Metal-Responsive Base Pair Switching of Ligand-type Uracil Nucleobases (Springer Theses)

In this thesis, the author proposes "metal-responsive base pair switching" of ligand-modified nucleobases as a novel tool for stimuli-responsive control of DNA assemblies. It is written to demonstrate broad applicability of the base pair switching in dynamic DNA nanotechnology and inspire researchers to use this technique. Based on specific interactions between ligand-type nucleobases and target metal ions, in this volume, DNA hybridization was dynamically controlled through strand displacement reactions. The base pair switching was further applied to develop metal-dependent DNA molecular machines. This novel strategy for stimuli-responsive regulation of DNA assemblies will greatly expand the scope of dynamic DNA nanotechnology. This volume uniquely features importance of elaborate molecular design based on chemistry for imparting stimuli responsiveness to DNA assemblies. Supervisor’s Foreword Acknowledgements Contents List of Published Articles Abbreviations 1 General Introduction 1.1 Programmable Self-Assembly of DNA 1.2 Dynamic Control of DNA Assemblies Based on Strand Displacement Reactions 1.3 Dynamic DNA Systems Driven by External Stimuli 1.4 Metal-Mediated Base Pairing 1.5 Bifacial Base-Pairing Behaviors of 5-Modified Uracil Bases 1.6 The Aim of This Study References 2 Metal-Responsive DNA Strand Displacement Reactions Driven by Base Pair Switching of 5-Hydroxyuracil Nucleobases 2.1 Introduction 2.2 Design and Synthesis of DNA Strands Containing 5-Hydroxyuracil Bases for Metal-Responsive DNA Strand Displacement Reactions 2.3 GdIII-Responsive Base Pair Switching of 5-Hydroxyuracil Bases 2.3.1 GdIII-Dependent Hybridization Preference of UOH-containing DNA Strands 2.3.2 GdIII-Responsive Base Pair Switching under Isothermal Conditions 2.3.3 Effects of the Introduction of an Additional G–C Pair at the Termini of DNA Duplexes 2.4 Metal-Responsive DNA Strand Displacement Reactions Driven by Base Pair Switching of 5-Hydroxyuracil Bases 2.5 Discussion 2.6 Experimental Section References 3 Metal-Dependent Base Pair Switching of N,N-Dicarboxymethyl-5-Aminouracil Nucleosides 3.1 Introduction 3.2 Synthesis of DNA Strands Containing N,N-Dicarboxymethyl-5-Aminouracil Bases 3.2.1 Overview 3.2.2 Synthesis of Methyl-Protected dcaU Nucleoside 3 (Fig. 3.3) 3.2.3 Synthesis of dcaU Nucleoside 4 (Fig. 3.9) 3.2.4 Synthesis of DMTr-Protected dcaU Nucleoside 5 (Fig. 3.12) 3.2.5 Synthesis of dcaU Phosphoramidite 6 (Fig. 3.14) 3.2.6 Synthesis of DNA Strands Containing the dcaU Base 3.3 Metal Complexation of N,N-Dicarboxymethyl-5-Aminouracil Nucleosides 3.4 Metal-Mediated Base Pairing of N,N-Dicarboxymethyl-5-Aminouracil Bases within DNA Duplexes 3.5 Base-Pairing Behaviors of N,N-Dicarboxymethyl-5-Aminouracil Bases with Natural Nucleobases 3.6 Metal-Dependent Switching of the DNA Hybridization Partner through Base Pair Switching of N,N-Dicarboxymethyl-5-Aminouracil Bases 3.7 Discussion 3.8 Experimental Section References 4 Metal-Responsive DNA Tweezers Driven by Base Pair Switching of 5-Hydroxyuracil Nucleobases 4.1 Introduction 4.2 Design of Metal-Responsive DNA Tweezers Containing 5-Hydroxyuracil Bases 4.3 Formation and Metal-Dependent Structural Conversion of DNA Tweezers Containing 5-Hydroxyuracil Bases 4.3.1 Optimization of the Base Sequences of the Tweezer Arms 4.3.2 Evaluation of the Structural Conversion by Fluorescence Measurement 4.3.3 Optimization of MgII Concentration 4.3.4 Optimization of GdIII Concentration 4.4 Metal-Responsive Operation of DNA Tweezers Containing 5-Hydroxyuracil Bases under Isothermal Conditions 4.5 Discussion 4.6 Experimental Section References 5 Conclusion 5.1 Conclusion References Curriculum Vitae Keita Mori