Biological Nanowires

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Biological Nanowires Biological Nanowires: Integration of the silver(I) base pair into DNA with nanotechnological and synthetic biological applications Simon Vecchioni Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences Columbia University 2019 © 2019 Simon Vecchioni All rights reserved Abstract Biological Nanowires: Integration of the silver(I) base pair into DNA with nanotechnological and synthetic biological applications Simon Vecchioni Modern computing and mobile device technologies are now based on semiconductor technology with nanoscale components, i.e., nanoelectronics, and are used in an increasing variety of consumer, scientific, and space-based applications. This rise to global prevalence has been accompanied by a similarly precipitous rise in fabrication cost, toxicity, and technicality; and the vast majority of modern nanotechnology cannot be repaired in whole or in part. In combination with looming scaling limits, it is clear that there is a critical need for fabrication technologies that rely upon clean, inexpensive, and portable means; and the ideal nanoelectronics manufacturing facility would harness micro- and nanoscale fabrication and self-assembly techniques. The field of molecular electronics has promised for the past two decades to fill fundamental gaps in modern, silicon-based, micro- and nanoelectronics; yet molecular electronic devices, in turn, have suffered from problems of size, dispersion and reproducibility. In parallel, advances in DNA nanotechnology over the past several decades have allowed for the design and assembly of nanoscale architectures with single-molecule precision, and indeed have been used as a basis for heteromaterial scaffolds, mechanically-active delivery mechanisms, and network assembly. The field has, however, suffered for lack of meaningful modularity in function: few designs to date interact with their surroundings in more than a mechanical manner. As a material, DNA offers the promise of nanometer resolution, self-assembly, linear shape, and connectivity into branched architectures; while its biological origin offers information storage, enzyme- compatibility and the promise of biologically-inspired fabrication through synthetic biological means. Recent advances in DNA chemistry have isolated and characterized an orthogonal DNA base pair using standard nucleobases: by bridging the gap between mismatched cytosine nucleotides, silver(I) ions can be selectively incorporated into the DNA helix with atomic resolution. The goal of this thesis is to explore how this approach to “metallize” DNA can be combined with structural DNA nanotechnology as a step toward creating electronically-functional DNA networks. This work begins with a survey of applications for such a transformative technology, including nanoelectronic component fabrication for low-resource and space-based applications. We then investigate the assembly of linear Ag+-functionalized DNA species using biochemical and structural analyses to gain an understanding of the kinetics, yield, morphology, and behavior of this orthogonal DNA base pair. After establishing a protocol for high yield assembly in the presence of varying Ag+ functionalization, we investigate these linear DNA species using electrical means. First a method of coupling orthogonal DNA to single-walled carbon nanotubes (SWCNTs) is explored for self-assembly into nanopatterned transistor devices. Then we carry out scanning tunneling microscope (STM) break junction experiments on short polycytosine, polycationic DNA duplexes and find increased molecular conductance of at least an order of magnitude relative to the most conductive DNA analog. With an understanding of linear species from both a biochemical and nanoelectronic perspective, we investigate the assembly of nonlinear Ag+-functionalized DNA species. Using rational design principles gathered from the analysis of linear species, a de novo mathematical framework for understanding generalized DNA networks is developed. This provides the basis for a computational model built in Matlab that is able to design DNA networks and nanostructures using arbitrary base parity. In this way, DNA nanostructures are able to be designed using the dC:Ag+:dC base pair, as well as any similar nucleobase or DNA-inspired system (dT:Hg2+:dT, rA:rU, G4, XNA, LNA, PNA, etc.). With this foundation, three general classes of DNA tiles are designed with embedded nanowire elements: single crossover Holliday junction (HJ) tiles, T-junction (TJ) units, and double crossover (DX) tile pairs and structures. A library of orthogonal chemistry DNA nanotechnology is described, and future applications to nanomaterials and circuit architectures are discussed. Contents List of Figures .......................................................................................................................................... v Acknowledgements ............................................................................................................................... xii Preface: Structure of this thesis ............................................................................................................. xiv Chapter 1 Introduction: Significance of DNA nanowire and nanostructure design ................................... 1 1.1. Mesoscale technologies for Earth- and space-based applications .................................................. 2 1.2. DNA as a building block ................................................................................................................. 4 1.3. Metallo-DNA: electrical potential in DNA ...................................................................................... 5 Chapter 2 Biochemical Analysis of DNA Nanowires: A foundation for nanotechnology ........................... 9 2.1. Chemical analysis: a framework .................................................................................................. 10 2.2. Characterization of Ag+ intercalation .......................................................................................... 11 2.2.1. Analysis by molecular weight: reaction kinetics, sequence design and enzyme compatibility 14 2.2.2. NMR..................................................................................................................................... 17 2.2.3. Single-molecule FRET via zero-mode waveguide (ZMW) ....................................................... 19 2.3. Stability of Ag+ intercalation ....................................................................................................... 23 2.3.1. Thermal denaturation and UV-Vis ........................................................................................ 23 2.3.2. Cluster analysis .................................................................................................................... 26 2.4. Best annealing protocol for Ag+ intercalation, devised by chemical analysis................................ 28 2.4.1. Buffer analysis using FRET quenching ................................................................................... 29 2.4.2. Protocol for high-yield DNA nanowire annealing and processing .......................................... 35 i 2.5. Synthetic biological integration of Ag+ intercalation .................................................................... 38 2.5.1. Enzyme compatibility ........................................................................................................... 38 2.5.2. Synthetic gene parts ............................................................................................................. 39 2.6. Discussion of Ag+ intercalation ................................................................................................... 42 Chapter 3 Finding the Spark: Electrical assay of silver(I) DNA nanowires .............................................. 48 3.1. Assay of DNA conductivity .......................................................................................................... 49 3.2. Nanofabricated molecular transistors ......................................................................................... 51 3.2.1. CNT linking chemistry—a route to SM leads ......................................................................... 51 3.2.2. Device nanofabrication ........................................................................................................ 57 3.2.3. Electrical assay, results, limitations....................................................................................... 60 3.3. STM break junction experiments: bridging the gap...................................................................... 62 3.3.1. Device design ....................................................................................................................... 63 3.3.2. Linking chemistry ................................................................................................................. 63 3.3.3. Atomically-flat gold surface preparation ............................................................................... 66 3.3.4. STM break junction assay and results ................................................................................... 76 Chapter 4 DNA by Design: De novo computational framework for DNA sequence design and nanotechnology .................................................................................................................................... 79 4.1. Use of Computational Modeling in
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