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Korolev N, Berezhnoy NV, Eom KD, Tam JP, Nordenskiöld L. A universal description for the experimental behavior of salt-(in)dependent oligocation-induced DNA condensation. Nucleic Acids Res 2009; 37:7137-50. [PMID: 19773427 PMCID: PMC2790876 DOI: 10.1093/nar/gkp683] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 08/03/2009] [Accepted: 08/03/2009] [Indexed: 01/19/2023] Open
Abstract
We report a systematic study of the condensation of plasmid DNA by oligocations with variation of the charge, Z, from +3 to +31. The oligocations include a series of synthetic linear epsilon-oligo(l-lysines), (denoted epsilonKn, n = 3-10, 31; n is the number of lysines equal to the ligand charge) and branched alpha-substituted homologues of epsilonK10: epsilonYK10, epsilonLK10 (Z = +10); epsilonRK10, epsilonYRK10 and epsilonLYRK10 (Z = +20). Data were obtained by light scattering, UV absorption monitored precipitation assay and isothermal titration calorimetry in a wide range concentrations of DNA and monovalent salt (KCl, C(KCl)). The dependence of EC(50) (ligand concentration at the midpoint of DNA condensation) on C(KCl) shows the existence of a salt-independent regime at low C(KCl) and a salt-dependent regime with a steep rise of EC(50) with increase of C(KCl). Increase of the ligand charge shifts the transition from the salt-independent to salt-dependent regime to higher C(KCl). A novel and simple relationship describing the EC(50) dependence on DNA concentration, charge of the ligand and the salt-dependent dissociation constant of the ligand-DNA complex is derived. For the epsilon-oligolysines epsilonK3-epsilonK10, the experimental dependencies of EC(50) on C(KCl) and Z are well-described by an equation with a common set of parameters. Implications from our findings for understanding DNA condensation in chromatin are discussed.
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Affiliation(s)
- Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | | | | | | | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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29
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Lin WJ, Chen TD, Liu CW. Synthesis and characterization of lactobionic acid grafted pegylated chitosan and nanoparticle complex application. POLYMER 2009. [DOI: 10.1016/j.polymer.2009.06.076] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Ma PL, Lavertu M, Winnik FM, Buschmann MD. New Insights into Chitosan−DNA Interactions Using Isothermal Titration Microcalorimetry. Biomacromolecules 2009; 10:1490-9. [DOI: 10.1021/bm900097s] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Pei Lian Ma
- Department of Chemical and Biomedical Engineering, Ecole Polytechnique de Montréal, P.O. 6079 Succ. Centre-Ville, Montreal, Quebec, H3C 3A7, Canada, and Department of Chemistry and Faculty of Pharmacy, Université de Montréal, P.O. 6128 Succ. Centre-Ville, Montreal, Quebec, H3C 3J7, Canada
| | - Marc Lavertu
- Department of Chemical and Biomedical Engineering, Ecole Polytechnique de Montréal, P.O. 6079 Succ. Centre-Ville, Montreal, Quebec, H3C 3A7, Canada, and Department of Chemistry and Faculty of Pharmacy, Université de Montréal, P.O. 6128 Succ. Centre-Ville, Montreal, Quebec, H3C 3J7, Canada
| | - Françoise M. Winnik
- Department of Chemical and Biomedical Engineering, Ecole Polytechnique de Montréal, P.O. 6079 Succ. Centre-Ville, Montreal, Quebec, H3C 3A7, Canada, and Department of Chemistry and Faculty of Pharmacy, Université de Montréal, P.O. 6128 Succ. Centre-Ville, Montreal, Quebec, H3C 3J7, Canada
| | - Michael D. Buschmann
- Department of Chemical and Biomedical Engineering, Ecole Polytechnique de Montréal, P.O. 6079 Succ. Centre-Ville, Montreal, Quebec, H3C 3A7, Canada, and Department of Chemistry and Faculty of Pharmacy, Université de Montréal, P.O. 6128 Succ. Centre-Ville, Montreal, Quebec, H3C 3J7, Canada
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