The DNA origami strategy for assembling designed supramolecular complexes requires ssDNA as a scaffold strand. A system is described that was designed approximately one third the length of the M13 bacteriophage genome for ease of ssDNA production. Folding of the 2404-base ssDNA scaffold into a variety of origami shapes with high assembly yields is demonstrated.

As bottom up DNA nanofabrication creates increasingly complex and dynamic mechanisms, the implementation of actuators within the DNA nanotechnology toolkit has grown increasingly important. One such actuator, the I-motif, is fairly simple in that it consists solely of standard DNA sequences and does not require any modification chemistry or special purification beyond that typical for DNA oligomer synthesis. This study presents a new implementation of parallel I-motif actuators, emphasizing their future potential as drivers of complex internal motion between substructures. Here we characterize internal motion between DNA origami substructures via AFM and image analysis. Such parallel I-motif design and quantification of actuation provide a useful step toward more complex and effective molecular machines.

Scaffolded DNA origami are a robust tool for building discrete nanoscale objects at high yield. This strategy ensures, in the design process, that the desired nanostructure is the minimum free energy state for the designed set of DNA sequences. Despite aiming for the minimum free energy structure, the folding process which leads to that conformation is difficult to characterize, although it has been the subject of much research. In order to shed light on the molecular folding pathways, this study intentionally frustrates the folding process of these systems by simultaneously annealing the staple pools for multiple target or parent origami structures, forcing competition. A surprising result of these competitive, simultaneous anneals is the formation of chimeric DNA origami which inherit structural regions from both parent origami. By comparing the regions inherited from the parent origami, relative stability of substructures were compared. This allowed examination of the folding process with typical characterization techniques and materials. Anneal curves were then used as a means to rapidly generate a phase diagram of anticipated behavior as a function of staple excess and parent staple ratio. This initial study shows that competitive anneals provide an exciting way to create diverse new nanostructures and may be used to examine the relative stability of various structural motifs.The commercial development of inexpensive and quickly produced DNA of arbitrary nucleobase sequence has fueled the growth of DNA nanotechnology as a field [1]. DNA nanotechnology has made promising advances toward light harvesting [2], computation [3], cancer treatement [4,5], and assembly of nanoelectronics [6]. While many DNA self-assembly strategies exist [7,8], scaffolded DNA origami has received significant attention as a convenient way to design and create discrete nanoscale objects [9]. Scaffolded DNA origami consist of single strand DNA (ssDNA) of two types, synthetic oligomers and circular viral genomes; the viral scaffold is forced to route through the designed structure by the binding of complementary subsequences on the synthetic oligomers, or staples. Staples are added in excess, often 10× relative to the scaffold concentration, strongly driving the viral ssDNA scaffold to fold into the target structure. Although 10× is a common staple excess anneals have been successfully performed as low as 2.5× staple excess. As this study involves multiple staple pools, staple excess will always refer to the total staple concentration relative to the scaffold, while the parent staple ratio will refer to how much of that total corresponds to the staple pool for each target origami. High production yield is achieved by thermal annealing and slow cooling of the system. Such annealing has also been performed chemically, isothermally, and mechanically [10][11][12].The hybridization of double strand DNA (dsDNA) has been well studied, particularly under physiological conditions [13,14]. The formation of dsDNA from ssDNA is driven by base stack...

Structural DNA nanotechnology has demonstrated both versatility and potential as a molecular manufacturing tool; the formation and processing of DNA nanostructures has therefore been subject to much interest. Characterization of the formation process itself is vital to understanding the role of design in production yield. We present our search for a robust new technique, chemical quenching, to arrest molecular folding in DNA systems for subsequent characterization. Toward this end we will introduce two miniM13 origami designs based on a 2.4 kb scaffold, each with diametrically opposed scaffold routing strategies (maximized scaffold crossovers versus maximized staple crossovers) to examine the relevance of design in the folding process. By chemically rendering single strand DNA inert and unable to hybridize, we probe the folding pathway of several scaffolded DNA origami structures.

Polyimides are well established as gas separation membranes due to their intrinsically low free volume and correspondingly high H2 selectivity relative to other gases such as CO2. Prior studies have established that H2/CO2 selectivity can be improved by crosslinking polyimides with diamines differing in spacer length. In this work, we follow the evolution of macroscopic and microscopic properties of a commercial polyimide over long crosslinking times (tx) with 1,3‐diaminopropane. According to spectroscopic analysis, the crosslinking reaction saturates after ≈24 h, whereas tensile, nanoindentation and stress relaxation tests reveal that the material stiffens, and possesses a long relaxation time that increases with increasing tx. Although differential scanning calorimetry shows that the glass transition temperature decreases systematically with increasing tx, permeation studies indicate that the permeabilities of H2 and CO2 decrease, while the H2/CO2 selectivity increases markedly, with increasing tx. At long tx, the polyimide becomes impermeable to CO2, suggesting that it could be used as a barrier material.magnified image

Structural DNA nanotechnology, as exemplified by DNA origami, has enabled the design and construction of molecularly-precise objects for a myriad of applications. However, limitations in imaging, and other characterization approaches, make a quantitative understanding of the folding process challenging. Such an understanding is necessary to determine the origins of structural defects, which constrain the practical use of these nanostructures. Here, we combine careful fluorescent reporter design with a novel affine transformation technique that, together, permit the rigorous measurement of folding thermodynamics. This method removes sources of systematic uncertainty and resolves problems with typical background-correction schemes. This in turn allows us to examine entropic corrections associated with folding and potential secondary and tertiary structure of the scaffold. Our approach also highlights the importance of heat-capacity changes during DNA melting. In addition to yielding insight into DNA origami folding, it is well-suited to probing fundamental processes in related self-assembling systems.

Here, a pH-induced nanomechanical switching of i-motif structures incorporated into DNA origami bound onto cysteamine-modified basal plane HOPG was electronically addressed, demonstrating for the first time the electrochemical read-out of the nanomechanics of DNA origami. This paves the way for construction of electrode-integrated bioelectronic nanodevices exploiting DNA origami patterns on conductive supports.

While the design and assembly of DNA origami are straightforward, its relative novelty as a nanofabrication technique means that the tools and methods for designing new structures have not been codified as well as they have for more mature technologies, such as integrated circuits. While design approaches cannot be truly formalized until design-property relationships are fully understood, this document attempts to provide a step-by-step guide to designing DNA origami nanostructures using the tools available at the current state of the art.