Rita S. Dias

DNA interactions with polymers and surfactants

Preface. Contributors. 1 Polyelectrolytes. Physicochemical Aspects and Biological Significance (Magnus Ullner). 1.1 Introduction. 1.2 Polyelectrolytes and Biological Function. 1.3 Electrostatic Interactions. 1.4 Solution Properties. 1.5 Flexibility. References. 2 Solution Behavior of Nucleic Acids (Rita S. Dias). 2.1 Biological Function of Nucleic Acids. 2.2 Discovery of DNA. 2.3 Structure of Nucleic Acids. 2.4 Nuclei Acids Nanostructures. 2.5 Behavior of DNA in Solution. 2.6 Melting of Double-Stranded DNA. Acknowledgments. References. 3 Single DNA Molecules: Compaction and Decompaction (Anatoly A. Zinchenko, Olga A. Pyshkina, Andrey V. Lezov, Vladimir G. Sergeyev, and Kenichi Yoshikawa). 3.1 Introduction. 3.2 Condensation and Compaction of DNA by Surfactants. 3.3 DNA Condensation by Cationic Liposomes. 3.4 DNA Compaction and Decompaction by Multivalent Cations. 3.5 DNA Compaction by Polycations. 3.6 Compaction of DNA in a Crowded Environment of Neutral Polymer. 3.7 Conclusion. References. 4 Interaction of DNA with Surfactants in Solution (Rita S. Dias, Kenneth Dawson, and Maria G. Miguel). 4.1 Introduction. 4.2 DNA-Cationic Surfactant Interactions. 4.3 DNA Covalent Gels and Their Interaction with Surfactants. 4.4 Applications. Acknowledgments. References. 5 Interaction of DNA with Cationic Polymers (Eric Raspaud, Adriana C. Toma, Francoise Livolant, and Joachim Radler). 5.1 Introduction. 5.2 Theory of DNA Interacting with Polycations. 5.3 Condensation of DNA, Phase Diagram, and Structure. 5.4 Formation of Polycation-DNA Complexes: Polyplexes. 5.5 DNA-Nanoparticles for Gene Delivery. 5.6 Cellular Uptake and Intracellular Interactions of Polyplexes. 5.7 Conclusion. Acknowledgment. References. 6 Interactions of Histones with DNA: Nucleosome Assembly, Stability, Dynamics, and Higher Order Structure (Karsten Rippe, Jacek Mazurkiewicz, and Nick Kepper). 6.1 Introduction. 6.2 Histones. 6.3 Structure of Histone-DNA Complexes. 6.4 Assembly of Nucleosomes and Chromatosomes. 6.5 Stability and Dynamics of Nucleosomes. 6.6 Higher Order Chromatin Structures. Acknowledgments. References. 7 Opening and Closing DNA: Theories on the Nucleosome (Igor M. Kulic and Helmut Schiessel). 7.1 Introduction. 7.2 Unwrapping Nucleosomes. 7.3 Nucleosome Sliding. 7.4 Transcription Through Nucleosomes. 7.5 Tail Bridging. 7.6 Discussion and Conclusion. Acknowledgment. References. 8 DNA-DNA Interactions (Lars Nordenskiold, Nikolay Korolev, and Alexander P. Lyubartsev). 8.1 Introduction. 8.2 The Statistical Polymer Solution Model Predicts DNA Collapse/Aggregation Phase Behavior. 8.3 DNA in Solution is Condensed to a Compact State by Multivalent Cationic Ligands. 8.4 Ion Correlation Effects Included in Theory and in Computer Modeling Explain DNA-DNA Attraction. 8.5 Conclusions and Future Prospects. References. 9 Hydration of DNA-Amphiphile Complexes (Cecilia Leal and Hakan Wennerstrom). 9.1 Introduction. 9.2 General Properties of DNA Double Helices and Cationic Aggregates. 9.3 Thermodynamics of DNA-Amphiphile Complexes. 9.4 Molecular Properties of DNA-Amphiphile Complexes. 9.5 Concluding Remarks. References. 10 DNA-Surfactant/Lipid Complexes at Liquid Interfaces (Dominique Langevin). 10.1 Introduction. 10.2 Soluble Surfactants. 10.3 Insoluble Surfactants. 10.4 Lipids. 10.5 Mixtures of Surfactants and Lipids. 10.6 Conclusion. References 286 11 DNA and DNA-Surfactant Complexes at Solid Surfaces (Marite Cardenas and Tommy Nylander). 11.1 Introduction. 11.2 Adsorption of DNA at Surfaces. 11.3 Attachment of DNA Surfaces-Strategies and Challenges. 11.4 DNA Structure on Surfaces-Comparison with Highly Charged Polyelectrolytes. 11.5 Some Applications-Arrays and Nanostamping. Acknowledgments. References. 12 Role of Correlation Forces for DNA-Cosolute Interactions (Malek O. Khan). 12.1 Introduction. 12.2 Experimental Evidence of DNA Condensation Induced by Electrostatic Agents. 12.3 Simulations Used to Characterize the DNA Compaction Mechanism. 12.4 Ion Correlations Limiting the Validity of DLVO Theory. 12.5 Ion Correlations Driving the Compaction of DNA. 12.6 Conformation of Compact DNA-The Coil to Toroid Transition. 12.7 Conclusions. References. 13 Simulations of Polyions: Compaction, Adsorption onto Surfaces, and Confinement (A.A.C.C. Pais and P. Linse). 13.1 Introduction. 13.2 Models. 13.3 Solutions of Polyions with Multivalent Counterions. 13.4 Polyion Adsorption onto Charged Surfaces. 13.5 Polyions in Confined Geometries. 13.6 Concluding Remarks. References. 14 Cross-linked DNA Gels and Gel Particles (Diana Costa, M. Carmen Moran, Maria G. Miguel, and Bjorn Lindman) 14.1 Introduction. 14.2 Covalently Cross-Linked DNA Gels. 14.3 ds-DNA versus ss-DNA: Skin Formation. 14.4 DNA Gel Particles. 14.5 Physical DNA Gels. References. 15 DNA as an Amphiphilic Polymer (Rita S. Dias, Maria G. Miguel, and Bjorn Lindman). 15.1 Some General Aspects of Self-Assembly. 15.2 Illustrations. References. 16 Lipid-DNA Interactions: Structure-Function Studies of Nanomaterials for Gene Delivery (Kai K. Ewert, Charles E. Samuel, and Cyrus R. Safinya). 16.1 Introduction. 16.2 Formation and Structures of CL-DNA Complexes. 16.3 Effect of the Lipid-DNA Charge Ratio ( r chg) on CL-DNA Complex Properties. 16.4 Effect of the Membrane Charge Density (sM) on CL-DNA Complex Properties. 16.5 Effect of Nonlamellar CL-DNA Complex Structure on the Transfection Mechanism. 16.6 Model of Transfection with Lamellar CL-DNA Complexes. 16.7 Model of Transfection with Inverted Hexagonal CL-DNA Complexes. 16.8 PEGylated CL-DNA Complexes: Surface Functionalization and Distinct DNA-DNA Interaction Regimes. 16.9 Conclusion and Summary. Acknowledgments. References. Index.

Modeling of DNA compaction by polycations

In this work we study polycations as efficient compacting agents of a medium size polyanion by means of Monte Carlo simulations. The systems are characterized in terms of a conformational analysis in which shape, overall dimensions, structure factors, radial distribution functions, and the degree of accumulation of the compaction agent near the polyanion are taken into consideration. Results show that the degree of compaction depends on the size of the positive chains and their number. The role of electrostatic interactions is paramount in the compaction process, and an increase in the number of molecules of the compacting agent or in the number of charges of each molecule leads to collapse, which may be followed by some unfolding in situations of overcharging. Compaction is associated with polycations promoting bridging between different sites in the polyanion. When the total charge of the polycations is significantly lower than that of the polyanion, interaction produces only a small degree of intrachain segregation in the latter, allowing for significant translational motion of the compacting agent along the longer chain. However, complete charge neutralization is not mandatory to achieve compact forms.

Effect of the head-group geometry of amino acid-based cationic surfactants on interaction with plasmid DNA.

The interaction between DNA and different types of amino acid-based cationic surfactants was investigated. Particular attention was directed to determine the extent of influence of surfactant head-group geometry toward tuning the interaction behavior of these surfactants with DNA. An overview is obtained by gel retardation assay, isothermal titration calorimetry, fluorescence spectroscopy, and circular dichroism at different mole ratios of surfactant/DNA; also, cell viability was assessed. The studies show that the surfactants with more complex/bulkier hydrophobic head group interact more strongly with DNA but exclude ethidium bromide less efficiently; thus, the accessibility of DNA to small molecules is preserved to a certain extent. The presence of more hydrophobic groups surrounding the positive amino charge also gave rise to a significantly lower cytotoxicity. The surfactant self-assembly pattern is quite different without and with DNA, illustrating the roles of electrostatic and steric effects in determining the effective shape of a surfactant molecule.

Condensation and Decondensation of DNA by Cationic Surfactant, Spermine, or Cationic Surfactant–Cyclodextrin Mixtures: Macroscopic Phase Behavior, Aggregate Properties, and Dissolution Mechanisms

The macroscopic phase behavior and other physicochemical properties of dilute aqueous mixtures of DNA and the cationic surfactant hexadecyltrimethylammounium bromide (CTAB), DNA and the polyamine spermine, or DNA, CTAB, and (2-hydroxypropyl)-β-cyclodextrin (2HPβCD) were investigated. When DNA is mixed with CTAB we found, with increasing surfactant concentration, (1) free DNA coexisting with surfactant unimers, (2) free DNA coexisting with aggregates of condensed DNA and CTAB, (3) a miscibility gap where macroscopic phase separation is observed, and (4) positively overcharged aggregates of condensed DNA and CTAB. The presence of a clear solution beyond the miscibility gap cannot be ascribed to self-screening by the charges from the DNA and/or the surfactant; instead, hydrophobic interactions among the surfactants are instrumental for the observed behavior. It is difficult to judge whether the overcharged mixed aggregates represent an equilibrium situation or not. If the excess surfactant was not initially present, but added to a preformed precipitate, redissolution was, in consistency with previous reports, not observed; thus, kinetic effects have major influence on the behavior. Mixtures of DNA and spermine also displayed a miscibility gap; however, positively overcharged aggregates were not identified, and redissolution with excess spermine can be explained by electrostatics. When 2HPβCD was added to a DNA-CTAB precipitate, redissolution was observed, and when it was added to the overcharged aggregates, the behavior was essentially a reversal of that of the DNA-CTAB system. This is attributed to an effectively quantitative formation of 1:1 2HPβCD-surfactant inclusion complexes, which results in a gradual decrease in the concentration of effectively available surfactant with increasing 2HPβCD concentration.

Cationic agents for DNA compaction

Fluorescence microscopy was used to investigate the conformational changes of individual T4 DNA molecules induced by different compacting agents, namely the cationic surfactants, cetyltrimethylammonium bromide (CTAB) and chloride (CTAC), iron(III), lysozyme, and protamine sulfate. A protocol for establishing size estimates is suggested to obtain reproducible results. Observations show that in the presence of lysozyme and protamine sulfate, DNA molecules exhibit a conformational change from an elongated coil structure to compact globules, usually interpreted as a first-order transition. The maximum degree of compaction that is attained when iron(III) or CTAB (CTAC) are used as compacting agents is considerably smaller, and intermediate structures (less elongated coils) are visible even for high concentrations of these agents. Dynamic light scattering experiments were carried out, for some of the systems, to assess the reliability of size estimates from fluorescence microscopy.

Cyclodextrin−Surfactant Complex: A New Route in DNA Decompaction

In the present work, we show a new approach for decompaction of DNA-cationic surfactant complexes, e.g., lipoplexes, by using beta-cyclodextrin (beta-CD). The DNA decompaction was achieved by dissolving the surfactant aggregates in the complex by making use of the high affinity between the beta-CD and the free surfactant in solution. The results from fluorescence microscopy and adiabatic compressibility measurements indicate that coils and globules do not coexist. The reported procedure using beta-CD is an efficient way to decompact DNA surfactant complexes because the association constant of surfactants with beta-CD is large. The surfactants interaction with beta-CD is specific and the nonspecific interaction between beta-CD and biological interfaces is small.

DNA condensation by pH-responsive polycations.

This work addresses the impact of pH variation on DNA-polyethylenimine (PEI) complex formation, in aqueous solution and at constant ionic strength. An initial potentiometric characterization of the acid-base behavior of PEI is carried out to measure the concentration of ionized species in the relevant systems. The characterization of the DNA-PEI complexes is performed by precipitation assays, agarose gel electrophoresis, photon correlation spectroscopy, and zeta potential analysis. It is observed that the variations on the electrophoretic mobility, size, and electrical properties of complexes display nonmonotonic, nontrivial trends with pH, if the same polycation/polyanion charge ratios are used for different values of pH. It is seen that both linear charge density and the relative number of chains of the condensing agent are important factors governing the condensation behavior. Complexes prepared at pH 4, for example, indicate strong binding and a large mean size, while those prepared at pH 8 are smaller, in a more uniform population. Finally, charge inversion was observed for all studied pH values (even below charge neutralization).

Role of linker groups between hydrophilic and hydrophobic moieties of cationic surfactants on oligonucleotide-surfactant interactions.

The interaction between DNA and amino-acid-based surfactants with different linker groups was investigated by gel electrophoresis, ethidium bromide exclusion assays, circular dichroism, and melting temperature determinations. The studies showed that the strength of the interaction between the oligonucleotides and the surfactants is highly dependent on the linker of the surfactant. For ester surfactants, no significant interaction was observed for surfactant-to-DNA charge ratios up to 12. On the other hand, amide surfactants were shown to interact strongly with the oligonucleotides; these surfactants could displace up to 75% of the ethidium bromide molecules bound to the DNA and induced significant changes in the circular dichroism spectra. When comparing the headgroups of the surfactants, it was observed that surfactants with more hydrophobic headgroups (proline vs alanine) interacted more strongly with the DNA, in good agreement with previous studies.

DNA compaction induced by a cationic polymer or surfactant impact gene expression and DNA degradation.

There is an increasing interest in achieving gene regulation in biotechnological and biomedical applications by using synthetic DNA-binding agents. Most studies have so far focused on synthetic sequence-specific DNA-binding agents. Such approaches are relatively complicated and cost intensive and their level of sophistication is not always required, in particular for biotechnological application. Our study is inspired by in vivo data that suggest that DNA compaction might contribute to gene regulation. This study exploits the potential of using synthetic DNA compacting agents that are not sequence-specific to achieve gene regulation for in vitro systems. The semi-synthetic in vitro system we use include common cationic DNA-compacting agents, poly(amido amine) (PAMAM) dendrimers and the surfactant hexadecyltrimethylammonium bromide (CTAB), which we apply to linearized plasmid DNA encoding for the luciferase reporter gene. We show that complexing the DNA with either of the cationic agents leads to gene expression inhibition in a manner that depends on the extent of compaction. This is demonstrated by using a coupled in vitro transcription-translation system. We show that compaction can also protect DNA against degradation in a dose-dependent manner. Furthermore, our study shows that these effects are reversible and DNA can be released from the complexes. Release of DNA leads to restoration of gene expression and makes the DNA susceptible to degradation by Dnase. A highly charged polyelectrolyte, heparin, is needed to release DNA from dendrimers, while DNA complexed with CTAB dissociates with the non-ionic surfactant C12E5. Our results demonstrate the relation between DNA compaction by non-specific DNA-binding agents and gene expression and gene regulation can be achieved in vitro systems in a reliable dose-dependent and reversible manner.

Cyclodextrins in DNA decompaction.

Individual T4DNA molecules, previously compacted by using a cationic surfactant (cetyltrimethylammonium bromide, CTAB), were successfully decompacted by the addition of an appropriate concentration of either alpha-cyclodextrin or beta-cyclodextrin (alpha-CD and beta-CD, respectively) due to the formation of inclusion complexes with the surfactant. The process was shown to be a non first-order transition from globules to coils. Density and sound velocity measurements as well as steady state fluorescence spectroscopy have confirmed the approximate CD concentration at which the globule-to-coil transition occurs. Phase maps of the DNA-CTA-CD systems were produced and the CTAB concentration range at which decompaction can be achieved was determined. Evidences for DNA-CD interaction were found, however, its nature and influence on the decompaction process was not yet determined.