Linker Engineering of Ligand‐Decorated DNA Origami Nanostructures Affects Biological Activity

News from an old acquaintance: The streptavidin (STV)-biotin binding system is frequently used for the decoration of DNA origami nanostructures (DON) to study biological systems. Here, a surprisingly high dynamic of the STV/DON interaction is reported, which is affected by the structure of the DNA linker system. Analysis of different mono- or bi-dentate linker architectures on DON with a novel high-speed atomic force microscope (HS-AFM) enabling acquisition times as short as 50 ms per frame gave detailed insights into the dynamics of the DON/STV interaction, revealing dwell times in the sub-100 millisecond range. The linker systems are also used to present biotinylated epidermal growth factor on DON to study the activation of the epidermal growth factor receptor signaling cascade in HeLa cells. The studies confirm that cellular activation correlated with the binding properties of linker-specific STV/DON interactions observed by HS-AFM. This work sheds more light on the commonly used STV/DON system and will help to further standardize the use of DNA nanostructures for the study of biological processes

Finding Correlations in Multimodal Data Using Decomposition Approaches

Dornbusch D, Haschke R, Menzel S, Wersing H. Finding Correlations in Multimodal Data Using Decomposition Approaches. In: Proc. ESANN 2010. Belgium: d-facto; 2010: 253-258.In this paper, we propose the application of standard decomposition approaches to find local correlations in multimodal data. In a test scenario, we apply these methods to correlate the local shape of turbine blades with their associated aerodynamic flow fields. We compare several decomposition algorithms, i.e., k-Means, Principal Component Analysis, Non-negative Matrix Factorization and Non-Negative Sparse Coding, with regards to their efficiency at finding local correlations and their ability to predict one modality from another

Decomposition of Multimodal Data for Affordance-based Identification of Potential Grasps

Dornbusch D, Haschke R, Menzel S, Wersing H. Decomposition of Multimodal Data for Affordance-based Identification of Potential Grasps. Presented at the International Conference on Pattern Recognition Applications and Methods, Vilamoura, Algarve, Portugal.In this paper, we apply standard decomposition approaches to the problem of finding local correlations in multi-modal and high-dimensional grasping data, particularly to correlate the local shape of cup-like objects to their associated local grasp configurations. We compare the capability of several decomposition methods to establish these task-relevant, inter-modal correlations and indicate how they can be exploited to find potential contact points and hand postures for novel, though similar, objects

Correlating shape and functional properties using decomposition approaches

Dornbusch D, Haschke R, Menzel S, Wersing H. Correlating shape and functional properties using decomposition approaches. In: Proc. FLAIRS-23. AAAI; 2010: 398-403.In this paper, we propose the application of standard decomposition approaches to find local correlations in multimodal data. In a test scenario, we apply these methods to correlate the local shape of turbine blades with their associated aerodynamic flow fields. We compare several decomposition algorithms, i.e., k-Means, Principal Component Analysis, Non-negative Matrix Factorization and Uni-orthogonal Non-negative Matrix Factorization, with regards to their efficiency at finding local, relevant correlations and their ability to predict one modality from another

A novel nanoscopic tool by combining AFM with STED microscopy

none5Benjamin Harke;Jenu Varghese Chacko;Heiko Haschke;Claudio Canale;Alberto DiasproBenjamin, Harke; Jenu Varghese Chacko, ; Heiko, Haschke; Canale, Claudio; Diaspro, ALBERTO GIOVANN

Structure and mechanics of the human Nuclear Pore Complex basket

Nuclear pore complexes (NPCs) are the only gateways between the nucleus and cytoplasm in eukaryotic cells. They restrict free diffusion to molecules below 5 nm while facilitating the active transport of selected cargoes, sometimes as large as the pore itself. This versatility implies an important pore plasticity. Recently, cryo-EM and AI-based protein modeling revealed with acute precision how most NPC constituents are arranged. But the basket, a fish trap-like structure capping the nucleoplasmic side of the pore, remains the missing piece in this puzzle. Here by Atomic Force Microscopy (AFM) coupled to Single Molecule Localization Microscopy (SMLM) we revealed that the basket is very soft and explores a large conformational landscape: apart from its canonical shape, it dives into the central pore channel or opens, with filaments reaching to the pore sides. Our observations enlighten how this structure can adapt and let morphologically diverse cargoes shuttling through NPCs