Biology subjects

Takahashi, C. N.

Publications and source records attributed to Takahashi, C. N..

5 recordsLinked to original sources

bioRxiv2026

DNA-GUARD: molecular access control as a physical security layer for DNA data storage

DNA data storage offers exceptional density and millennial-scale stability, with advances in encoding schemes and reduced synthesis costs making large-scale archiving increasingly viable. However, while efforts have focused on reliable data retrieval, securing DNA-encoded information against unauthorized access remains largely unexplored. Here, we introduce DNA-GUARD (DNA Gated Unlocking and Access Restriction of Data), a molecular-level access control system that physically restricts data retrieval rather than relying on computational encryption. DNA-GUARD integrates with PCR-based random access by selectively blocking amplification of protected sequences. Chemically modified "locker strands" outcompete PCR primers and block polymerase extension through 3 inverted dT modifications, preventing amplification of key sequences required for file decoding. To restore access, complementary "password strands" tethered to magnetic particles sequester locker strands, enabling their removal and restoring data access. We demonstrate DNA-GUARDs scalability from 550-byte to 1-MB files without performance loss, orthogonal control of multiple files within mixed libraries, and reliable repeated locking-unlocking cycles. This approach enables physical access control compatible with established DNA storage workflows, providing a foundation for secure archival storage with implications for molecular information security that complements cryptographic data protection methods.

synthetic biology↗

bioRxiv2026

Characterizing the Assembly and Functional Properties of Gene-Length Mixed DNA Monolayers on Electrodes for Cell-Free Expression

Gold electrodes are attractive substrates for bioelectronic and cell-free synthetic biology platforms because they are conductive, chemically stable, biocompatible, and readily functionalized through thiol-gold chemistry. Here, gene-length DNA monolayers assembled on planar gold electrodes as reusable templates for cell-free protein expression are investigated. Using thiol-modified sfGFP genes, DNA surface density is shown to be tunable by changing the DNA concentration during incubation, with the immobilized genes able to support cell-free sfGFP expression directly from the electrode surface. Further, the effects of applied voltage, storage, repeated reactions, reducing agents, and protein fouling on monolayer stability and expression output are examined. While some conditions lead to loss of reusable expression activity, dense chemisorbed monolayers can retain partial function under neutral, non-reducing conditions and are relatively robust to protein exposure. In contrast, low-density physisorbed monolayers show a stronger relationship between DNA loss and expression output. Finally, when using gold-mediated fluorescence quenching to monitor changes in DNA conformation, surface-bound DNA demonstrates electrophoretic addressability. Together, these results establish DNA- functionalized planar electrodes as a promising foundation for modular, addressable cell-free expression platforms.

bioengineering↗

bioRxiv2019

Quantifying Molecular Bias in DNA Data Storage

DNA has recently emerged as an attractive medium for future digital data storage because of its extremely high information density and potential longevity. Recent work has shown promising results in developing proof-of-principle prototype systems. However, very uneven (biased) sequencing coverage distributions have been reported, which indicates inefficiencies in the storage process and points to optimization opportunities. These deviations from the average coverage in oligonucleotide copy distribution result in sequence drop-out and make error-free data retrieval from DNA more challenging. The uneven copy distribution was believed to stem from the underlying molecular processes, but the interplay between these molecular processes and the copy number distribution has been poorly understood until now. In this paper, we use millions of unique sequences from a DNA-based digital data archival system to study the oligonucleotide copy unevenness problem and show that two important sources of bias are the synthesis process and the Polymerase Chain Reaction (PCR) process. By mapping the sequencing coverage of a large complex oligonucleotide pool back to its spatial distribution on the synthesis chip, we find that significant bias comes from array-based oligonucleotide synthesis. We also find that PCR stochasticity is another main driver of oligonucleotide copy variation. Based on these findings, we develop a statistical model for each molecular process as well as the overall process and compare the predicted bias with our experimental data. We further use our model to explore the trade-offs between synthesis bias, storage physical density and sequencing redundancy, providing insights for engineering efficient, robust DNA data storage systems.

synthetic biology↗

bioRxiv2018

Demonstration of End-to-End Automation of DNA Data Storage

We developed a complete end-to-end DNA data storage device. The device enables the encoding of data, which is then written to a DNA oligonucleotide using a custom DNA synthesizer, pooled for liquid storage, and read using a nanopore sequencer and a novel, minimal preparation protocol. We demonstrate an automated 5-byte write, store, and read cycle with the ability to expand as new technology is available.

synthetic biology↗

bioRxiv2017

Accelerating Evolutionary Hill Climbs in Parallel Turbidostats

Evolution has been used to address many engineering problems. Within the context of metabolic engineering and synthetic biology, directed evolution has natural appli-cations. However, most research concerning optimizing microbial evolution has been focused on library generation and screening, while accelerating evolutionary hill climbs and been largely ignored. Here, we develop a model to explore how population struc-ture can accelerate evolutionary hill climbs. We show that by adjusting the population size, environmental challenge, and meta-population dynamics that the rate of evolution can be accelerated in parallel turbidostats. Our analyses leads to two surprising results: small populations are favored over conventionally large microbial populations, and propagating modest fitness improvements is favored over propagating mutants with large beneficial mutations. When combined with rational design and other optimization techniques our theory can accelerate strain development for applications such as consolidated bioprocessing, and bioremidation systems.

synthetic biology↗