Biology subjects

Barisic, I.

Publications and source records attributed to Barisic, I..

4 recordsLinked to original sources

bioRxiv2026

DNA Staples: An oligonucleotide library for data storage and computing

DNA offers exceptional information density and stability, making it a promising medium for long-term data storage. However, the high cost of DNA synthesis and data retrieval remain key barriers to large-scale deployment. In this paper, we present DNA staples, a multipurpose library of short single-stranded DNA sequences that enables the encoding of arbitrary digital data by enzymatic assembly. Flexible encoding schemes allow the same presynthesized strand library to be used across applications, significantly reducing synthesis requirements while supporting diverse data representations. Using a restricted library also confers inherent error correction. In addition to storage, the library enables creation of computational DNA modules that perform highly parallel operations directly on stored data. This framework provides a cost-efficient approach to molecular data storage and supports integrated storage-computation at the DNA level.

synthetic biology↗

bioRxiv2020

Twist of the mitotic spindle culminates at anaphase onset and depends on microtubule-associated proteins along with external forces

Forces produced by motor proteins and microtubule dynamics within the mitotic spindle are crucial for proper chromosome segregation. In addition to linear forces, rotational forces or torques are present in the spindle, reflected in the left-handed twisted shapes of microtubule bundles that make the spindle chiral. However, the biological role and molecular origins of spindle chirality are unknown. By developing methods for measuring spindle twist, we show that spindles are most chiral near the metaphase-to-anaphase transition. To assess the role of chirality in maintaining spindle robustness under force, we compressed the spindles along their axis. This resulted in stronger left-handed twist, suggesting that the twisted shape allows for a mechanical response to forces. Inhibition or depletion of motor proteins that perform chiral stepping, Eg5/kinesin-5, Kif18A/kinesin-8, MKLP1/kinesin-6, and dynein, decreased the left-handed twist or led to right-handed twist, implying that these motors regulate the twist by rotating microtubules within their antiparallel overlaps or at the spindle pole. Right-handed twist was also observed after the depletion of the microtubule nucleator augmin, indicating its contribution to the twist through the nucleation of antiparallel bridging microtubules. The uncovered switch from left-handed to right-handed twist reveals the existence of competing mechanisms that promote twisting in opposite directions. As round spindles were more twisted than elongated ones, we infer that bending and twisting moments are generated by similar molecular mechanisms and propose a physiological role for spindle chirality in allowing the spindle to absorb mechanical load.

cell biology↗

bioRxiv2019

Adenita: Interactive 3D modeling and visualization of DNA nanostructures

We present Adenita, a novel software tool for the design of DNA nanostructures in a user-friendly integrated environment for molecular modeling. Adenita is capable of handling large DNA origami structures, re-use them as building blocks of new designs and provide on demand feedback, thus overcoming effectively some of the limitations of existing tools. Additionally, it integrates all major established approaches to DNA nanostructure design (DNA origami, wireframe nanostructures and DNA tiles) and allows to combine them. We show-case Adenita by re-using a large nanorod designed with Cadnano [1] to create a new nanostructure through user interactions that employ different editors to modify the original nanorod.

bioinformatics↗

bioRxiv2019

Enzyme Catalytic Activity Emulated Within DNA-based Nanodevice

Artificial enzymes hold a great potential in the field of biotechnology. The currently available design strategies are limited to recruit and organise secondary and tertiary structural elements, and functional motifs of native enzymes. Here, we demonstrate an approach towards the bottom-up development of an artificial enzyme based on DNA nanotechnology. Structural analyses of the FlaI ATPase were used to identify a set of amino acids essential for the catalytic reaction. The selected amino acids were used to design four peptide-oligonucleotide conjugates (POCs). The POCs were integrated into a DNA nanostructure and reconstituted the catalytic site of FlaI. DNA origami technology was employed to maintain the relative orientations of the amino acids and their positions analogous to those in the protein catalytic site. The substrate turnover rates were found to be comparable in our artificial nanozyme (kcat = 0.3622 s-1) and the native enzyme (kcat {approx} 0.016 s-1). The nanozymes could be recycled using an ultrafiltration protocol and reused in multiple experiments allowing a reliable reproduction of the measurements. The emulation of enzymatic activity, by this novel and computable technological framework, can be of high relevance in many different areas.

synthetic biology↗