Svenja Moench

Karlsruhe Institute of Technology

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Christof M. Niemeyer

Karlsruhe Institute of Technology

Carmen M. Domínguez

Karlsruhe Institute of Technology

Kersten S. Rabe

Karlsruhe Institute of Technology

Phillip Lemke

Karlsruhe Institute of Technology

Christoph Bickmann

Karlsruhe Institute of Technology

Martin Peng

Karlsruhe Institute of Technology

Róisı́n M. Owens

University of Cambridge

Alessa Schipperges

Karlsruhe Institute of Technology

Yong Hu

Tongji University

Claude Oelschlaeger

Karlsruhe Institute of Technology

Cooperative Institutions

Karlsruhe Institute of Technology

University of Cambridge

TU Dortmund University

Karlsruhe University of Education

Hitachi (United Kingdom)

EdgeWave (Germany)

University of Duisburg-Essen

Institute of Micro and Nanotechnology

Universidad Complutense de Madrid

Centro Nacional de Microelectrónica

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Micromechanical Indentation Platform for Rapid Analysis of Viscoelastic Biomolecular Hydrogels

Small Methods (2024)

Phillip Lemke Svenja Moench Paula S. Jäger Claude Oelschlaeger Kersten S. Rabe

Abstract The advent of biomedical applications of soft bioinspired materials has entailed an increasing demand for streamlined and expedient characterization methods meant for both research and quality control objectives. Here, a novel measurement system for the characterization of biological hydrogels with volumes as low as 75 µL was developed. The system is based on an indentation platform equipped with micrometer drive actuators that allow the determination of both the fracture points and Young's moduli of relatively stiff polymers, including agarose, as well as the measurements of viscosity for exceptionally soft and viscous hydrogels, such as DNA hydrogels. The sensitivity of the method allows differentiation between DNA hydrogels produced by rolling circle amplification based on different template sequences and synthesis protocols. In addition, the polymerization kinetics of the hydrogels can be determined by time‐resolved measurements, and the apparent viscosities of even more complex DNA‐based nanocomposites can be measured. The platform presented here thus offers the possibility to characterize a broad variety of soft biomaterials in a targeted, fast, and cost‐effective manner, holding promises for applications in fundamental materials science and ensuring reproducibility in the handling of complex materials.

Characterization

Indentation

Micrometer

Soft materials

Agarose

10.1002/smtd.202400251

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A Critical View on the Use of DNA Hydrogels in Cell‐Free Protein Synthesis

Angewandte Chemie International Edition (2024)

Svenja Moench Phillip Lemke Anders J. Hansen Christoph Bickmann Martin Peng

Numerous studies have reported in the past that the use of protein-encoding DNA hydrogels as templates for cell-free protein synthesis (CFPS) leads to better yields than the use of conventional templates such as plasmids or PCR fragments. Systematic investigation of different types of bulk materials from pure DNA hydrogels and DNA hydrogel composites using a commercially available CFPS kit showed no evidence of improved expression efficiency. However, protein-coding DNA hydrogels were advantageously used in microfluidic reactors as immobilized templates for repetitive protein production, suggesting that DNA-based materials offer potential for future developments in high-throughput profiling or rapid in situ characterization of proteins.

Template

Cell-free protein synthesis

10.1002/anie.202414480

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Chiral plasmonic metasurface assembled by DNA origami

Optics Express (2024)

Niels Gieseler Svenja Moench Dominik Beutel Wolfgang Pfeifer Carmen M. Domínguez

Chiral materials are essential to perceive photonic devices that control the helicity of light. However, the chirality of natural materials is rather weak, and relatively thick films are needed for noticeable effects. To overcome this limitation, artificial photonic materials were suggested to affect the chiral response in a much more substantial manner. Ideally, a single layer of such a material, a metasurface, should already be sufficient. While various structures fabricated with top-down nanofabrication technologies have already been reported, here we propose to utilize scaffolded DNA origami technology, a scalable bottom-up approach for metamolecule production, to fabricate a chiral metasurface. We introduce a chiral plasmonic metamolecule in the shape of a tripod and simulate its optical properties. By fixing the metamolecule to a rectangular planar origami, the tripods can be assembled into a 2D DNA origami crystal that forms a chiral metasurface. We simulate the optical properties but also fabricate selected devices to assess the experimental feasibility of the suggested approach critically.

DNA origami

Tripod (photography)

Chirality

Nanophotonics

10.1364/oe.520522

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Formulation of DNA Nanocomposites: Towards Functional Materials for Protein Expression

Polymers (2021)

Alessa Schipperges Yong Hu Svenja Moench Simone Weigel Johannes Reith

DNA hydrogels are an emerging class of materials that hold great promise for numerous biotechnological applications, ranging from tissue engineering to targeted drug delivery and cell-free protein synthesis (CFPS). In addition to the molecular programmability of DNA that can be used to instruct biological systems, the formulation of DNA materials, e.g., as bulk hydrogels or microgels, is also relevant for specific applications. To advance the state of knowledge in this research area, the present work explores the scope of a recently developed class of complex DNA nanocomposites, synthesized by RCA polymerization of DNA-functionalized silica nanoparticles (SiNPs) and carbon nanotubes (CNTs). SiNP/CNT–DNA composites were produced as bulk materials and microgels which contained a plasmid with transcribable genetic information for a fluorescent marker protein. Using confocal microscopy and flow cytometry, we found that the materials are very efficiently taken up by various eukaryotic cell lines, which were able to continue dividing while the ingested material was evenly distributed to the daughter cells. However, no expression of the encoded protein occurred within the cells. While the microgels did not induce production of the marker protein even in a CFPS procedure with eukaryotic cell lysate, the bulk composites proved to be efficient templates for CFPS. This work contributes to the understanding of the molecular interactions between DNA composites and the functional cellular machinery. Implications for the use of such materials for CFPS procedures are discussed.

Template

10.3390/polym13152395

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Citations (9)

Quantitative Characterization of RCA‐based DNA Hydrogels – Towards Rational Design

Chemistry - A European Journal (2024)

Svenja Moench Phillip Lemke Julia Weisser Iliya D. Stoev Kersten S. Rabe

DNA hydrogels hold significant promise for biomedical applications and can be synthesized through enzymatic Rolling Circle Amplification (RCA). Due to the exploratory nature of this emerging field, standardized RCA protocols specifying the impact of reaction parameters are currently lacking. This study varied template sequences and reagent concentrations, evaluating RCA synthesis efficiency and hydrogel mechanical properties through quantitative PCR (qPCR) and indentation measurements, respectively. Primer concentration and stabilizing additives showed minimal impact on RCA efficiency, while changes in polymerase and nucleotide concentrations had a stronger effect. Concentration of the circular template exerted the greatest influence on RCA productivity. An exponential correlation between hydrogel viscosity and DNA amplicon concentration was observed, with nucleobase sequence significantly affecting both amplification efficiency and material properties, particularly through secondary structures. This study suggests that combining high-throughput experimental methods with structural folding prediction offers a viable approach for systematically establishing structure-property relationships, aiding the rational design of DNA hydrogel material systems.

Rational design

Characterization

10.1002/chem.202401788

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Activity-enhanced DNAzyme for design of label-free copper(ii) biosensor

Nanoscale (2023)

William Etheridge Frederic S. F. Brossard Sitan Zheng Svenja Moench Suraj Pavagada

Metal ion-driven, DNA-cleaving DNAzymes are characterised by high selectivity and specificity. However, their use for metal ion sensing remains largely unexplored due to long reaction times and poor reaction yields relative to RNA-cleaving DNAzymes and other sensing strategies. Herein we present a study demonstrating a significant rate enhancement of a copper-selective DNA cleaving DNAzyme by both polydopamine (PDA) and gold (Au) nanoparticles (NPs). PDA NPs enhance the reaction through the production of hydrogen peroxide, while for AuNPs the enhancement is aided by the presence of citrate surface moeities, both of which drive the oxidative cleavage of the substrate. A 50-fold enhancement for PDA NPs makes the combination of PDA and DNAzyme suitable for a practical application as a sensitive biosensor for Cu(II) ions. Using DNAzyme deposition onto a gold electrode followed by Polydopamine Assisted DNA Immobilisation (PADI), we achieve a cost-effective, label-free and fast (within 15 min) electrochemical biosensor with a limit of detection of 180 nmol (11 ppm), thus opening a route for the rational design of a new generation of hybrid DNAzyme-based biosensors.

Deoxyribozyme

Cleave

10.1039/d3nr02169f

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A Critical View on the Use of DNA Hydrogels in Cell‐Free Protein Synthesis

Angewandte Chemie (2024)

Svenja Moench Phillip Lemke Anna–Lena Hansen Christoph Bickmann Martin Peng

Abstract Numerous studies have reported in the past that the use of protein‐encoding DNA hydrogels as templates for cell‐free protein synthesis (CFPS) leads to better yields than the use of conventional templates such as plasmids or PCR fragments. Systematic investigation of different types of bulk materials from pure DNA hydrogels and DNA hydrogel composites using a commercially available CFPS kit showed no evidence of improved expression efficiency. However, protein‐coding DNA hydrogels were advantageously used in microfluidic reactors as immobilized templates for repetitive protein production, suggesting that DNA‐based materials offer potential for future developments in high‐throughput profiling or rapid in situ characterization of proteins.

10.1002/ange.202414480

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