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INSTITUTE FOR BIOFUNCTIONAL POLYMER MATERIALS

PROGRAMMABLE NANOMATERIALS AND DEVICES BASED ON DNA

Independent Research associates & joint labs

Elisha Krieg

We use DNA as a key component for the construction of reconfigurable, stimuli-responsive nanomaterials and functional biomolecular devices.

Research

Biological systems use self-assembly and self-organization to build complex materials (e.g. the cytoskeleton) and to construct and operate sophisticated macromolecular devices (e.g. motor proteins). Inspired by biology’s refined design principles, we engineer nanomaterials and devices with programmable and reconfigurable properties. We use DNA as the quintessential component for these artificial systems, as it enables us to assemble structures with custom size, shape, mechanical properties, and stimuli-responsiveness. Our functional nanosystems will address current challenges in molecular biology, biophysics and materials science.

Adaptive nanomaterials

We aim to establish design rules for DNA-based materials, in particular polyacrylamide-DNA copolymers. We correlate their bulk characteristics with the nanomechanical properties of their components, and use external chemical, optical, and mechanical signals to enable reversible switching between different functional configurations. We will study the performance of these materials as tools for molecular biology, tissue engineering, and diagnostics.

Multi-component nanodevices

Using the DNA origami method, we seek to construct discrete molecular machines that can perform complex tasks. DNA origami structures serve as pegboards to assemble multiple components with well-defined tasks and positions, enabling them to work together synergistically, in a manner that is unachievable by the individual building blocks alone.


Improving the performance, stability and accessibility of self-assembled nanosystems

The success and real-life application of DNA-based materials would greatly benefit from lower cost and higher robustness under relevant conditions. We develop methods for the isolation of chemically modified, low-cost DNA strands with access to a wide sequence space. We study the performance of these alternative DNA precursors for assembly of DNA origami and DNA-based copolymers with superior properties.

 

 

Design (top) and TEM images (bottom) of three different DNA origami structures. Adapted from E. Krieg and W. M. Shih, Angew. Chem. Int. Ed. 2018, 57, 714.
Example of a reconfigurable and stimuli-responsive nanomaterial that can be programmed to selectively capture molecular targets, isolate, and finally release them back into solution.

Methods and Expertise

  • DNA nanotechnology
  • Organic, supramolecular and polymer chemistry
  • Standard methods in molecular biology
  • Nanoparticle synthesis and purification
  • Nanomaterial characterization: electron microscopy, atomic force microscopy, oscillatory rheology, steady-state and time-resolved UV/Vis and fluorescence spectroscopy, dynamic light scattering, gel permeation chromatography

Patents

Elisha Krieg and William M. Shih, Acrylamide copolymerization for sequestration and production of single-stranded nucleic acid. PCT application filed on Sept 11, 2017.

Boris Rybtchinski, Elisha M. Krieg, Haim Weissman, Shira Weissman, Yaron Tidhar, Separation of nanoparticles. WO2012025928A1 (2012), EP2608874A1 (2013), US9067181B2 (2015).

Boris Rybtchinski, Elijah Shirman, Alona Ustinov, Netanel Ben-Shitrit, Haim Weissman, Elisha M. Krieg, Galina Golubkov, Jonathan Baram, Doubly reduced perylene-diimides and supramolecular polymers derived from perylene-diimides. WO2009118742A1 (2009), US8968886B2 (2015), EP3067354A1 (2016).

Funding

BMBF NanoMatFutur

TU Dresden Open Topic Postdoc Programme

Contact

email: krieg@ipfdd.de

phone: +49(0)351-4658-644

Publications (see google scholar)

Minev, D.; Guerra, R.; Kishi, J.; Smith, C.; Krieg, E.; Said, K.; Hornick, A.; Sasaki, H.; Filsinger, G.; Beliveau, B.; Yin, P.; Church, G. M.; Shih, W. M. Rapid and Scalable in Vitro Production of Single-Stranded DNA. bioRxiv 558429 (2019). https://doi.org/10.1101/558429.

Krieg, E.; Gupta, K.; Dahl, A.; Lesche, M.; Boye, S.; Lederer, A.; Shih, W. M. A Smart Polymer for Sequence-Selective Binding, Pulldown and Release of DNA Targets. bioRxiv 573030 (2019). https://doi.org/10.1101/573030.

Krieg E., Shih W.M. Selective Nascent Polymer Catch and Release Enables Scalable Isolation of Multi-Kilobase Single-Stranded DNA. Angewandte Chemie International Edition 57, 714 (2018).

Lewis F.D., Mishra A.K., Weissman H., Krieg E., Voltaw K.A., McCullagh M., Rybtchinski B. Self-assembly of perylenediimide-single strand DNA conjugates: Employing hydrophobic interactions and DNA base pairing to create a diverse structural space. Chemistry - A European Journal 23, 10328–10337 (2017).

Krieg E.*, Bastings M.M.C., Besenius P.*, Rybtchinski B.*; Supramolecular polymers in aqueous media. Chemical Reviews 116, 2414–2477 (2016). (*corresponding authors)

Tsarfati Y., Strauss V., Kuhri S., Krieg E., Weissman H., Shimoni E., Baram J., Guldi D.M., Rybtchinski B. Dispersing perylene diimide/SWCNT hybrids: structural insights at the molecular level and fabricating advanced materials. Journal of the American Chemical Society 137, 7429–7440 (2015).

Krieg E., Weissman H., Shimoni E., On A.B., Rybtchinski B.Understanding the effect of fluorocarbons in aqueous supramolecular polymerization: ultra-strong noncovalent binding and cooperativity. Journal of the American Chemical Society 136, 9443–9452 (2014).

Krieg E., Albeck S., Weissman H., Shimoni E., Rybtchinski B. Separation, immobilization, and biocatalytic utilization of proteins by a supramolecular membrane. PLoS One8, e63188 (2013).

Krieg E., Weissman,h. Shimoni E., Shirman E., Rybtchinski B. A recyclable supramolecular membrane for size-selective separation of nanoparticles. Nature Nanotechnology 6, 141– 146 (2011). Highlighted in: Chem. World 2011, 8, 27; Nature Nanotech. 2011, 6, 136–137; American Scientist 2014, 102, 94–97.

Krieg E., Rybtchinski B. Noncovalent water-based materials: robust yet adaptive. Chemistry - A European Journal 17, 9016–9026 (2011).

Gunderson V.L., Krieg E., Vagnini M.T., Iron M.A., Rybtchinski B., Wasielewski M.R. Photoinduced singlet charge transfer in a ruthenium(II) perylene-3,4:9,10- bis(dicarboximide) complex. Journal of Physical Chemistry B 115, 7533–7540 (2011).

Krieg E., Shirman E., Weissman H., Shimoni E., Wolf S., Pinkas I., Rybtchinski B. Supramolecular gel based on a perylene diimide dye: multiple stimuli responsiveness, robustness, and photofunction. Journal of the American Chemical Society 131, 14365–14373 (2009).