Lifeng Zhou

Programmable motion of DNA origami mechanisms

Significance Folding DNA into complex 3D shapes (DNA origami) has emerged as a powerful method for the precise design and fabrication of self-assembled nanodevices. Current efforts have focused largely on developing static objects or structures with small movements and/or unspecified motion paths. Here we establish a basis for developing DNA-based nanomachines by creating dynamic mechanisms with well-defined motion. We demonstrate the design of nanoscale 1D, 2D, and 3D motion by integrating concepts from engineering machine design with DNA origami nanotechnology. DNA origami enables the precise fabrication of nanoscale geometries. We demonstrate an approach to engineer complex and reversible motion of nanoscale DNA origami machine elements. We first design, fabricate, and characterize the mechanical behavior of flexible DNA origami rotational and linear joints that integrate stiff double-stranded DNA components and flexible single-stranded DNA components to constrain motion along a single degree of freedom and demonstrate the ability to tune the flexibility and range of motion. Multiple joints with simple 1D motion were then integrated into higher order mechanisms. One mechanism is a crank–slider that couples rotational and linear motion, and the other is a Bennett linkage that moves between a compacted bundle and an expanded frame configuration with a constrained 3D motion path. Finally, we demonstrate distributed actuation of the linkage using DNA input strands to achieve reversible conformational changes of the entire structure on ∼minute timescales. Our results demonstrate programmable motion of 2D and 3D DNA origami mechanisms constructed following a macroscopic machine design approach.

DNA Origami Compliant Nanostructures with Tunable Mechanical Properties

DNA origami enables fabrication of precise nanostructures by programming the self-assembly of DNA. While this approach has been used to make a variety of complex 2D and 3D objects, the mechanical functionality of these structures is limited due to their rigid nature. We explore the fabrication of deformable, or compliant, objects to establish a framework for mechanically functional nanostructures. This compliant design approach is used in macroscopic engineering to make devices including sensors, actuators, and robots. We build compliant nanostructures by utilizing the entropic elasticity of single-stranded DNA (ssDNA) to locally bend bundles of double-stranded DNA into bent geometries whose curvature and mechanical properties can be tuned by controlling the length of ssDNA strands. We demonstrate an ability to achieve a wide range of geometries by adjusting a few strands in the nanostructure design. We further developed a mechanical model to predict both geometry and mechanical properties of our compliant nanostructures that agrees well with experiments. Our results provide a basis for the design of mechanically functional DNA origami devices and materials.

Direct Design of an Energy Landscape with Bistable DNA Origami Mechanisms

Structural DNA nanotechnology provides a feasible technique for the design and fabrication of complex geometries even exhibiting controllable dynamic behavior. Recently we have demonstrated the possibility of implementing macroscopic engineering design approaches to construct DNA origami mechanisms (DOM) with programmable motion and tunable flexibility. Here, we implement the design of compliant DNA origami mechanisms to extend from prescribing motion to prescribing an energy landscape. Compliant mechanisms facilitate motion via deformation of components with tunable stiffness resulting in well-defined mechanical energy stored in the structure. We design, fabricate, and characterize a DNA origami nanostructure with an energy landscape defined by two stable states (local energy minima) separated by a designed energy barrier. This nanostructure is a four-bar bistable mechanism with two undeformed states. Traversing between those states requires deformation, and hence mechanical energy storage, in a compliant arm of the linkage. The energy barrier for switching between two states was obtained from the conformational distribution based on a Boltzmann probability function and closely follows a predictive mechanical model. Furthermore, we demonstrated the ability to actuate the mechanism into one stable state via additional DNA inputs and then release the actuation via DNA strand displacement. This controllable multistate system establishes a foundation for direct design of energy landscapes that regulate conformational dynamics similar to biomolecular complexes.

Directing folding pathways for multi-component DNA origami nanostructures with complex topology

Molecular self-assembly has become a well-established technique to design complex nanostructures and hierarchical mesoscale assemblies. The typical approach is to design binding complementarity into nucleotide or amino acid sequences to achieve the desired final geometry. However, with an increasing interest in dynamic nanodevices, the need to design structures with motion has necessitated the development of multi-component structures. While this has been achieved through hierarchical assembly of similar structural units, here we focus on the assembly of topologically complex structures, specifically with concentric components, where post-folding assembly is not feasible. We exploit the ability to direct folding pathways to program the sequence of assembly and present a novel approach of designing the strand topology of intermediate folding states to program the topology of the final structure, in this case a DNA origami slider structure that functions much like a piston-cylinder assembly in an engine. The ability to program the sequence and control orientation and topology of multi-component DNA origami nanostructures provides a foundation for a new class of structures with internal and external moving parts and complex scaffold topology. Furthermore, this work provides critical insight to guide the design of intermediate states along a DNA origami folding pathway and to further understand the details of DNA origami self-assembly to more broadly control folding states and landscapes.

Pseudorigid-Body Models of Compliant DNA Origami Mechanisms

In this paper, we introduce a strategy for the design and computational analysis of compliant DNA origami mechanism (CDOM), which are compliant nanomechanisms fabricated with DNA origami self-assembly. The rigid, compliant and flexible parts are constructed by bundles of many double-stranded DNA (dsDNA) helices, bundles of a few dsDNA helices or a single dsDNA helix, and single-stranded DNA (ssDNA) strands respectively. Just like in macroscopic compliant mechanisms, a CDOM generates its motion via deformation of at least one structural member. During the motion, strain energy is stored and released in the compliant components. Therefore, these CDOM have the advantage of suppressing thermal fluctuations due to the internal mechanical energy barrier for motion. Here we show that classic Pseudo-rigid-body (PRB) models for compliant mechanism are successfully employed to the analysis of these DNA origami nanomechanisms and can serve to guide the design and analysis method, an example of compliant hinge joint and a bistable four-bar CDOM fabricated with DNA origami are presented.

Mobility Analysis and Type Synthesis with Screw Theory: From Rigid Body Linkages to Compliant Mechanisms

Mobility analysis is one of fundamental problems in kinematics and an important tool in type synthesis of linkages. In this paper, we will review screw theory as a mathematical tool for mobility analysis of overconstrained linkages and compliant mechanisms. Established by Ball in late 1800, screw theory has become one of the fundamental theories for characterizing instantaneous kinematics of spatial movements. In mid to late 1960, Waldron was one of the first modern kinematicians who systematically developed screw theory and its applications to the constraint analysis and synthesis of overconstrained linkages. Due to the screw theory, several overconstrained spatial linkages have been invented and designed, including the well known Waldron six-bar loop overconstrained linkage. In recent years, mobility analysis has been extended to compliant mechanisms which achieve motion through deflection of flexure joints. By the concept of relative compliance/ stiffness, we can also define mobility of compliant mechanisms similar to their rigid body counterparts. This paper will summarize some recent work on applying screw theory to mobility analysis and synthesis of compliant mechanisms.

Paper Origami-Inspired Design and Actuation of DNA Nanomachines with Complex Motions

Significant progress in DNA nanotechnology has accelerated the development of molecular machines with functions like macroscale machines. However, the mobility of DNA self-assembled nanorobots is still dramatically limited due to challenges with designing and controlling nanoscale systems with many degrees of freedom. Here, an origami-inspired method to design transformable DNA nanomachines is presented. This approach integrates stiff panels formed by bundles of double-stranded DNA connected with foldable creases formed by single-stranded DNA. To demonstrate the method, a DNA version of the paper origami mechanism called a waterbomb base (WBB) consisting of six panels connected by six joints is constructed. This nanoscale WBB can follow four distinct motion paths to transform between five distinct configurations including a flat square, two triangles, a rectangle, and a fully compacted trapezoidal shape. To achieve this, the sequence specificity of DNA base-pairing is leveraged for the selective actuation of joints and the ion-sensitivity of base-stacking interactions is employed for the flattening of joints. In addition, higher-order assembly of DNA WBBs into reconfigurable arrays is achieved. This work establishes a foundation for origami-inspired design for next generation synthetic molecular robots and reconfigurable nanomaterials enabling more complex and controllable motion.

Cation-Activated Avidity for Rapid Reconfiguration of DNA Nanodevices

The ability to design and control DNA nanodevices with programmed conformational changes has established a foundation for molecular-scale robotics with applications in nanomanufacturing, drug delivery, and controlling enzymatic reactions. The most commonly used approach for actuating these devices, DNA binding and strand displacement, allows devices to respond to molecules in solution, but this approach is limited to response times of minutes or greater. Recent advances have enabled electrical and magnetic control of DNA structures with sub-second response times, but these methods utilize external components with additional fabrication requirements. Here, we present a simple and broadly applicable actuation method based on the avidity of many weak base-pairing interactions that respond to changes in local ionic conditions to drive large-scale conformational transitions in devices on sub-second time scales. To demonstrate such ion-mediated actuation, we modified a DNA origami hinge with short, weakly complementary single-stranded DNA overhangs, whose hybridization is sensitive to cation concentrations in solution. We triggered conformational changes with several different types of ions including mono-, di-, and trivalent ions and also illustrated the ability to engineer the actuation response with design parameters such as number and length of DNA overhangs and hinge torsional stiffness. We developed a statistical mechanical model that agrees with experimental data, enabling effective interpretation and future design of ion-induced actuation. Single-molecule Förster resonance energy-transfer measurements revealed that closing and opening transitions occur on the millisecond time scale, and these transitions can be repeated with time resolution on the scale of one second. Our results advance capabilities for rapid control of DNA nanodevices, expand the range of triggering mechanisms, and demonstrate DNA nanomachines with tunable analog responses to the local environment.

Pseudo-Rigid-Body Models of Compliant DNA Origami Mechanisms

In this paper, we introduce the strategy of designing and analyzing compliant nanomechanisms fabricated with DNA origami which we call compliant DNA origami mechanism (CDOM). The rigid, compliant and flexible parts are constructed by a bunch of double-stranded DNA (dsDNA) helices, fewer dsDNA helices and single-stranded DNA (ssDNA) strands respectively. Just like in macroscopic compliant mechanisms, a CDOM generates its motion via deformation of at least one structural member. During the motion, strain energy is stored and released in the mechanism. These CDOM can suppress thermal fluctuations due to the internal mechanical energy barrier for motion. An example of compliant hinge joint and a bistable four-bar CDOM fabricated with DNA origami are discussed at the end of this paper. The classic pseudo-rigid-body (PRB) model for compliant mechanism is successfully employed to the analysis of these DNA origami nanomechanisms. This PRB model has been used to guide the design of a bistable CDOM for a desired energy landscape.Copyright

The Kinematic Principle for Designing DNA Origami Mechanisms: Challenges and Opportunities

DNA origami nanotechnology is a recently developed self-assembly process for design and fabrication of complex 3D nanostructures using DNA as functional materials. This paper aims to review our recent progress in applying DNA origami to design of kinematic mechanisms of nanometer scale. These nanomechanisms, which we call DNA Origami Mechanisms (DOM), are made of relatively stiff bundles of double-stranded DNA (dsDNA) which function as rigid links, connected by highly compliant single-stranded DNA (ssDNA) strands which function as kinematic joints. The designs of kinematic joints such as revolute, prismatic, cylindrical, universal and spherical are presented. The steps as well as necessary software or experimental tools for designing DOM with DNA origami links and joints are detailed. To demonstrate the designs, we presented the designs of Bennett 4-bar and crank-slider linkages. At last, a list of technical challenges such as design automation, computational modeling are presented. These challenges could also be opportunities for mechanism and robotics community to apply the well developed kinematic theories and computational tools to design of nanorobots and nanomachines.Copyright