Authors' Preface ............................................... xi
Editor's Preface ............................................. xiii
Foreword ....................................................... xv
Introduction ................................................. xvii
Outline .................................................... xxxiii
SECTION I The Liquid-Crystalline State of the DNA
Chapter 1 The Condensed State of the High-Molecular-Mass
Double-Stranded DNA ............................................. 3
1.1 The DNA Condensation and Aggregation ....................... 3
1.2 Polyphosphates as a Simplified DNA Model ................... 4
1.3 Models of High-Molecular-Mass DNA Condensation in
Water-Polymeric Solutions ................................. 10
1.4 Grosberg Model of High-Molecular-Mass DNA Condensation .... 20
1.5 Summary ................................................... 27
References ..................................................... 28
Chapter 2 Liquid-Crystalline Phases of the Low-Molecular-
Mass Double-Stranded DNA Molecules ............................. 33
2.1 Ordering of Low-Molecular-Mass Double-Stranded DNAs ....... 33
2.2 Brief Concept of Types of Liquid-Crystalline Phases ....... 34
2.3 Liquid-Crystalline Phases of Low-Molecular-Mass
Double-Stranded DNA Molecules ............................. 36
2.4 Summary ................................................... 41
References ..................................................... 41
Chapter 3 Dispersions of Low-Molecular-Mass Double-Stranded
DNA Molecules .................................................. 43
3.1 Low-Molecular-Mass Double-Stranded DNA Dispersions
in Water-Polymer Solutions ................................ 43
3.2 Formation of DNA Dispersions in PEG-Containing Solutions .. 43
3.3 Summary ................................................... 47
References ..................................................... 48
Chapter 4 Circular Dichroism of Nucleic Acid Dispersions ...... 49
4.1 Circular Dichroism as a Method of Proof of Cholesteric
Packing of Nucleic Acid Molecules in Dispersion
Particles and Analysis of Their Properties ................ 49
4.2 Effect of Different Factors on Formation and Properties
of CLCD Particles ......................................... 63
4.2.1 Factors Determining CLCD Particle's Structure
at "Moment of Formation" ........................... 63
4.2.1.1 DNA Molecule's Length ..................... 63
4.2.1.2 Structure of Rigid, Double-Stranded,
Nucleic Acid Molecules .................... 64
4.2.1.3 Osmotic Pressure of PEG-Containing
Solutions ................................. 65
4.2.1.4 Effect of Ionic Composition of the
Solvent on DNA CLCD Formation ............. 66
4.2.1.5 Ionic Content of Solutions and
Efficiency of DNA CLCD Formation .......... 70
4.2.1.6 Dielectric Constants of PEG Water-
Salt Solution ............................. 73
4.2.2 Factors Influencing Type of Nucleic Acid
Molecules' Spatial Packing in CLCD Particles
after Their Formation .............................. 74
4.2.2.1 Role of Solution Temperature .............. 74
4.2.2.2 Change in Mode of Interaction between
Adjacent DNA Molecules Fixed in
Structure of CLCD Particles ............... 77
4.3 Order Parameter of Nucleic Acid Molecules in CLCD
Particles ................................................. 78
4.4 Summary ................................................... 81
References ..................................................... 82
Chapter 5 Polymorphism of Liquid-Crystalline Structures
Formed by (DNA-Polycation) Complexes ........................... 85
5.1 Some Peculiarities of Interaction of DNA Molecules with
Polycations ............................................... 85
5.2 Specificity of Chitosan Binding to DNA .................... 90
5.3 Formation of Dispersions of (DNA-Chitosan) Complexes ...... 91
5.4 CD Spectra of Dispersions Formed by (DNA-Chitosan)
Complexes ................................................. 92
5.5 X-Ray Parameters of Phases Formed by (DNA-Chitosan)
Complexes ................................................. 93
5.6 Dependence of Efficiency of CLCD Formation by
(DNA-Chitosan) Complexes on Various Factors ............... 95
5.7 Peculiarities of Interaction of Chitosan Molecules with
Nucleic Acids ............................................. 98
5.8 Attempt at a Theoretical Description of Interactions
Occurring in the (DNA-Chitosan) Complexes and Resulting
in the Formation of Liquid-Crystalline Dispersions with
Different Optical Properties ............................. 101
5.9 Summary .................................................. 111
References .................................................... 111
Chapter 6 Liquid-Crystalline State of DNA Circular
Molecules ..................................................... 115
6.1 Phase Exclusion of Circular Molecules of Nucleic Acids ... 115
6.2 Formation of Dispersions from Circular Superhelical DNA .. 116
6.3 CD Spectra of Circular Superhelical DNA Dispersions
under Conditions That Modify Parameters of Their
Secondary Structure ...................................... 118
6.4 Packing Density and Rearrangement of the Spatial
Structure of Superhelical DNA Molecules in LCD
Particles ................................................ 124
6.5 Topological Forms and Rearrangement of the Spatial
Organization of Superhelical DNA Molecules in LCD
Particles ................................................ 126
6.6 Summary .................................................. 134
References .................................................... 134
Section I Summary ............................................. 136
SECTION II DNA LIQUID-CRYSTALLINE FORMS AND THEIR
BIOLOGICAL ACTIVITY
Chapter 7 Liquid-Crystalline State of DNA in Biological
Objects ....................................................... 141
7.1 DNA and Biological Objects ............................... 141
7.2 Summary .................................................. 148
References .................................................... 148
Chapter 8 DNA Reactions under Conditions Causing Liquid-
Crystalline Dispersions ....................................... 149
8.1 Molecular Crowding ....................................... 149
8.2 Condensation of DNA under the Effect of Chitosan in
Conditions Causing Molecular Crowding .................... 150
8.3 Activity of Nucleolytic Enzymes under Conditions of
Molecular Crowding ....................................... 154
8.3.1 Effect of Nucleases on Superhelical DNA-
Forming LCD Particles ............................. 154
8.3.2 Specificity of Nuclease Action under Conditions
of Molecular Crowding ............................. 154
8.4 Activity of Proteolytic Enzymes under Conditions of
Molecular Crowding ....................................... 157
8.5 Other Biochemical Processes under Conditions of
Molecular Crowding ....................................... 161
8.6 Summary .................................................. 165
References .................................................... 165
Section II Summary ............................................ 167
SECTION III DNA LIQUID-CRYSTALLINE DISPERSIONS IN
NANOTECHNOLOGY AND BIOSENSORICS
Chapter 9 Nanoconstructions Based on Nucleic Acid Molecules .. 171
9.1 The General Concept of Nanotechnology .................... 171
9.2 Biological Molecules as a Background for Nanodesign ...... 183
9.3 Two Strategies of Nanodesign Based on NA Molecules ....... 185
9.3.1 Nanoconstructions Created by Modification of
Linear NA Molecule Structure ...................... 185
9.3.2 Theoretical Approaches to the Problem of Guest
Accumulation in Nanoconstructions Based on
Nucleic Acid Molecules ............................ 193
9.3.3 Nanoconstructions Based on NA Molecules
Ordered by Entropy Condensation ................... 197
9.3.4 Nanoconstructions Based on NA Molecules Ordered
as a Result of Enthalpy Condensation .............. 205
9.4 Summary .................................................. 210
References .................................................... 210
Chapter 10 Biosensors Based on Nucleic Acids .................. 215
10.1 General Concept of Construction and Operation of
Biosensors ............................................... 215
10.2 Double-Stranded DNA Molecule as Polyfunctional
Biosensing Unit .......................................... 220
10.3 Content and Principle of Operation of an Optical
Biosensor Based on DNA Liquid-Crystalline Dispersions .... 222
10.4 DNA CLCD Particles as Sensing Units ...................... 224
10.4.1 Detection of ВАС Causing Distortion of Double-
Stranded DNA Structure (First Approach) ........... 225
10.4.2 Detection of Colored ВАС ("External
Chromophores") Intercalating between DNA
Nitrogen Base Pairs in CLCD Particles (The
Second Approach) .................................. 227
10.4.3 Synthetic Polymer Matrixes Containing DNA
CLCD as Film-Type Biosensing Units ................ 231
10.5 Sandwich-Type Biosensing Units Based on
(DNA-Polycation) Liquid-Crystalline Dispersions .......... 234
10.6 DNA Nanoconstruction as a Sensing Unit (New Type of
Biodetectors) ............................................ 238
10.7 Hydrogels Containing DNA NaCs as New "Film-Type"
Biodetectors ............................................. 242
10.8 Summary .................................................. 245
References .................................................... 245
Section III Summary ........................................... 248
Index ......................................................... 251
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