Dynamic self-assembling DNA nanosystems: design and engineering

Over the last thirty years, DNA has proven to be a great candidate for engineering nanoscale architectures. These DNA nanostructures have been applied in areas such as single-molecular analyses, nanopatterning, diagnostics and therapeutics. One of the most commonly-used techniques to engineer DNA-based two- and three-dimensional functional nanostructures is DNA origami, wherein a long single-stranded DNA (called scaffold) is folded into a predetermined shape with the help of a set of shorter oligonucleotides (called staples). This thesis discusses a brief overview of DNA nanotechnology (design, assembly and applications) and three primary projects undertaken in the area of dynamic self-assembling DNA nanosystems: 1, a self-assembly design strategy that vastly expands the utility of DNA origami, 2, a DNA origami-based reconfigurable nanosystem with potential as a force/energy balance and diagnostic tool, and 3, a collaborative initiative on computational analyses and experimental verification for improving efficiency of DNA nanoengineering

Complex DNA Nanostructures from Oligonucleotide Ensembles

The first synthetic DNA nanostructures were created by self-assembly of a small number of oligonucleotides. Introduction of the DNA origami method provided a new paradigm for designing and creating two- and three-dimensional DNA nanostructures by folding a large single-stranded DNA and ‘stapling’ it together with a library of oligonucleotides. Despite its power and wide-ranging implementation, the DNA origami technique suffers from some limitations. Foremost among these is the limited number of useful single-stranded scaffolds of biological origin. This report describes a new approach to creating large DNA nanostructures exclusively from synthetic oligonucleotides. The essence of this approach is to replace the single-stranded scaffold in DNA origami with a library of oligonucleotides termed “scaples” (scaffold staples). Scaples eliminate the need for scaffolds of biological origin and create new opportunities for producing larger and more diverse DNA nanostructures as well as simultaneous assembly of distinct structures in a “single-pot” reaction

Probing the Security of DNA Origami

DNA origami is a method used to program the self-assembly of nanoscale computational systems. The contribution of this paper is to probe the security of a canonical DNA origami that is often reused. The paper describes the techniques we used to design probes whose input targets the origami systems’ integrity. Experimental results show that the probes successfully caused up to a third of the systems to fail. Moreover, our approach identified a single, small input whose addition was able to cause the failure of a quarter of the systems. Extending such probes to other DNA origami systems may aid in understanding how to enhance their reliability

Automated requirements analysis for a molecular watchdog timer

Dynamic systems in DNA nanotechnology are often programmed using a chemical reaction network (CRN) model as an intermediate level of abstraction. In this paper, we design and analyze a CRN model of a watchdog timer, a device commonly used to monitor the health of a safety critical system. Our process uses incremental design practices with goal-oriented requirements engineering, software verification tools, and custom software to help automate the software engineering process. The watchdog timer is comprised of three components: an absence detector, a threshold filter, and a signal amplifier. These components are separately designed and verified, and only then composed to create the molecular watchdog timer. During the requirements-design iterations, simulation, model checking, and analysis are used to verify the system. Using this methodology several incomplete requirements and design flaws were found, and the final verified model helped determine specific parameters for biological experiments

Pursuing Excitonic Energy Transfer with Programmable DNA-Based Optical Breadboards

DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond

Dynamic self-assembling DNA nanosystems: design and engineering

Over the last thirty years, DNA has proven to be a great candidate for engineering nanoscale architectures. These DNA nanostructures have been applied in areas such as single-molecular analyses, nanopatterning, diagnostics and therapeutics. One of the most commonly-used techniques to engineer DNA-based two- and three-dimensional functional nanostructures is DNA origami, wherein a long single-stranded DNA (called scaffold) is folded into a predetermined shape with the help of a set of shorter oligonucleotides (called staples). This thesis discusses a brief overview of DNA nanotechnology (design, assembly and applications) and three primary projects undertaken in the area of dynamic self-assembling DNA nanosystems: 1, a self-assembly design strategy that vastly expands the utility of DNA origami, 2, a DNA origami-based reconfigurable nanosystem with potential as a force/energy balance and diagnostic tool, and 3, a collaborative initiative on computational analyses and experimental verification for improving efficiency of DNA nanoengineering.</p

Complex DNA Nanostructures from Oligonucleotide Ensembles

The first synthetic DNA nanostructures were created by self-assembly of a small number of oligonucleotides. Introduction of the DNA origami method provided a new paradigm for designing and creating two- and three-dimensional DNA nanostructures by folding a large single-stranded DNA and ‘stapling’ it together with a library of oligonucleotides. Despite its power and wide-ranging implementation, the DNA origami technique suffers from some limitations. Foremost among these is the limited number of useful single-stranded scaffolds of biological origin. This report describes a new approach to creating large DNA nanostructures exclusively from synthetic oligonucleotides. The essence of this approach is to replace the single-stranded scaffold in DNA origami with a library of oligonucleotides termed “scaples” (scaffold staples). Scaples eliminate the need for scaffolds of biological origin and create new opportunities for producing larger and more diverse DNA nanostructures as well as simultaneous assembly of distinct structures in a “single-pot” reaction.Reprinted (adapted) with permission from Complex DNA Nanostructures from Oligonucleotide Ensembles. Divita Mathur and Eric R. Henderson. ACS Synthetic Biology 2013 2 (4), 180-185. DOI: 10.1021/sb3000518. Copyright 2012 American Chemical Society.</p

The Role of Environmental Assumptions in Failures of DNA Nanosystems

Many failures arise from complex and imperfectly understood interactions of a computational system with aspects of the environment in which it operates. By environment we mean the computational system's broader context, also called the problem world. In this work, we propose a new analysis technique called failure frames, a variation of Jackson's problem frames, to identify and model classes of environmental assumptions whose violation is known from experience to have prevented the requirements from being satisfied. We use instances of failure frames, called failure diagrams, to make explicit in the requirements model the environmental assumptions that contributed to past failures. Developers want to reuse such knowledge of past failures to prevent failures in similar, new systems. We show that failure frames and failure diagrams can capture environmental assumptions that developers need to check in order to prevent recurrence of certain failures in similar application areas. The new failure frame approach that we describe arose from our work in molecular programming of DNA nanosystems. Inaccurate assumptions about the environment are a source of many failures in DNA nanosystems and can be extremely challenging to resolve. We describe the structure of a failure catalog for DNA nanosystems that we have prototyped for use by molecular programmers. We hypothesize that the failure frame approach and catalog can be broadly useful for reducing failure recurrence in other large, distributed applications with autonomous or nondeterministic behavior that must operate in uncertain environments

Complex DNA Nanostructures from Oligonucleotide Ensembles

The first synthetic DNA nanostructures were created by self-assembly of a small number of oligonucleotides. Introduction of the DNA origami method provided a new paradigm for designing and creating two- and three-dimensional DNA nanostructures by folding a large single-stranded DNA and ‘stapling’ it together with a library of oligonucleotides. Despite its power and wide-ranging implementation, the DNA origami technique suffers from some limitations. Foremost among these is the limited number of useful single-stranded scaffolds of biological origin. This report describes a new approach to creating large DNA nanostructures exclusively from synthetic oligonucleotides. The essence of this approach is to replace the single-stranded scaffold in DNA origami with a library of oligonucleotides termed “scaples” (<u>sca</u>ffold sta<u>ples</u>). Scaples eliminate the need for scaffolds of biological origin and create new opportunities for producing larger and more diverse DNA nanostructures as well as simultaneous assembly of distinct structures in a “single-pot” reaction

Probing the Security of DNA Origami

DNA origami is a method used to program the self-assembly of nanoscale computational systems. The contribution of this paper is to probe the security of a canonical DNA origami that is often reused. The paper describes the techniques we used to design probes whose input targets the origami systems’ integrity. Experimental results show that the probes successfully caused up to a third of the systems to fail. Moreover, our approach identified a single, small input whose addition was able to cause the failure of a quarter of the systems. Extending such probes to other DNA origami systems may aid in understanding how to enhance their reliability.This is a manuscript of a proceeding from C. Koehler, D. Mathur, E. Henderson and R. Lutz, "Probing the Security of DNA Origami," 2018 IEEE International Symposium on Software Reliability Engineering Workshops (ISSREW), Memphis, TN, 2018, pp. 138-139, doi: 10.1109/ISSREW.2018.00-14. Posted with permission.</p