Final Report Summary - DNA MACHINES (Nanomachines based on interlocked DNA architectures)
DNA nanotechnology uses DNA self-organization for the assembly of complex structures that can perform specific functions. The ERC project „DNA machines“ aimed at building nanomachines based on interlocked DNA-architectures. Interlocked DNA nanostructures represent highly versatile devices for nanorobotics and nanomechanics because they possess unique mechanical properties. Our project aimed at generating interlocked DNA-architectures wherein individual components can be set in motion in a controlled manner.
We started our project by synthesizing the first DNA-rotaxane. It contains a movable interlocked DNA-ring as a prototype interlocked DNA-architecture. During the first half of the project we achieved the controlled regulation of the dynamic properties of interlocked DNA nanostructures by employing external stimuli. For this purpose we implemented three orthogonal methods to reversibly switch between different conformations in DNA nanoarchitectures. Switching can be triggered either by light irradiation, by toehold-extended oligodeoxynucleotides or by pseudo-complementary peptide nucleic acids. Furthermore, we succeeded in modulating the mechanical stiffness in DNA-rotaxanes, by introducing paranemic crossover structures.
Another important goal of DNA machines was to functionalize DNA-nanostructures with components that can be employed as a control element or switch. To that end we introduced the so-called i-motif into DNA-nanocircles. Depending on the DNA sequence and the pH-value of the environment, the DNA-nanorings could be reversibly contracted and expanded. Thereby, our modified DNA-nanorings served as a prototype to ultimately develop DNA-muscles and autonomous DNA-motors. DNA-architectures that can undergo structural rearrangements often face the technical problem of a low reversibility of the switching process, depending on the switching efficiency of each individual step. To further improve the dynamic properties of our DNA-architectures we designed and assembled DNA-catenanes. These DNA-architectures contain 2, 3 or more interlocked double-stranded rings that are able to switch reversibly and quantitatively. To come closer to “DNA-muscles” we also constructed another class of rotaxanes, called daisy chain rotaxanes. This interlocked DNA structure comprises a macrocycle connected to an axle bearing a stopper at its end that circumscribes the axle of a second such unit and vice versa. This design results in two interwoven, dumbbell-shaped structures that can be pushed toward each other linearly along their interwoven axles. It results in moving structures that can function as transmissions for nanomachines or molecular slide bearings.
Furthermore, have synthesized a variety of different chemically modified nucleotides and have incorporated them into DNA-architectures. DNA-protein hybrids and modified nucleotides enhance functionality of our DNA-architectures towards performing individual tasks.
DNA nanostructures are mainly analyzed by AFM and fluorescence quenching experiments. Atomic force microscopy (AFM), a technique implemented in our lab with the help of the ERC Grant 'DNA Machines', was very useful for obtaining high-resolution images of DNA-nanoarchitectures in the size range of 50 nm. Images obtained have proven to be crucial for understanding the assembly of dynamic DNA-nanoarchitectures.
We started our project by synthesizing the first DNA-rotaxane. It contains a movable interlocked DNA-ring as a prototype interlocked DNA-architecture. During the first half of the project we achieved the controlled regulation of the dynamic properties of interlocked DNA nanostructures by employing external stimuli. For this purpose we implemented three orthogonal methods to reversibly switch between different conformations in DNA nanoarchitectures. Switching can be triggered either by light irradiation, by toehold-extended oligodeoxynucleotides or by pseudo-complementary peptide nucleic acids. Furthermore, we succeeded in modulating the mechanical stiffness in DNA-rotaxanes, by introducing paranemic crossover structures.
Another important goal of DNA machines was to functionalize DNA-nanostructures with components that can be employed as a control element or switch. To that end we introduced the so-called i-motif into DNA-nanocircles. Depending on the DNA sequence and the pH-value of the environment, the DNA-nanorings could be reversibly contracted and expanded. Thereby, our modified DNA-nanorings served as a prototype to ultimately develop DNA-muscles and autonomous DNA-motors. DNA-architectures that can undergo structural rearrangements often face the technical problem of a low reversibility of the switching process, depending on the switching efficiency of each individual step. To further improve the dynamic properties of our DNA-architectures we designed and assembled DNA-catenanes. These DNA-architectures contain 2, 3 or more interlocked double-stranded rings that are able to switch reversibly and quantitatively. To come closer to “DNA-muscles” we also constructed another class of rotaxanes, called daisy chain rotaxanes. This interlocked DNA structure comprises a macrocycle connected to an axle bearing a stopper at its end that circumscribes the axle of a second such unit and vice versa. This design results in two interwoven, dumbbell-shaped structures that can be pushed toward each other linearly along their interwoven axles. It results in moving structures that can function as transmissions for nanomachines or molecular slide bearings.
Furthermore, have synthesized a variety of different chemically modified nucleotides and have incorporated them into DNA-architectures. DNA-protein hybrids and modified nucleotides enhance functionality of our DNA-architectures towards performing individual tasks.
DNA nanostructures are mainly analyzed by AFM and fluorescence quenching experiments. Atomic force microscopy (AFM), a technique implemented in our lab with the help of the ERC Grant 'DNA Machines', was very useful for obtaining high-resolution images of DNA-nanoarchitectures in the size range of 50 nm. Images obtained have proven to be crucial for understanding the assembly of dynamic DNA-nanoarchitectures.