100 research outputs found
Molecular robots guided by prescriptive landscapes
Traditional robots rely for their function on computing, to store internal representations of their goals and environment and to coordinate sensing and any actuation of components required in response. Moving robotics to the single-molecule level is possible in principle, but requires facing the limited ability of individual molecules to store complex information and programs. One strategy to overcome this problem is to use systems that can obtain complex behaviour from the interaction of simple robots with their environment. A first step in this direction was the development of DNA walkers, which have developed from being non-autonomous, to being capable of directed but brief motion on one-dimensional tracks. Here we demonstrate that previously developed random walkersâso-called molecular spiders that comprise a streptavidin molecule as an inert âbodyâ and three deoxyribozymes as catalytic âlegsââshow elementary robotic behaviour when interacting with a precisely defined environment. Single-molecule microscopy observations confirm that such walkers achieve directional movement by sensing and modifying tracks of substrate molecules laid out on a two-dimensional DNA origami landscape. When using appropriately designed DNA origami, the molecular spiders autonomously carry out sequences of actions such as âstartâ, âfollowâ, âturnâ and âstopâ. We anticipate that this strategy will result in more complex robotic behaviour at the molecular level if additional control mechanisms are incorporated. One example might be interactions between multiple molecular robots leading to collective behaviour; another might be the ability to read and transform secondary cues on the DNA origami landscape as a means of implementing Turing-universal algorithmic behaviour
Nanostructured luminescently labeled nucleic acids
Important and emerging trends at the interface of luminescence, nucleic acids and nanotechnology
are: (i) the conventional luminescence labeling of nucleic acid nanostructures (e.g. DNA tetrahedron);
(ii) the labeling of bulk nucleic acids (e.g. singleâstranded DNA, doubleâstranded DNA) with
nanostructured luminescent labels (e.g. copper nanoclusters); and (iii) the labeling of nucleic acid
nanostructures (e.g. origami DNA) with nanostructured luminescent labels (e.g. silver
nanoclusters). This review surveys recent advances in these three different approaches to the
generation of nanostructured luminescently labeled nucleic acids, and includes both direct and
indirect labeling methods
Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns
Self-assembled DNA nanostructures enable nanometre-precise patterning that can be used to create programmable molecular machines and arrays of functional materials. DNA origami is particularly versatile in this context because each DNA strand in the origami nanostructure occupies a unique position and can serve as a uniquely addressable pixel. However, the scale of such structures has been limited to about 0.05 square micrometres, hindering applications that demand a larger layout and integration with more conventional patterning methods. Hierarchical multistage assembly of simple sets of tiles can in principle overcome this limitation, but so far has not been sufficiently robust to enable successful implementation of larger structures using DNA origami tiles. Here we show that by using simple local assembly rules that are modified and applied recursively throughout a hierarchical, multistage assembly process, a small and constant set of unique DNA strands can be used to create DNA origami arrays of increasing size and with arbitrary patterns. We illustrate this method, which we term âfractal assemblyâ, by producing DNA origami arrays with sizes of up to 0.5 square micrometres and with up to 8,704 pixels, allowing us to render images such as the Mona Lisa and a rooster. We find that self-assembly of the tiles into arrays is unaffected by changes in surface patterns on the tiles, and that the yield of the fractal assembly process corresponds to about 0.95^(mâââ1) for arrays containing m tiles. When used in conjunction with a software tool that we developed that converts an arbitrary pattern into DNA sequences and experimental protocols, our assembly method is readily accessible and will facilitate the construction of sophisticated materials and devices with sizes similar to that of a bacterium using DNA nanostructures
Direct Atomic Force Microscopy Observation of DNA Tile Crystal Growth at the Single-Molecule Level
DNA Nanostructures as Models for Evaluating the Role of Enthalpy and Entropy in Polyvalent Binding
Surface treatments to improve adhesion to cured butyl rubber
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Synthesis of pdCpAs and transfer RNAs activated with thiothreonine and derivatives
N,S-diprotected L-thiothreonine and L-allo-thiothreonine derivatives were synthesized using a novel chemical strategy, and used for esterification of the dinucleotide pdCpA. The aminoacylated dinucleotides were then employed for the preparation of activated suppressor tRNA(CUA) transcripts. Thiothreonine and allo-thiothreonine were incorporated into a predetermined position of a catalytically competent dihydrofolate reductase (DHFR) analogue lacking cysteine, and the elaborated proteins were derivatized site-specifically at the thiothreonine residue with a fluorophore
Mapping the Thermal Behavior of DNA Origami Nanostructures
Understanding
the thermodynamic properties of complex DNA nanostructures,
including rationally designed two- and three-dimensional (2D and 3D,
respectively) DNA origami, facilitates more accurate spatiotemporal
control and effective functionalization of the structures by other
elements. In this work fluorescein and tetramethylrhodamine (TAMRA),
a FoÌrster resonance energy transfer (FRET) dye pair, were incorporated
into selected staples within various 2D and 3D DNA origami structures.
We monitored the temperature-dependent changes in FRET efficiency
that occurred as the dye-labeled structures were annealed and melted
and subsequently extracted information about the associative and dissociative
behavior of the origami. In particular, we examined the effects of
local and long-range structural defects (omitted staple strands) on
the thermal stability of common DNA origami structures. The results
revealed a significant decrease in thermal stability of the structures
in the vicinity of the defects, in contrast to the negligible long-range
effects that were observed. Furthermore, we probed the global assembly
and disassembly processes by comparing the thermal behavior of the
FRET pair at several different positions. We demonstrated that the
staple strands located in different areas of the structure all exhibit
highly cooperative hybridization but have distinguishable melting
temperatures depending on their positions. This work underscores the
importance of understanding fundamental aspects of the self-assembly
of DNA nanostructures and can be used to guide the design of more
complicated DNA nanostructures, to optimize annealing protocol and
manipulate functionalized DNA nanostructures
Reconfigurable DNA Origami to Generate Quasifractal Patterns
The specificity of WatsonâCrick base pairing,
unique mechanical
properties of DNA, and intrinsic stability of DNA double helices makes
DNA an ideal material for the construction of dynamic nanodevices.
Rationally designed strand displacement reactions can be used to produce
dynamic reconfiguration of DNA nanostructures postassembly. Here we
describe a âfoldâreleaseâfoldâ strategy
of multiple strand displacement and hybridization reactions to reconfigure
a simple DNA origami structure into a complex, quasifractal pattern,
demonstrating a complex transformation of DNA nanoarchitectures
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