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Bos I, Brink E, Michels L, Sprakel J. DNA dynamics in complex coacervate droplets and micelles. SOFT MATTER 2022; 18:2012-2027. [PMID: 35191449 PMCID: PMC8905490 DOI: 10.1039/d1sm01787j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Single stranded DNA (ssDNA), or another polyanion, can be mixed with polycations to form liquid-like complex coacervates. When the polycations are replaced by cationic-neutral diblock copolymers, complex coacervate core micelles (C3Ms) can be formed instead. In both complex coacervates and C3Ms, dynamics plays an important role. Yet, to date, the effect of chain length on the dynamics effect is still not fully understood. The DNA complexes provide a versatile platform to further elucidate these chain length effects because the DNA is monodisperse and its length can be easily adapted. Therefore, we study in this paper the dynamics of fluorescently labelled ssDNA in both complex coacervate droplets and micelles. The DNA dynamics in the complex coacervate droplets is probed by fluorescence recovery after photobleaching (FRAP). We observe that the DNA diffusion coefficient depends more strongly on the DNA length than predicted by the sticky Rouse model and we show that this can be partly explained by changes in complex coacervate density, but that also other factors might play a role. We measure the molecular exchange of C3Ms by making use of Förster resonance energy transfer (FRET) and complement these measurements with Langevin dynamics simulations. We conclude that chain length polydispersity is the main cause of a broad distribution of exchange rates. We hypothesise that the different exchange rates that we observe for the monodisperse DNA are mainly caused by differences in dye interactions and show that the dye can indeed have a large effect on the C3M exchange. In addition, we show that a new description of the C3M molecular exchange is required that accounts among others for the effect of the length of the oppositely charged core species. Together our findings can help to better understand the dynamics in both specific DNA systems and in complex coacervate droplets and micelles in general.
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Affiliation(s)
- Inge Bos
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Eline Brink
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Lucile Michels
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Joris Sprakel
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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2
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Perico A. Electrostatic theory of the assembly of PAMAM dendrimers and DNA. Biopolymers 2016; 105:276-86. [PMID: 26756793 DOI: 10.1002/bip.22805] [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: 09/25/2015] [Revised: 12/21/2015] [Accepted: 12/30/2015] [Indexed: 11/05/2022]
Abstract
The electrostatic interactions mediated by counterions between a cationic PAMAM dendrimer, modelized as a sphere of radius and cationic surface charge highly increasing with generation, and a DNA, modelized as an anionic elastic line, are analytically calculated in the framework of condensation theory. Under these interactions the DNA is wrapped around the sphere. For excess phosphates relative to dendrimer primary amines, the free energy of the DNA-dendrimer complex displays an absolute minimum when the complex is weakly negatively overcharged. This overcharging opposes gene delivery. For a highly positive dendrimer and a DNA fixed by experimental conditions to a number of phosphates less than the number of dendrimer primary amines, excess amine charges, the dendrimer may at the same time bind stably DNA and interact with negative cell membranes to activate cell transfection in fair agreement with molecular simulations and experiments.
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Affiliation(s)
- Angelo Perico
- National Research Council (CNR), Institute for Macromolecular Studies (ISMAC), Genova, via De Marini 6, Genova, 16149, Italy
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Campbell MJ, Turner BM. Altered histone modifications in cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 754:81-107. [PMID: 22956497 DOI: 10.1007/978-1-4419-9967-2_4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In human health and disease the choreographed actions of a wide armory of transcription factors govern the regulated expression of coding and nonprotein coding genes. These actions are central to human health and are evidently aberrant in cancer. Central components of regulated gene expression are a variety of epigenetic mechanisms that include histone modifications. The post-translational modifications of histones are widespread and diverse, and appear to be spatial--temporally regulated in a highly intricate manner. The true functional consequences of these patterns of regulation are still emerging. Correlative evidence supports the idea that these patterns are distorted in malignancy on both a genome-wide and a discrete gene loci level. These patterns of distortion also often reflect the altered expression of the enzymes that control these histone states. Similarly gene expression patterns also appear to reflect a correlation with altered histone modifications at both the candidate loci and genome-wide level. Clarity is emerging in resolving these relationships between histone modification status and gene expression -patterns. For example, altered transcription factor interactions with the key co-activator and co-repressors, which in turn marshal many of the histone-modifying enzymes, may distort regulation of histone modifications at specific gene loci. In turn these aberrant transcriptional processes can trigger other altered epigenetic events such as DNA methylation and underline the aberrant and specific gene expression patterns in cancer. Considered in this manner, altered expression and recruitment of histone-modifying enzymes may underline the distortion to transcriptional responsiveness observed in malignancy. Insight from understanding these processes addresses the challenge of targeted epigenetic therapies in cancer.
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Affiliation(s)
- Moray J Campbell
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA.
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Spruijt E, van den Berg SA, Cohen Stuart MA, van der Gucht J. Direct measurement of the strength of single ionic bonds between hydrated charges. ACS NANO 2012; 6:5297-5303. [PMID: 22559075 DOI: 10.1021/nn301097y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The strength of ionic bonds is essentially unknown, despite their widespread occurrence in natural and man-made assemblies. Here, we use single-molecule force spectroscopy to measure their strength directly. We disrupt a complex between two oppositely charged polyelectrolyte chains and find two modes of rupture: one ionic bond at a time, or cooperative rupture of many bonds at once. For both modes, disruption of the ionic bonds can be described quantitatively as an activated process. The height of the energy barrier is not only lowered by added salt, but also by the applied force. We extract unperturbed ionic bond lifetimes that range from milliseconds for single ionic bonds at high salt concentration to tens of years for small complexes of five ionic bonds at low salt concentration.
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Affiliation(s)
- Evan Spruijt
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands.
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Shao N, Zhang K, Chen Y, He X, Zhang Y. Preparation and characterization of DNA aptamer based spin column for enrichment and separation of histones. Chem Commun (Camb) 2012; 48:6684-6. [PMID: 22644042 DOI: 10.1039/c2cc32376a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Core histones play a critical role in the regulation of chromatin-templated biological process. Here we have developed a novel approach to enrich histone proteins based on the recognition of a specific aptamer. The method shows good selectivity toward histone proteins and is able to extract histones directly from complex whole cell lysates.
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Affiliation(s)
- Nan Shao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, P. R. China
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6
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Perico A, Rapallo A. Clusters in strong polyelectrolyte solutions in the condensation theory approach. J Chem Phys 2011; 134:055108. [DOI: 10.1063/1.3533276] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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7
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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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8
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La Penna G, Perico A. Wrapped-around models for the lac operon complex. Biophys J 2010; 98:2964-73. [PMID: 20550909 PMCID: PMC2884243 DOI: 10.1016/j.bpj.2010.03.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Revised: 03/11/2010] [Accepted: 03/12/2010] [Indexed: 11/28/2022] Open
Abstract
The protein-DNA complex, involved in the lac operon of enteric bacteria, is paradigmatic in understanding the extent of DNA bending and plasticity due to interactions with protein assemblies acting as DNA regulators. For the lac operon, two classes of structures have been proposed: 1), with the protein tetramer lying away from the DNA loop (wrapped-away model); and 2), with the protein tetramer lying inside the DNA loop (wrapped-around model). A recently developed electrostatic analytical model shows that the size and net charge of the Lac protein tetramer allow the bending of DNA, which is consistent with another wrapped-around model from the literature. Coarse-grained models, designed based on this observation, are extensively investigated and show three kinds of wrapped-around arrangements of DNA and a lower propensity for wrapped-away configurations. Molecular dynamics simulations of an all-atom model, built on the basis of the most tightly collapsed coarse-grained model, show that most of the DNA double-helical architecture is maintained in the region between O3 and O1 DNA operators, that the DNA distortion is concentrated in the chain beyond the O1 operator, and that the protein tetramer can adapt the N-terminal domains to the DNA tension.
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Affiliation(s)
- Giovanni La Penna
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo-Metallici, Sesto Fiorentino, Florence, Italy.
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Donati I, Asaro F, Paoletti S. Experimental evidence of counterion affinity in alginates: the case of nongelling ion Mg2+. J Phys Chem B 2009; 113:12877-86. [PMID: 19736959 DOI: 10.1021/jp902912m] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The present contribution aims at testing experimentally the theoretical model previously devised (Donati, I.; Cesaro, A.; Paoletti, S.; Biomacromolecules 2006, 7, 281-287) for the description of the interaction between alginate and nongelling Mg(2+) ions. The model, based on an extension of the counterion condensation theory, introduces a contribution of free energy of affinity, DeltaG(aff,0), which depends on the monomer composition of the polyuronate. In the present work, three different alginates separately mimicking the mannuronan (polyM), the guluronan (polyG), and the polyalternating (polyMG) components of alginate, together with a natural alginate isolated from Laminaria hyperborea ( L. hyperborea ), were examined. They were treated with Mg(2+) ions, and relative variations in scattered light intensity, isothermal calorimetry (DeltaH(mix)), specific viscosity, and (23)Na NMR longitudinal relaxation rates were monitored with respect to samples at the same ionic strength but containing only Na(+) ions. The fraction of condensed magnesium counterions was found to be strongly dependent on alginate composition, increasing along the series mannuronan < polyalternating approximately L. hyperborea < guluronan, thus in good agreement with the theoretical predictions.
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Affiliation(s)
- Ivan Donati
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 1, I-34127 Trieste, Italy.
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Cinacchi G, La Penna G, Perico A. Anisotropic Internucleosome Interactions and Geometrical Constraints in the Organization of Chromatin. Macromolecules 2007. [DOI: 10.1021/ma071343l] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giorgio Cinacchi
- Università di Pisa, Dipartimento di Chimica e Chimica Industriale, Via Risorgimento 35, 56126 Pisa, Italy
| | - Giovanni La Penna
- Consiglio Nazionale delle Ricerche, Istituto per la Chimica dei Composti Organo-Metallici, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy
| | - Angelo Perico
- Consiglio Nazionale delle Ricerche, Istituto per lo Studio delle Macromolecole, Via De Marini 6, 16149 Genova, Italy
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12
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Engelhardt M. Choreography for nucleosomes: the conformational freedom of the nucleosomal filament and its limitations. Nucleic Acids Res 2007; 35:e106. [PMID: 17704136 PMCID: PMC2018644 DOI: 10.1093/nar/gkm560] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Eukaryotic DNA is organized into nucleosomes by coiling around core particles of histones, forming a nucleosomal filament. The significance for the conformation of the filament of the DNA entry/exit angle (alpha) at the nucleosome, the angle of rotation (beta) of nucleosomes around their interconnecting DNA (linker DNA) and the length of the linker DNA, has been studied by means of wire models with straight linkers. It is shown that variations in alpha and beta endow the filament with an outstanding conformational freedom when alpha is increased beyond 60-90 degrees, owing to the ability of the filament to change between forward right-handed and backward left-handed coiling. A wealth of different helical and looped conformations are formed in response to repeated beta sequences, and helical conformations are shown to be able to contract to a high density and to associate pairwise into different types of double fibers. Filaments with random beta sequences are characterized by relatively stable loop clusters connected by segments of higher flexibility. Displacement of core particles along the DNA in such fibers, combined with limited twisting of the linkers, can generate the beta sequence necessary for compaction into a regular helix, thus providing a model for heterochromatinization.
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Affiliation(s)
- Mogens Engelhardt
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
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Arcesi L, La Penna G, Perico A. Generalized electrostatic model of the wrapping of DNA around oppositely charged proteins. Biopolymers 2007; 86:127-35. [PMID: 17330872 DOI: 10.1002/bip.20711] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Histonelike proteins in prokaryotes and histone octamers in eukaryotes carry large positive charges, which are responsible of strong electrostatic interactions with DNA. As a result, DNA wraps around proteins and genetic information is condensed. We describe a generalized model of these electrostatic interactions mediated by salt that explains the wrapping of DNA around the nucleosome octamer, around remodeling factors in eukaryotes and around histonelike proteins in prokaryotes. It comes out that small changes in protein dimension and charge produce large effects in the supramolecular DNA-protein architecture.
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Affiliation(s)
- Luca Arcesi
- Consiglio Nazionale delle Ricerche, Institute for Macromolecular Studies, Genova, Via De Marini 6, 16149 Genova, Italy
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14
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La Penna G, Furlan S, Perico A. Modeling H3 histone N-terminal tail and linker DNA interactions. Biopolymers 2006; 83:135-47. [PMID: 16691563 DOI: 10.1002/bip.20538] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Molecular dynamics computer simulations were performed for the 25-residue N-terminal tail of the H3 histone protein in the proximity of a DNA segment of 10 base pairs (bp), representing a model for the linker DNA in chromatin. Several least biased configurations were used as initial configurations. The secondary structure content of the protein was increased by the presence of DNA close to it, but the locations of the secondary motifs were different for different initial orientations of the DNA grooves with respect to the protein. As a common feature to all simulations, the electrostatic attraction between negatively charged DNA and positively charged protein was screened by the water solvent and counterbalanced by the intrinsic compaction of the protein due to hydrophobic effects. The protein secondary structure limited the covering of DNA by the protein to 4-5 bp. The degree of compaction and charge density of the bound protein suggests a possible role of H3 tail in a nonspecific bending and plasticity of the linker DNA when the protein is located in the crowded dense chromatin.
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Affiliation(s)
- Giovanni La Penna
- National Research Council, Institute for Macromolecular Studies, Via De Marini 6, 16149 Genova, Italy.
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