Biomat04 - Engineered Crystalline Biomaterials (EngCryBio)

Research outline

Natural macromolecular 'machines' exploit complicated 3D scaffolds of proteins and nucleic acids to position structural features with near-atomic precision in order to fulfill their complicated tasks. These structures have inspired many researchers to design synthetic objects that achieve functionalities known today only from natural complexes. A candidate route toward achieving this goals builds on molecular self-assembly with DNA. Large, densely-packed DNA objects obtained by DNA origami methods have proven useful in applications that rest on discrete shapes fabricated to a precision of several nanometer. Yet, high resolution 3D structural information on these objects has not been reported so far, thus stalling further progress in the design of objects to meet subnanometer-precise specifications. Our aim is to combine crystallography and electron microscopy to contribute to the creation of a comprehensive picture of structure, dynamics and interactions of the origami structures during their folding pathway. Central focus is to engineer discrete DNA objects such that they become amenable to crystallization, exploring crystallization conditions, and structural analysis once crystals have become available as well as addressing the kinetics during the origami assembly. The objectives of the engineering partner of the project (Dietz) comprise the design, production, and electron microscopy analysis of synthetic DNA based objects. The science partner of the project (Groll) has extensive expertise in the characterisation, purification and crystallographic analysis of large protein complexes.

Publications

Wagenbauer, K., Engelhardt, F., Stahl, E. , Ketterer, P. et al.: "How we make DNA origami", 2017.

Funke, Jonas J., Ketterer, P. et al. : "Uncovering the forces between nucleosomes using DNA origami", 2016.

Funke, Jonas J., Ketterer, P. et al.: "Exploring nucleosome unwrapping using DNA origami", 2016.

Ketterer, P., Willner, E.M., and Dietz, H.: "Nanoscale rotary apparatus formed from tight-fitting 3D DNA components", 2016.

Lieleg, C., Ketterer, P. et al.: "Nucleosome Spacing Generated by ISWI and CHD1 Remodelers Is Constant Regardless of Nucleosome Density", 2015.

Plesa, C., van Loo, N., Ketterer, P. et al.: "Velocity of DNA during Translocation through a Solid-State Nanopore", 2015.

Team

Project team leader

Evi Stahl
Biomolecular Nanotechnology

Alumnus

Dr. rer. nat. Philip Ketterer
Biomolecular Nanotechnology

Principal investigator

Professor Hendrik Dietz
Biomolecular Nanotechnology

Principal investigator

Professor Michael Groll
Biochemistry