Biology subjects

Katzmeier, F.

Publications and source records attributed to Katzmeier, F..

5 recordsLinked to original sources

bioRxiv2026

OrthoSeq: A Design Workflow for Thermodynamically Orthogonal DNA Sequence-Pair Libraries

Programmable DNA hybridization underlies many technologies in DNA nanotechnology, fluorescence imaging, and synthetic DNA sequence assembly. A common design challenge is to generate large sequence libraries in which each strand binds strongly to its intended partner while avoiding cross-hybridization and self-folding. Here, we introduce OrthoSeq, a workflow for designing thermodynamically orthogonal DNA sequence-pair libraries under user-defined experimental conditions. OrthoSeq uses NUPACK to evaluate intended binding, cross-hybridization, and self-folding. Within OrthoSeq, candidate sequence pairs form vertices in a conflict graph, while pairwise cross-hybridization conflicts define the edges. Library selection is then formulated as an independent-set problem and addressed using search strategies tailored to the computational regime considered here, in which thermodynamic evaluations dominate the computational cost. In benchmark comparisons, these strategies identify larger sequence-pair libraries than the commonly employed sequential candidate-addition strategy under the same thermodynamic constraints and computational budget. We further show that sequence-level barcode libraries can serve as candidate pools for thermodynamic refinement with OrthoSeq. To support practical use, OrthoSeq provides a graphical user interface that implements the complete workflow. Altogether, OrthoSeq provides an application-agnostic framework for designing DNA sequence-pair libraries under explicit thermodynamic constraints.

bioinformatics↗

bioRxiv2026

A computational framework for designing micron-scale crisscross DNA megastructures

Crisscross polymerization enables the assembly of hundreds of unique DNA origami slats into micron-sized structures with nanoscale precision. To design these megastructures, thousands of handle sequences from a fixed library must be assigned to individual slats to encode the desired binding architecture. This complexity presents two major challenges: handles must be selected to minimize parasitic interactions that compete with desired assembly, and the fabrication of hundreds of unique slats creates a substantial logistical burden. Here, we develop a unified framework that standardizes the design and fabrication of crisscross megastructures. We use an evolutionary algorithm to optimize handle assignment and minimize parasitic binding between slats, paired with a graph-based algorithm that expands the handle library. Together, these algorithms enable the assembly of large, multi-layered megastructures that otherwise would be produced at negligible yields. We have released this framework as #-CAD, an open-source graphical application that integrates these algorithms, streamlines laboratory workflows, and makes crisscross DNA origami more broadly accessible.

synthetic biology↗

bioRxiv2025

Digital Phage Biology in Droplets

Since their discovery, bacteriophages - viruses that infect bacteria - have been an invaluable source of insight for molecular biology and have provided a plethora of molecular components for biotechnology. Driven by the imminent global antibiotic crisis, interest in using bacteriophages as antimicrobial agents has strongly increased in the past few years. While standard quantification of phage counts and infectivity by double-layer plaque assays (DLA) have provided foundational insights, they are limited by their inability to monitor infection dynamics over time and the inflexibility in experimental setups. Here, we introduce a novel high-throughput method using droplet microfluidics to quantify individual phage infection events, enhancing the understanding of phage-host dynamics at the single-event level. By co-encapsulating individual phages and bacteria in microfluidic droplets, we can control key experimental parameters such as exposure time and the ratio of phages to bacteria. Our system allows for precise quantification of lysis events and the direct observation of lysis kinetics unaffected by the continuous release of progeny phages that is typical in bulk cultures. Moreover, our method is potentially applicable to any phage-host pair. Our findings suggest that droplet microfluidics can provide a more accurate and dynamic understanding of phage biology. This approach could be particularly valuable in the development of phage-based antimicrobial strategies in the face of rising antibiotic resistance.

biophysics↗

bioRxiv2022

Shape primed AC-electrophoretic microrobots

Second-order electrokinetic flow around colloidal particles caused by concentration polarization electro-osmosis (CPEO) can result in a phoretic motion of asymmetric particle dimers in a homogeneous AC electrical field, which we refer to as concentration polarization electro-phoresis (CPEP). To demonstrate this actuation mechanism, we created particle dimers from micron-sized silica spheres with sizes 1.0 {micro}m and 2.1 {micro}m by connecting them with DNA linker molecules. The dimers can be steered along arbitrarily chosen paths within a 2D plane by controlling the orientation of the AC electric field in a fluidic chamber with the joystick of a gamepad. Further utilizing induced dipole-dipole interactions, we demonstrate that particle dimers can be used to controllably pick up monomeric particles and release them at any desired position, and also to assemble several particles into groups. Systematic experiments exploring the dependence of the dimer migration speed on the electric field strength, frequency, and buffer composition align with the theoretical framework of CPEO and provide parameter ranges for the operation of our microrobots.

biophysics↗

bioRxiv2019

A low-cost fluorescence reader for in vitro transcription and nucleic acid detection with Cas13a

Point-of-care testing (POCT) in low-resource settings requires tools that can operate independent of typical laboratory infrastructure. Due to its favorable signal-to-background ratio, a wide variety of biomedical tests utilize fluorescence as a readout. However, fluorescence techniques often require expensive or complex instrumentation and can be difficult to adapt for POCT. To address this issue, we developed a pocket-sized fluorescence detector costing less than $15 that is easy to manufacture and can operate in low-resource settings. It is built from standard electronic components, including an LED and a light dependent resistor, filter foils and 3D printed parts, and reliably detected less than 10 nM fluorescein concentrations (with a lower limit of detection of {approx}6.8 nM), which is sufficient to follow typical biochemical reactions used in POCT applications. All assays are conducted on filter paper, which allows for a flat detector architecture to improve signal collection. We validate the device by quantifying in vitro RNA transcription and also demonstrate sequence-specific detection of target RNAs in the nanomolar range using a Cas13a-based fluorescence assay. Cas13a is a RNA-guided, RNA-targeting CRISPR effector with promiscuous RNase activity upon recognition of its RNA target. Cas13a sensing is highly specific and adaptable and in combination with our detector represents a promising approach for nucleic acid POCT. Furthermore, our open-source device architecture could be a valuable educational tool that integrates hardware, software and biochemistry concepts.

bioengineering↗