DNA Interactions with Polymers and Surfactants Book

Preface     xiii
Contributors     xv
Polyelectrolytes. Physicochemical Aspects and Biological Significance   Magnus Ullner     1
Introduction     1
Polyelectrolytes and Biological Function     1
Electrostatic Interactions     3
Ion Distributions and the Poisson-Boltzmann Equation     3
Debye-Huckel Theory     9
Solution Properties     13
Flexibility     17
The Concept of Persistence Length     17
Interactions and the Separation of Length Scales     23
Polyelectrolyte Behavior: Electrostatic Persistence Length     26
DNA Persistence Length     29
References     31
Solution Behavior of Nucleic Acids   Rita S. Dias     41
Biological Function of Nucleic Acids     41
Discovery of DNA     41
Structure of Nucleic Acids     43
DNA     43
RNA     47
Analogues of Nucleic Acids     48
Nuclei Acids Nanostructures     48
DNA     48
RNA     50
Behavior of DNA in Solution     51
Ionization Equilibrium     51
Flexibility of NucleicAcids     51
Melting of Double-Stranded DNA     52
Effect of Base Composition     53
Effect of Ionic Strength     53
Effect of pH     53
Dependence on DNA Chain Length     54
Dependence on DNA Concentration     54
Acknowledgments     55
References     55
Single DNA Molecules: Compaction and Decompaction   Anatoly A. Zinchenko   Olga A. Pyshkina   Andrey V. Lezov   Vladimir G. Sergeyev   Kenichi Yoshikawa     59
Introduction     59
Condensation and Compaction of DNA by Surfactants     60
Linear DNA Condensation/Compaction by Positively Charged Surfactants     60
Compaction of Plasmid DNA with Surfactants     63
Non-ionic Surfactants     64
Zwitterionic Surfactants     64
Decompaction of DNA-Surfactant Complex     65
DNA Condensation by Cationic Liposomes     65
DNA Compaction and Decompaction by Multivalent Cations     74
DNA Compaction by Polycations     77
Compaction of DNA in a Crowded Environment of Neutral Polymer     81
Conclusion     82
References     82
Interaction of DNA with Surfactants in Solution   Rita S. Dias   Kenneth Dawson   Maria G. Miguel     89
Introduction     89
Surfactants     89
Polymer-Surfactant Interactions     93
Polyelectrolyte-Oppositely Charged Surfactant Interactions     94
DNA-Surfactant Interactions     95
DNA-Cationic Surfactant Interactions     96
Solution Behavior     96
Effect of the Surfactant Chain Length     99
Effect of the Surfactant Head-group     101
Structure of DNA-Surfactant Complexes     102
DNA Is an Amphiphilic Polyelectrolyte     105
DNA Covalent Gels and Their Interaction with Surfactants     106
Applications     108
Control of DNA Compaction/Decompaction     108
Purification     110
Gene Transfection     110
Acknowledgments     111
References     111
Interaction of DNA with Cationic Polymers   Eric Raspaud   Adriana C. Toma   Francoise Livolant   Joachim Radler     119
Introduction     119
Theory of DNA Interacting with Polycations     120
Manning Condensation     120
Counterion Release      121
Short-Range Attractive Force due to Ion Correlations     121
Phase Diagrams of Condensed DNA-Polycation Phases     121
Finite-Size Aggregates     122
Condensation of DNA, Phase Diagram, and Structure     122
Short Polycations and Multivalent Cations     123
Long Polycations and Basic Proteins     123
Formation of Polycation-DNA Complexes: Polyplexes     125
DNA-Nanoparticles for Gene Delivery     126
Artificial Viruses     126
Cytotoxicity     127
Cellular Uptake and Intracellular Interactions of Polyplexes     127
Conclusion     129
Acknowledgment     129
References     129
Interactions of Histones with DNA: Nucleosome Assembly, Stability, Dynamics, and Higher Order Structure   Karsten Rippe   Jacek Mazurkiewicz   Nick Kepper     135
Introduction     135
Histones     136
Core Histones     136
Linker Histones     137
Histone Variants     138
Posttranslational Modifications of Histones     141
Structure of Histone-DNA Complexes     142
Nucleosome     142
Chromatosome      144
Assembly of Nucleosomes and Chromatosomes     144
Chaperone-Guided Nucleosome Assembly     146
Chromatin Remodeling Complexes     147
Stability and Dynamics of Nucleosomes     148
Accessibility of Nucleosomal DNA     148
DNA Sequence Specificity of Nucleosome Binding     149
Thermodynamic and Kinetic Parameters for Nucleosome Formation under Physiological Conditions     150
Higher Order Chromatin Structures     154
Assembly of Chromatin Fibers     154
Higher Order Folding of Chromatin Fibers     157
Acknowledgments     158
References     158
Opening and Closing DNA: Theories on the Nucleosome   Igor M. Kulic   Helmut Schiessel     173
Introduction     173
Unwrapping Nucleosomes     176
Nucleosome Sliding     180
Transcription Through Nucleosomes     187
Tail Bridging     194
Discussion and Conclusion     202
Acknowledgment     204
References     204
DNA-DNA Interactions   Lars Nordenskiold   Nikolay Korolev   Alexander P. Lyubartsev     209
Introduction     209
The Statistical Polymer Solution Model Predicts DNA Collapse/Aggregation Phase Behavior     211
DNA in Solution is Condensed to a Compact State by Multivalent Cationic Ligands     214
DNA Compaction in Solution     214
Experimental Studies on Chromatin and Nucleosome Condensation     219
Measurement of DNA-DNA Forces from Osmotic Stress     221
Ion Correlation Effects Included in Theory and in Computer Modeling Explain DNA-DNA Attraction     222
Analytical Theories of DNA-DNA Interactions     222
Computer Simulations of DNA-DNA Interactions     224
Modeling DNA-DNA Interactions in Chromatin and NCP     227
Conclusions and Future Prospects     230
References     231
Hydration of DNA-Amphiphile Complexes   Cecilia Leal   Hakan Wennerstrom     239
Introduction     239
General Properties of DNA Double Helices and Cationic Aggregates     240
Thermodynamics of DNA-Amphiphile Complexes     243
Molecular Properties of DNA-Amphiphile Complexes     247
Concluding Remarks     249
References     250
DNA-Surfactant/Lipid Complexes at Liquid Interfaces   Dominique Langevin     253
Introduction     253
Soluble Surfactants      255
DNA-DTAB Surface Layers     255
Other DNA-Cationic Surfactants Systems     261
DNA Surfactants     262
Insoluble Surfactants     262
DNA-DODAB Surface Layers     263
DNA-TODAB Surface Layers     267
DNA-ODA Surface Layers     271
DNA Binding with Other Surfactant Layers     273
Lipids     274
Cationic Lipids-DNA Surface Layers     275
DSPC-Divalent Ion-DNA Surface Layers     276
DPPC-Divalent Ion-DNA Surface Layers     278
DMPE-Divalent Ion-DNA Surface Layers     279
Other Types of Binding     283
Mixtures of Surfactants and Lipids     284
Conclusion     285
References     286
DNA and DNA-Surfactant Complexes at Solid Surfaces   Marite Cardenas   Tommy Nylander     291
Introduction     291
Adsorption of DNA at Surfaces     292
Attachment of DNA Surfaces-Strategies and Challenges     294
DNA Structure on Surfaces-Comparison with Highly Charged Polyelectrolytes     297
Regulating the DNA Compaction by Compaction Agents at Interfaces to Control the Structure     297
Cationic Surfactants and DNA at Hydrophobic Surfaces     298
Cationic Surfactants and DNA at Negatively Charged Surfaces     304
Some Applications-Arrays and Nanostamping     307
Acknowledgments     310
References     310
Role of Correlation Forces for DNA-Cosolute Interactions   Malek O. Khan     317
Introduction     317
Experimental Evidence of DNA Condensation Induced by Electrostatic Agents     317
Simulations Used to Characterize the DNA Compaction Mechanism     319
Ion Correlations Limiting the Validity of DLVO Theory     320
Ion Correlations Driving the Compaction of DNA     322
Conformation of Compact DNA-The Coil to Toroid Transition     328
Conclusions     332
References     334
Simulations of Polyions: Compaction, Adsorption onto Surfaces, and Confinement   A.A.C.C. Pais   P. Linse     337
Introduction     337
Models     339
Solutions of Polyions with Multivalent Counterions     340
Polyion Conformation     340
Small-Ion Distribution     341
Other Aspects     343
Polyion Adsorption onto Charged Surfaces     343
Surfaces with Homogeneous Surface Charge Densities      344
Surfaces with Heterogeneous Surface Charge Densities     344
Polyions in Confined Geometries     346
Structural Aspects     347
Free Energies     347
Concluding Remarks     349
References     349
Cross-linked DNA Gels and Gel Particles   Diana Costa   M. Carmen Moran   Maria G. Miguel   Bjorn Lindman     353
Introduction     353
Covalently Cross-Linked DNA Gels     354
Volumetric Behavior of DNA Gel Probes DNA-Cosolute Interactions     354
Swelling Reversibility     357
ds-DNA versus ss-DNA: Skin Formation     357
DNA Gel Particles     358
Particle Characterization     358
Particle Swelling and Deswelling Kinetics     359
Kinetics of DNA Release     360
Physical DNA Gels     361
Phase Behavior     361
Rheological Studies     362
References     363
DNA as an Amphiphilic Polymer   Rita S. Dias   Maria G. Miguel   Bjorn Lindman     367
Some General Aspects of Self-Assembly     367
Illustrations     369
Solubilization of Hydrophobic Molecules in ds-DNA     370
Adsorption on Hydrophobic Surfaces     372
Effects of Hydrophobic Cosolutes on DNA Melting     372
Differences in Interactions (Phase Separation) of Cationic Surfactants between ss-DNA and ds-DNA     373
DNA-Protein Interaction     374
Dependence of DNA Melting on Base Sequence     374
DNA Physical and Chemical Gels     374
References     375
Lipid-DNA Interactions: Structure-Function Studies of Nanomaterials for Gene Delivery   Kai K. Ewert   Charles E. Samuel   Cyrus R. Safinya     377
Introduction     377
Formation and Structures of CL-DNA Complexes     378
Effect of the Lipid-DNA Charge Ratio ([rho subscript chg]) on CL-DNA Complex Properties     383
Physicochemical Effects and Phase Behavior of CL-DNA Lipids     383
Biological Effects     386
Effect of the Membrane Charge Density ([sigma subscript M]) on CL-DNA Complex Properties     387
Effect of Nonlamellar CL-DNA Complex Structure on the Transfection Mechanism     391
Model of Transfection with Lamellar CL-DNA Complexes     393
Model of Transfection with Inverted Hexagonal CL-DNA Complexes     395
PEGylated CL-DNA Complexes: Surface Functionalization and Distinct DNA-DNA Interaction Regimes     396
DNA-DNA Interaction Regimes in PEG-Lipid CL-DNA Complexes     396
Surface Functionalization of CL-DNA Complexes with PEG-Lipids     397
Conclusion and Summary     400
Acknowledgments     400
References     401
Index     405