Synthetic DNA Nanostructures Research Articles

The Physics of DNA in Confinement

Throughout all kingdoms of life, DNA is found to form compact structures. DNA is neatly wound inside a viral capsid, DNA forms hierarchical structures in cell nuclei, DNA could even be woven into complex 3D structures known as DNA origami. Such a ubiquitous compaction is surprising, as it contradicts, at the first look, the very basic physical properties of DNA: the high electrostatic charge and resistance to bending at the scale of 50 nm or less. Experimental work has shown that counterions surrounding DNA can considerably alter its properties, for example, turning electrostatic self-repulsion into attraction. Yet, elucidating the precise microscopic structure and mechanism of DNA-DNA interaction in confined environment remains beyond the experimental capability. Here, we report the results of all-atom molecular dynamics simulations that investigated the microscopic structure of dense DNA assemblies and the physics of interactions that makes such assemblies possible. First, we show that a refined parameterization of ion-DNA interaction [1] permits the all-atom MD method to quantitatively reproduce experimentally known properties [2,3] of dense DNA arrays. Next we characterize the microscopic structure of the arrays, elucidating their ionic atmosphere, preferred azimuthal orientation of DNA molecules, the pair-wise additivity of DNA-DNA forces, the longitudinal friction forces between DNA molecules, and the role of solvation force. Our study demonstrates the ability of all-atom molecular dynamics simulations to provide quantitative, accurate information about dense DNA systems, opening exciting opportunities for future work in the area of synthetic DNA nanostructures, DNA packaging in viral capsids and cell nuclei.[1] J Phys Chem Lett 3:45-50.[2] Proc Natl Acad Sci U S A 81:2621-2625.[3] Biophys J 94:4775-82.

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.

HolT Hunter: Software for identifying and characterizing low-strain DNA holliday triangles

Synthetic DNA nanostructures are most commonly held together via Holliday junctions. These junctions allow for a wide variety of different angles between the double helices they connect. Nevertheless, only constructs with a very limited selection of angles have been built, to date, because of the computational complexity of identifying structures that fit together with low strain at odd angles. I have developed an algorithm that finds over 95% of the possible solutions by breaking the problem down into two portions. First, there is a problem of how smooth rods can form triangles by lying across one another. This problem is easily handled by numerical computation. Second, there is the question of how distorted DNA double helices would need to be to fit onto the rod structure. This strain is calculated directly. The algorithm has been implemented in a Mathematica 8 notebook called Holliday Triangle Hunter. A large database of solutions has been identified. Additional interface software is available to facilitate drawing and viewing models.

DNA Nanostructures as Models for Evaluating the Role of Enthalpy and Entropy in Polyvalent Binding

DNA nanotechnology allows the design and construction of nanoscale objects that have finely tuned dimensions, orientation, and structure with remarkable ease and convenience. Synthetic DNA nanostructures can be precisely engineered to model a variety of molecules and systems, providing the opportunity to probe very subtle biophysical phenomena. In this study, several such synthetic DNA nanostructures were designed to serve as models to study the binding behavior of polyvalent molecules and gain insight into how small changes to the ligand/receptor scaffolds, intended to vary their conformational flexibility, will affect their association equilibrium. This approach has yielded a quantitative identification of the roles of enthalpy and entropy in the affinity of polyvalent DNA nanostructure interactions, which exhibit an intriguing compensating effect.

Recent advances in DNA-based directed assembly on surfaces

In the last decade, "small" and "integrated" have been keywords in the field of device fabrication as the desire to exploit nanoscale phenomena and make electronic, photonic and magnetic arrays has grown. In an effort to improve resolution and control costs, much work has been dedicated to developing alternatives to conventional microfabrication technology. For this purpose, biomolecular assembly and DNA nanotechnology in particular are appealing owing to their inherent size and capacity for molecular recognition. Herein, we review recent achievements in DNA-based directed assembly on substrates. These include novel methods for patterning and depositing nanomaterials on DNA-modified surfaces as well as using synthetic DNA nanostructures such as DNA tiles and origami as templates to direct the assembly of nanoscale components. Particular attention is paid to integrating self-assembly with top-down lithography, and some possible directions for future work are discussed.