DNA Interactions with Polymers and Surfactants
Wiley-Interscience (Verlag)
978-0-470-25818-7 (ISBN)
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Due to the potential benefits of biotechnology, interest in the interaction between DNA and surfactants and polymers has become increasingly significant. Now, DNA Interactions with Polymers and Surfactants provides an extensive, up-to-date overview of the subject, giving readers a basis for understanding the factors leading to complexation between DNA and different cosolutes, including metal ions, polyelectrolytes, spermine, spermidine, surfactants and lipids, and proteins.
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).
Preface xiii
Contributors xv
1 Polyelectrolytes. Physicochemical Aspects and Biological Significance 1
Magnus Ullner
1.1 Introduction 1
1.2 Polyelectrolytes and Biological Function 1
1.3 Electrostatic Interactions 3
1.3.1 Ion Distributions and the Poisson–Boltzmann Equation 3
1.3.2 Debye–H€uckel Theory 9
1.4 Solution Properties 13
1.5 Flexibility 17
1.5.1 The Concept of Persistence Length 17
1.5.2 Interactions and the Separation of Length Scales 23
1.5.3 Polyelectrolyte Behavior: Electrostatic Persistence Length 26
1.5.4 DNA Persistence Length 29
References 31
2 Solution Behavior of Nucleic Acids 41
Rita S. Dias
2.1 Biological Function of Nucleic Acids 41
2.2 Discovery of DNA 41
2.3 Structure of Nucleic Acids 43
2.3.1 DNA 43
2.3.2 RNA 47
2.3.3 Analogues of Nucleic Acids 48
2.4 Nuclei Acids Nanostructures 48
2.4.1 DNA 48
2.4.2 RNA 50
2.5 Behavior of DNA in Solution 51
2.5.1 Ionization Equilibrium 51
2.5.2 Flexibility of Nucleic Acids 51
2.6 Melting of Double-Stranded DNA 52
2.6.1 Effect of Base Composition 53
2.6.2 Effect of Ionic Strength 53
2.6.3 Effect of pH 53
2.6.4 Dependence on DNA Chain Length 54
2.6.5 Dependence on DNA Concentration 54
Acknowledgments 55
References 55
3 Single DNA Molecules: Compaction and Decompaction 59
Anatoly A. Zinchenko, Olga A. Pyshkina, Andrey V. Lezov, Vladimir G. Sergeyev, and Kenichi Yoshikawa
3.1 Introduction 59
3.2 Condensation and Compaction of DNA by Surfactants 60
3.2.1 Linear DNA Condensation/Compaction by Positively Charged Surfactants 60
3.2.2 Compaction of Plasmid DNA with Surfactants 63
3.2.3 Non-ionic Surfactants 64
3.2.4 Zwitterionic Surfactants 64
3.2.5 Decompaction of DNA–Surfactant Complex 65
3.3 DNA Condensation by Cationic Liposomes 65
3.4 DNA Compaction and Decompaction by Multivalent Cations 74
3.5 DNA Compaction by Polycations 77
3.6 Compaction of DNA in a Crowded Environment of Neutral Polymer 81
3.7 Conclusion 82
References 82
4 Interaction of DNA with Surfactants in Solution 89
Rita S. Dias, Kenneth Dawson, and Maria G. Miguel
4.1 Introduction 89
4.1.1 Surfactants 89
4.1.2 Polymer–Surfactant Interactions 93
4.1.3 Polyelectrolyte–Oppositely Charged Surfactant Interactions 94
4.1.4 DNA–Surfactant Interactions 95
4.2 DNA–Cationic Surfactant Interactions 96
4.2.1 Solution Behavior 96
4.2.2 Effect of the Surfactant Chain Length 99
4.2.3 Effect of the Surfactant Head-group 101
4.2.4 Structure of DNA–Surfactant Complexes 102
4.2.5 DNA Is an Amphiphilic Polyelectrolyte 105
4.3 DNA Covalent Gels and Their Interaction with Surfactants 106
4.4 Applications 108
4.4.1 Control of DNA Compaction/Decompaction 108
4.4.2 Purification 110
4.4.3 Gene Transfection 110
Acknowledgments 111
References 111
5 Interaction of DNA with Cationic Polymers 119
Eric Raspaud, Adriana C. Toma, Francoise Livolant, and Joachim R€adler
5.1 Introduction 119
5.2 Theory of DNA Interacting with Polycations 120
5.2.1 Manning Condensation 120
5.2.2 Counterion Release 121
5.2.3 Short-Range Attractive Force due to Ion Correlations 121
5.2.4 Phase Diagrams of Condensed DNA–Polycation Phases 121
5.2.5 Finite-Size Aggregates 122
5.3 Condensation of DNA, Phase Diagram, and Structure 122
5.3.1 Short Polycations and Multivalent Cations 123
5.3.2 Long Polycations and Basic Proteins 123
5.4 Formation of Polycation–DNA Complexes: Polyplexes 125
5.5 DNA-Nanoparticles for Gene Delivery 126
5.5.1 Artificial Viruses 126
5.5.2 Cytotoxicity 127
5.6 Cellular Uptake and Intracellular Interactions of Polyplexes 127
5.7 Conclusion 129
Acknowledgment 129
References 129
6 Interactions of Histones with DNA: Nucleosome Assembly, Stability, Dynamics, and Higher Order Structure 135
Karsten Rippe, Jacek Mazurkiewicz, and Nick Kepper
6.1 Introduction 135
6.2 Histones 136
6.2.1 Core Histones 136
6.2.2 Linker Histones 137
6.2.3 Histone Variants 138
6.2.4 Posttranslational Modifications of Histones 141
6.3 Structure of Histone–DNA Complexes 142
6.3.1 Nucleosome 142
6.3.2 Chromatosome 144
6.4 Assembly of Nucleosomes and Chromatosomes 144
6.4.1 Chaperone-Guided Nucleosome Assembly 146
6.4.2 Chromatin Remodeling Complexes 147
6.5 Stability and Dynamics of Nucleosomes 148
6.5.1 Accessibility of Nucleosomal DNA 148
6.5.2 DNA Sequence Specificity of Nucleosome Binding 149
6.5.3 Thermodynamic and Kinetic Parameters for Nucleosome Formation under Physiological Conditions 150
6.6 Higher Order Chromatin Structures 154
6.6.1 Assembly of Chromatin Fibers 154
6.6.2 Higher Order Folding of Chromatin Fibers 157
Acknowledgments 158
References 158
7 Opening and Closing DNA: Theories on the Nucleosome 173
Igor M. Kuli_c and Helmut Schiessel
7.1 Introduction 173
7.2 Unwrapping Nucleosomes 176
7.3 Nucleosome Sliding 180
7.4 Transcription Through Nucleosomes 187
7.5 Tail Bridging 194
7.6 Discussion and Conclusion 202
Acknowledgment 204
References 204
8 DNA–DNA Interactions 209
Lars Nordenski€old, Nikolay Korolev, and Alexander P. Lyubartsev
8.1 Introduction 209
8.2 The Statistical Polymer Solution Model Predicts DNA Collapse/Aggregation Phase Behavior 211
8.3 DNA in Solution is Condensed to a Compact State by Multivalent Cationic Ligands 214
8.3.1 DNA Compaction in Solution 214
8.3.2 Experimental Studies on Chromatin and Nucleosome Condensation 219
8.3.3 Measurement of DNA–DNA Forces from Osmotic Stress 221
8.4 Ion Correlation Effects Included in Theory and in Computer Modeling Explain DNA–DNA Attraction 222
8.4.1 Analytical Theories of DNA–DNA Interactions 222
8.4.2 Computer Simulations of DNA–DNA Interactions 224
8.4.3 Modeling DNA–DNA Interactions in Chromatin and NCP 227
8.5 Conclusions and Future Prospects 230
References 231
9 Hydration of DNA–Amphiphile Complexes 239
Cecilia Leal and Hakan Wennerström
9.1 Introduction 239
9.2 General Properties of DNA Double Helices and Cationic Aggregates 240
9.3 Thermodynamics of DNA–Amphiphile Complexes 243
9.4 Molecular Properties of DNA–Amphiphile Complexes 247
9.5 Concluding Remarks 249
References 250
10 DNA–Surfactant/Lipid Complexes at Liquid Interfaces 253
Dominique Langevin
10.1 Introduction 253
10.2 Soluble Surfactants 255
10.2.1 DNA–DTAB Surface Layers 255
10.2.2 Other DNA–Cationic Surfactants Systems 261
10.2.3 DNA Surfactants 262
10.3 Insoluble Surfactants 262
10.3.1 DNA–DODAB Surface Layers 263
10.3.2 DNA–TODAB Surface Layers 267
10.3.3 DNA–ODA Surface Layers 271
10.3.4 DNA Binding with Other Surfactant Layers 273
10.4 Lipids 274
10.4.1 Cationic Lipids–DNA Surface Layers 275
10.4.2 DSPC-Divalent Ion–DNA Surface Layers 276
10.4.3 DPPC-Divalent Ion–DNA Surface Layers 278
10.4.4 DMPE-Divalent Ion–DNA Surface Layers 279
10.4.5 Other Types of Binding 283
10.5 Mixtures of Surfactants and Lipids 284
10.6 Conclusion 285
References 286
11 DNA and DNA–Surfactant Complexes at Solid Surfaces 291
Marité Cárdenas and Tommy Nylander
11.1 Introduction 291
11.2 Adsorption of DNA at Surfaces 292
11.3 Attachment of DNA Surfaces—Strategies and Challenges 294
11.4 DNA Structure on Surfaces—Comparison with Highly Charged Polyelectrolytes 297
11.4.1 Regulating the DNA Compaction by Compaction Agents at Interfaces to Control the Structure 297
11.4.2 Cationic Surfactants and DNA at Hydrophobic Surfaces 298
11.4.3 Cationic Surfactants and DNA at Negatively Charged Surfaces 304
11.5 Some Applications—Arrays and Nanostamping 307
Acknowledgments 310
References 310
12 Role of Correlation Forces for DNA–Cosolute Interactions 317
Malek O. Khan
12.1 Introduction 317
12.2 Experimental Evidence of DNA Condensation Induced by Electrostatic Agents 317
12.3 Simulations Used to Characterize the DNA Compaction Mechanism 319
12.4 Ion Correlations Limiting the Validity of DLVO Theory 320
12.5 Ion Correlations Driving the Compaction of DNA 322
12.6 Conformation of Compact DNA—The Coil to Toroid Transition 328
12.7 Conclusions 332
References 334
13 Simulations of Polyions: Compaction, Adsorption onto Surfaces, and Confinement 337
A.A.C.C. Pais and P. Linse
13.1 Introduction 337
13.2 Models 339
13.3 Solutions of Polyions with Multivalent Counterions 340
13.3.1 Polyion Conformation 340
13.3.2 Small-Ion Distribution 341
13.3.3 Other Aspects 343
13.4 Polyion Adsorption onto Charged Surfaces 343
13.4.1 Surfaces with Homogeneous Surface Charge Densities 344
13.4.2 Surfaces with Heterogeneous Surface Charge Densities 344
13.5 Polyions in Confined Geometries 346
13.5.1 Structural Aspects 347
13.5.2 Free Energies 347
13.6 Concluding Remarks 349
References 349
14 Cross-linked DNA Gels and Gel Particles 353
Diana Costa, M. Carmen Morán, Maria G. Miguel, and Björn Lindman
14.1 Introduction 353
14.2 Covalently Cross-Linked DNA Gels 354
14.2.1 Volumetric Behavior of DNA Gel Probes DNA–Cosolute Interactions 354
14.2.2 Swelling Reversibility 357
14.3 ds-DNA versus ss-DNA: Skin Formation 357
14.4 DNA Gel Particles 358
14.4.1 Particle Characterization 358
14.4.2 Particle Swelling and Deswelling Kinetics 359
14.4.3 Kinetics of DNA Release 360
14.5 Physical DNA Gels 361
14.5.1 Phase Behavior 361
14.5.2 Rheological Studies 362
References 363
15 DNA as an Amphiphilic Polymer 367
Rita S. Dias, Maria G. Miguel, and Björn Lindman
15.1 Some General Aspects of Self-Assembly 367
15.2 Illustrations 369
15.2.1 Solubilization of Hydrophobic Molecules in ds-DNA 370
15.2.2 Adsorption on Hydrophobic Surfaces 372
15.2.3 Effects of Hydrophobic Cosolutes on DNA Melting 372
15.2.4 Differences in Interactions (Phase Separation) of Cationic Surfactants between ss-DNA and ds-DNA 373
15.2.5 DNA–Protein Interaction 374
15.2.6 Dependence of DNA Melting on Base Sequence 374
15.2.7 DNA Physical and Chemical Gels 374
References 375
16 Lipid–DNA Interactions: Structure–Function Studies of Nanomaterials for Gene Delivery 377
Kai K. Ewert, Charles E. Samuel, and Cyrus R. Safinya
16.1 Introduction 377
16.2 Formation and Structures of CL–DNA Complexes 378
16.3 Effect of the Lipid–DNA Charge Ratio (rchg) on CL–DNA Complex Properties 383
16.3.1 Physicochemical Effects and Phase Behavior of CL–DNA Lipids 383
16.3.2 Biological Effects 386
16.4 Effect of the Membrane Charge Density (sM) on CL–DNA Complex Properties 387
16.5 Effect of Nonlamellar CL–DNA Complex Structure on the Transfection Mechanism 391
16.6 Model of Transfection with Lamellar CL–DNA Complexes 393
16.7 Model of Transfection with Inverted Hexagonal CL–DNA Complexes 395
16.8 PEGylated CL–DNA Complexes: Surface Functionalization and Distinct DNA–DNA Interaction Regimes 396
16.8.1 DNA–DNA Interaction Regimes in PEG-Lipid CL–DNA Complexes 396
16.8.2 Surface Functionalization of CL–DNA Complexes with PEG–Lipids 397
16.9 Conclusion and Summary 400
Acknowledgments 400
References 401
Index 405
| Sprache | englisch |
|---|---|
| Maße | 163 x 244 mm |
| Gewicht | 748 g |
| Einbandart | gebunden |
| Themenwelt | Informatik ► Weitere Themen ► Bioinformatik |
| Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie | |
| Naturwissenschaften ► Chemie ► Organische Chemie | |
| Naturwissenschaften ► Chemie ► Physikalische Chemie | |
| ISBN-10 | 0-470-25818-7 / 0470258187 |
| ISBN-13 | 978-0-470-25818-7 / 9780470258187 |
| Zustand | Neuware |
| Informationen gemäß Produktsicherheitsverordnung (GPSR) | |
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