Signal replication in a DNA nanostructure (original) (raw)
Related papers
2012
This chapter overviews the current state of the emerging discipline of DNA nanorobotics that make use of synthetic DNA to self-assemble operational molecular-scale devices. Recently there have been a series of quite astonishing experimental results—which have taken the technology from a state of intriguing possibilities into demonstrated capabilities of quickly increasing scale and complexity. We first state the challenges in molecular robotics and discuss why DNA as a nanoconstruction material is ideally suited to overcome these. We then review the design and demonstration of a wide range of molecular-scale devices; from DNA nanomachines that change conformation in response to their environment to DNA walkers that can be programmed to walk along predefined paths on nanostructures while carrying cargo or performing computations, to tweezers that can repeatedly switch states. We conclude by listing major challenges in the field along with some possible future directions.
A Two-State DNA Lattice Switched by DNA Nanoactuator
Angewandte Chemie International Edition, 2003
Controlled mechanical movement in molecular scale devices is one of the key goals of nanotechnology. DNA is an excellent candidate for the construction of such devices due to the specificity of base pairing and its robust physicochemical properties. Well-known as the genetic material, DNA has recently been explored as a smart material for constructing periodically patterned structures and nanomechanical devices. A variety of DNA-based molecular machines displaying rotational and open/close movements have recently been demonstrated. Reversible shifting of the equilibrium between two conformational states is triggered by changes in external conditions or by the addition of a "DNA fuel strand" that provides the driving force for such changes. Incorporation of DNA devices into arrays could lead to complex structural states suitable for nanorobotic applications if each individual device can be addressed separately. Yan et al. have recently demonstrated a linear one-dimensional DNA array displaying a switch of cis and trans conformations through the rotational motion of a robust sequence-dependent DNA nanodevice. In the further exploration of the potential applications of DNA-based molecule machines in nanorobotics, a major challenge is to implement molecular machines into two-dimensional (2D) or threedimensional (3D) patterned arrays. This has numerous potential applications. 1) The size and shape of the lattice could be programmed through the control of sequencedependent devices, leading to controlled nanofabrication of molecular nanoelectronic wires with "on" and "off" states. For example, the tunneling effect of quantum-dot cellular automata could be actuated by controlling the distance between adjacent cells. 2) Molecules or nanoparticles could be selectively manipulated, for example, sorted and transported, by using molecular motor devices arranged on DNA
Autonomous programmable DNA nanorobotic devices using DNAzymes
Theoretical Computer Science, 2009
A major challenge in nanoscience is the design of synthetic molecular devices that run autonomously (that is, without externally mediated changes per work-cycle) and are programmable (that is, their behavior can be modified without complete redesign of the device). DNA-based synthetic molecular devices have the advantage of being relatively simple to design and engineer, due to the predictable secondary structure of DNA nanostructures and the well-established biochemistry used to manipulate DNA nanostructures. However, ideally we would like to minimize the use of protein enzymes in the design of a DNA-based synthetic molecular device. We present the design of a class of DNA-based molecular devices using DNAzyme. These DNAzyme based devices are autonomous, programmable, and further require no protein enzymes. The basic principle involved is inspired by a simple but ingenious molecular device due to Mao et al that used DNAzyme to traverse on a DNA nanostructure, but was not programmable in the sense defined above (it did not execute computations).
Regulation at a distance of biomolecular interactions using a DNA origami nanoactuator
The creation of nanometre-sized structures that exhibit controllable motions and functions is a critical step towards building nanomachines. Recent developments in the field of DNA nanotechnology have begun to address these goals, demonstrating complex static or dynamic nanostructures made of DNA. Here we have designed and constructed a rhombus-shaped DNA origami 'nanoactuator' that uses mechanical linkages to copy distance changes induced on one half ('the driver') to be propagated to the other half ('the mirror'). By combining this nanoactuator with split enhanced green fluorescent protein (eGFP), we have constructed a DNA–protein hybrid nanostructure that demonstrates tunable fluorescent behaviours via long-range allosteric regulation. In addition, the nanoactuator can be used as a sensor that responds to specific stimuli, including changes in buffer composition and the presence of restriction enzymes or specific nucleic acids.
A DNA Tile Actuator with Eleven Discrete States
Angewandte Chemie International Edition, 2011
The dynamic nature of DNA hybridization has been utilized to design nanostructures that can switch between geometrically well-defined states. [1] Seeman and co-workers pioneered the design of DNA devices that could reversibly switch between two different states. [2] One of these structures was recently applied as a DNA robot arm in a nanoscale assembly line. Extension and contraction of nanostructures between 2 or 3 states have been executed by using DNA hairpins. Herein we report on a novel DNA actuator design that undergoes a sliding type motion between 11 discrete states. The actuator can be locked in any of the 2 nucleotide-spaced states, as shown by fluorescence resonance energy transfer (FRET) and by the strict control of a chemical reaction. By strand displacement reactions, the actuator can be switched between the states. The actuator operates as a nanoscale extendable arm and the integration of one or more actuators in larger nanostructures holds promise for designing more sophisticated dynamic DNA devices.
Design, Simulation, and Experimental Demonstration of Self-assembled DNA Nanostructures and Motors
Lecture Notes in Computer Science, 2005
Self-assembly is the spontaneous self-ordering of substructures into superstructures, driven by the selective affinity of the substructures. Complementarity of DNA bases renders DNA an ideal material for programmable selfassembly of nanostructures. DNA self-assembly is the most advanced and versatile system that has been experimentally demonstrated for programmable construction of patterned systems on the molecular scale. The methodology of DNA self-assembly begins with the synthesis of single strand DNA molecules that self-assemble into macromolecular building blocks called DNA tiles. These tiles have single strand "sticky ends" that complement the sticky ends of other DNA tiles, facilitating further assembly into larger structures known as DNA tiling lattices. In principle, DNA tiling assemblies can form any computable two or three-dimensional pattern, however complex, with the appropriate choice of the tiles' component DNA. Two-dimensional DNA tiling lattices composed of hundreds of thousands of tiles have been demonstrated experimentally. These assemblies can be used as programmable scaffolding to position molecular electronics and robotics components with precision and specificity, facilitating fabrication of complex nanoscale devices. We overview the evolution of DNA self-assembly techniques from pure theory, through simulation and design, and then to experimental practice. In particular, we begin with an overview of theoretical models and algorithms for DNA lattice self-assembly. Then we describe our software for the simulation and design of DNA tiling assemblies and DNA nano-mechanical devices. As an example, we discuss models, algorithms, and computer simulations for the key problem of error control in DNA lattice self-assembly. We then briefly discuss our laboratory demonstrations of DNA lattices and motors, including those using the designs aided by our software. These experimental demonstrations of DNA self-assemblies include the assembly of patterned objects at the molecular scale, the execution of molecular computations, and the autonomous DNA walking and computing devices.
Autonomous Programmable Nanorobotic Devices Using DNAzymes
Lecture Notes in Computer Science, 2008
A major challenge in nanoscience is the design of synthetic molecular devices that run autonomously and are programmable. DNA-based synthetic molecular devices have the advantage of being relatively simple to design and engineer, due to the predictable secondary structure of DNA nanostructures and the well-established biochemistry used to manipulate DNA nanostructures. We present the design of a class of DNAzyme based molecular devices that are autonomous, programmable, and further require no protein enzymes. The basic principle involved is inspired by a simple but ingenious molecular device due to Mao et al [25]. Our DNAzyme based designs include (1) a finite state automata device, DNAzyme FSA that executes finite state transitions using DNAzymes, (2) extensions to it including probabilistic automata and non-deterministic automata, (3) its application as a DNAzyme router for programmable routing of nanostructures on a 2D DNA addressable lattice, and (4) a medical-related application, DNAzyme doctor that provide transduction of nucleic acid expression: it can be programmed to respond to the underexpression or overexpression of various strands of RNA, with a response by release of an RNA.
Investigating the dynamics of surface-immobilized DNA nanomachines
Scientific Reports, 2016
Surface immobilization of molecules can have a profound in uence on their structure function and dynamics. Toehold-mediated strand displacement is often used in solution to drive synthetic nanomachines made from DNA but the e ects of surface immobilization on the mechanism and kinetics of this reaction have not yet been fully elucidated. Here we show that the kinetics of strand displacement in surface immobilized nanomachines are signi cantly di erent to those of the solution phase reaction and we attribute this to the e ects of intermolecular interactions within the DNA layer We demonstrate that the dynamics of strand displacement can be manipulated by changing strand length, concentration and G/C content. By inserting mismatched bases it is also possible to tune the rates of the constituent displacement processes (toehold-binding and branch migration) independently, and information can be encoded in the time dependence of the overall reaction Our ndings will facilitate the rational design of surface-immobilized dynamic DNA nanomachines, including computing devices and track-based motors.