DNA Interactions with Polymers and Surfactants

Rita S. Dias, PhD, is a postdoctoral scientist in the Department of Physical Chemistry at Lund University, Sweden. Her current research involves the control of DNA condensation using surfactant mixtures and Monte Carlo simulations on the compaction of DNA and interaction of macromolecules with coarse-grained lipid membranes. Björn Lindman, PhD, has served as Full Professor at Lund University for the past three decades. Dr. Lindman's contributions have included the determination of the structure of microemulsions, the development of novel delivery systems for pharmaceuticals, and new systems for eliminating adhesions in surgery. He was the first to establish phase diagrams for mixed polymer-surfactant solutions as well as the bicontinuity of microemulsions. Dr. Lindman is the author of hundreds of scientific publications and has coauthored or edited several books, including Surfactants and Polymers in Aqueous Solution, Second Edition (Wiley).

"Aims to give readers an overview of the subject and a basis for understanding the factors leading to the complexation between DNA and different co-salutes." (TCE - The Chemical Engineer, July 2008)

• Preface xiiiContributors xv1 Polyelectrolytes. Physicochemical Aspects and Biological Significance 1Magnus Ullner1.1 Introduction 11.2 Polyelectrolytes and Biological Function 11.3 Electrostatic Interactions 31.3.1 Ion Distributions and the Poisson–Boltzmann Equation 31.3.2 Debye–H€uckel Theory 91.4 Solution Properties 131.5 Flexibility 171.5.1 The Concept of Persistence Length 171.5.2 Interactions and the Separation of Length Scales 231.5.3 Polyelectrolyte Behavior: Electrostatic Persistence Length 261.5.4 DNA Persistence Length 29References 312 Solution Behavior of Nucleic Acids 41Rita S. Dias2.1 Biological Function of Nucleic Acids 412.2 Discovery of DNA 412.3 Structure of Nucleic Acids 432.3.1 DNA 432.3.2 RNA 472.3.3 Analogues of Nucleic Acids 482.4 Nuclei Acids Nanostructures 482.4.1 DNA 482.4.2 RNA 502.5 Behavior of DNA in Solution 512.5.1 Ionization Equilibrium 512.5.2 Flexibility of Nucleic Acids 512.6 Melting of Double-Stranded DNA 522.6.1 Effect of Base Composition 532.6.2 Effect of Ionic Strength 532.6.3 Effect of pH 532.6.4 Dependence on DNA Chain Length 542.6.5 Dependence on DNA Concentration 54Acknowledgments 55References 553 Single DNA Molecules: Compaction and Decompaction 59Anatoly A. Zinchenko, Olga A. Pyshkina, Andrey V. Lezov, Vladimir G. Sergeyev, and Kenichi Yoshikawa3.1 Introduction 593.2 Condensation and Compaction of DNA by Surfactants 603.2.1 Linear DNA Condensation/Compaction by Positively Charged Surfactants 603.2.2 Compaction of Plasmid DNA with Surfactants 633.2.3 Non-ionic Surfactants 643.2.4 Zwitterionic Surfactants 643.2.5 Decompaction of DNA–Surfactant Complex 653.3 DNA Condensation by Cationic Liposomes 653.4 DNA Compaction and Decompaction by Multivalent Cations 743.5 DNA Compaction by Polycations 773.6 Compaction of DNA in a Crowded Environment of Neutral Polymer 813.7 Conclusion 82References 824 Interaction of DNA with Surfactants in Solution 89Rita S. Dias, Kenneth Dawson, and Maria G. Miguel4.1 Introduction 894.1.1 Surfactants 894.1.2 Polymer–Surfactant Interactions 934.1.3 Polyelectrolyte–Oppositely Charged Surfactant Interactions 944.1.4 DNA–Surfactant Interactions 954.2 DNA–Cationic Surfactant Interactions 964.2.1 Solution Behavior 964.2.2 Effect of the Surfactant Chain Length 994.2.3 Effect of the Surfactant Head-group 1014.2.4 Structure of DNA–Surfactant Complexes 1024.2.5 DNA Is an Amphiphilic Polyelectrolyte 1054.3 DNA Covalent Gels and Their Interaction with Surfactants 1064.4 Applications 1084.4.1 Control of DNA Compaction/Decompaction 1084.4.2 Purification 1104.4.3 Gene Transfection 110Acknowledgments 111References 1115 Interaction of DNA with Cationic Polymers 119Eric Raspaud, Adriana C. Toma, Francoise Livolant, and Joachim R€adler5.1 Introduction 1195.2 Theory of DNA Interacting with Polycations 1205.2.1 Manning Condensation 1205.2.2 Counterion Release 1215.2.3 Short-Range Attractive Force due to Ion Correlations 1215.2.4 Phase Diagrams of Condensed DNA–Polycation Phases 1215.2.5 Finite-Size Aggregates 1225.3 Condensation of DNA, Phase Diagram, and Structure 1225.3.1 Short Polycations and Multivalent Cations 1235.3.2 Long Polycations and Basic Proteins 1235.4 Formation of Polycation–DNA Complexes: Polyplexes 1255.5 DNA-Nanoparticles for Gene Delivery 1265.5.1 Artificial Viruses 1265.5.2 Cytotoxicity 1275.6 Cellular Uptake and Intracellular Interactions of Polyplexes 1275.7 Conclusion 129Acknowledgment 129References 1296 Interactions of Histones with DNA: Nucleosome Assembly, Stability, Dynamics, and Higher Order Structure 135Karsten Rippe, Jacek Mazurkiewicz, and Nick Kepper6.1 Introduction 1356.2 Histones 1366.2.1 Core Histones 1366.2.2 Linker Histones 1376.2.3 Histone Variants 1386.2.4 Posttranslational Modifications of Histones 1416.3 Structure of Histone–DNA Complexes 1426.3.1 Nucleosome 1426.3.2 Chromatosome 1446.4 Assembly of Nucleosomes and Chromatosomes 1446.4.1 Chaperone-Guided Nucleosome Assembly 1466.4.2 Chromatin Remodeling Complexes 1476.5 Stability and Dynamics of Nucleosomes 1486.5.1 Accessibility of Nucleosomal DNA 1486.5.2 DNA Sequence Specificity of Nucleosome Binding 1496.5.3 Thermodynamic and Kinetic Parameters for Nucleosome Formation under Physiological Conditions 1506.6 Higher Order Chromatin Structures 1546.6.1 Assembly of Chromatin Fibers 1546.6.2 Higher Order Folding of Chromatin Fibers 157Acknowledgments 158References 1587 Opening and Closing DNA: Theories on the Nucleosome 173Igor M. Kuli_c and Helmut Schiessel7.1 Introduction 1737.2 Unwrapping Nucleosomes 1767.3 Nucleosome Sliding 1807.4 Transcription Through Nucleosomes 1877.5 Tail Bridging 1947.6 Discussion and Conclusion 202Acknowledgment 204References 2048 DNA–DNA Interactions 209Lars Nordenski€old, Nikolay Korolev, and Alexander P. Lyubartsev8.1 Introduction 2098.2 The Statistical Polymer Solution Model Predicts DNA Collapse/Aggregation Phase Behavior 2118.3 DNA in Solution is Condensed to a Compact State by Multivalent Cationic Ligands 2148.3.1 DNA Compaction in Solution 2148.3.2 Experimental Studies on Chromatin and Nucleosome Condensation 2198.3.3 Measurement of DNA–DNA Forces from Osmotic Stress 2218.4 Ion Correlation Effects Included in Theory and in Computer Modeling Explain DNA–DNA Attraction 2228.4.1 Analytical Theories of DNA–DNA Interactions 2228.4.2 Computer Simulations of DNA–DNA Interactions 2248.4.3 Modeling DNA–DNA Interactions in Chromatin and NCP 2278.5 Conclusions and Future Prospects 230References 2319 Hydration of DNA–Amphiphile Complexes 239Cecilia Leal and Hakan Wennerström9.1 Introduction 2399.2 General Properties of DNA Double Helices and Cationic Aggregates 2409.3 Thermodynamics of DNA–Amphiphile Complexes 2439.4 Molecular Properties of DNA–Amphiphile Complexes 2479.5 Concluding Remarks 249References 25010 DNA–Surfactant/Lipid Complexes at Liquid Interfaces 253Dominique Langevin10.1 Introduction 25310.2 Soluble Surfactants 25510.2.1 DNA–DTAB Surface Layers 25510.2.2 Other DNA–Cationic Surfactants Systems 26110.2.3 DNA Surfactants 26210.3 Insoluble Surfactants 26210.3.1 DNA–DODAB Surface Layers 26310.3.2 DNA–TODAB Surface Layers 26710.3.3 DNA–ODA Surface Layers 27110.3.4 DNA Binding with Other Surfactant Layers 27310.4 Lipids 27410.4.1 Cationic Lipids–DNA Surface Layers 27510.4.2 DSPC-Divalent Ion–DNA Surface Layers 27610.4.3 DPPC-Divalent Ion–DNA Surface Layers 27810.4.4 DMPE-Divalent Ion–DNA Surface Layers 27910.4.5 Other Types of Binding 28310.5 Mixtures of Surfactants and Lipids 28410.6 Conclusion 285References 28611 DNA and DNA–Surfactant Complexes at Solid Surfaces 291Marité Cárdenas and Tommy Nylander11.1 Introduction 29111.2 Adsorption of DNA at Surfaces 29211.3 Attachment of DNA Surfaces—Strategies and Challenges 29411.4 DNA Structure on Surfaces—Comparison with Highly Charged Polyelectrolytes 29711.4.1 Regulating the DNA Compaction by Compaction Agents at Interfaces to Control the Structure 29711.4.2 Cationic Surfactants and DNA at Hydrophobic Surfaces 29811.4.3 Cationic Surfactants and DNA at Negatively Charged Surfaces 30411.5 Some Applications—Arrays and Nanostamping 307Acknowledgments 310References 31012 Role of Correlation Forces for DNA–Cosolute Interactions 317Malek O. Khan12.1 Introduction 31712.2 Experimental Evidence of DNA Condensation Induced by Electrostatic Agents 31712.3 Simulations Used to Characterize the DNA Compaction Mechanism 31912.4 Ion Correlations Limiting the Validity of DLVO Theory 32012.5 Ion Correlations Driving the Compaction of DNA 32212.6 Conformation of Compact DNA—The Coil to Toroid Transition 32812.7 Conclusions 332References 33413 Simulations of Polyions: Compaction, Adsorption onto Surfaces, and Confinement 337A.A.C.C. Pais and P. Linse13.1 Introduction 33713.2 Models 33913.3 Solutions of Polyions with Multivalent Counterions 34013.3.1 Polyion Conformation 34013.3.2 Small-Ion Distribution 34113.3.3 Other Aspects 34313.4 Polyion Adsorption onto Charged Surfaces 34313.4.1 Surfaces with Homogeneous Surface Charge Densities 34413.4.2 Surfaces with Heterogeneous Surface Charge Densities 34413.5 Polyions in Confined Geometries 34613.5.1 Structural Aspects 34713.5.2 Free Energies 34713.6 Concluding Remarks 349References 34914 Cross-linked DNA Gels and Gel Particles 353Diana Costa, M. Carmen Morán, Maria G. Miguel, and Björn Lindman14.1 Introduction 35314.2 Covalently Cross-Linked DNA Gels 35414.2.1 Volumetric Behavior of DNA Gel Probes DNA–Cosolute Interactions 35414.2.2 Swelling Reversibility 35714.3 ds-DNA versus ss-DNA: Skin Formation 35714.4 DNA Gel Particles 35814.4.1 Particle Characterization 35814.4.2 Particle Swelling and Deswelling Kinetics 35914.4.3 Kinetics of DNA Release 36014.5 Physical DNA Gels 36114.5.1 Phase Behavior 36114.5.2 Rheological Studies 362References 36315 DNA as an Amphiphilic Polymer 367Rita S. Dias, Maria G. Miguel, and Björn Lindman15.1 Some General Aspects of Self-Assembly 36715.2 Illustrations 36915.2.1 Solubilization of Hydrophobic Molecules in ds-DNA 37015.2.2 Adsorption on Hydrophobic Surfaces 37215.2.3 Effects of Hydrophobic Cosolutes on DNA Melting 37215.2.4 Differences in Interactions (Phase Separation) of Cationic Surfactants between ss-DNA and ds-DNA 37315.2.5 DNA–Protein Interaction 37415.2.6 Dependence of DNA Melting on Base Sequence 37415.2.7 DNA Physical and Chemical Gels 374References 37516 Lipid–DNA Interactions: Structure–Function Studies of Nanomaterials for Gene Delivery 377Kai K. Ewert, Charles E. Samuel, and Cyrus R. Safinya16.1 Introduction 37716.2 Formation and Structures of CL–DNA Complexes 37816.3 Effect of the Lipid–DNA Charge Ratio (rchg) on CL–DNA Complex Properties 38316.3.1 Physicochemical Effects and Phase Behavior of CL–DNA Lipids 38316.3.2 Biological Effects 38616.4 Effect of the Membrane Charge Density (sM) on CL–DNA Complex Properties 38716.5 Effect of Nonlamellar CL–DNA Complex Structure on the Transfection Mechanism 39116.6 Model of Transfection with Lamellar CL–DNA Complexes 39316.7 Model of Transfection with Inverted Hexagonal CL–DNA Complexes 39516.8 PEGylated CL–DNA Complexes: Surface Functionalization and Distinct DNA–DNA Interaction Regimes 39616.8.1 DNA–DNA Interaction Regimes in PEG-Lipid CL–DNA Complexes 39616.8.2 Surface Functionalization of CL–DNA Complexes with PEG–Lipids 39716.9 Conclusion and Summary 400Acknowledgments 400References 401Index 405