Biology subjects

Wisna, G. B. M.

Publications and source records attributed to Wisna, G. B. M..

4 recordsLinked to original sources

bioRxiv2025

Small amphiphilic DNA for programmable transmembrane signaling and amplification

Interrogating the sequence-specific DNA/RNA content of a living cell without destroying it, is an elusive goal in biology and diagnostics with transformative potential. A DNA/RNA-based approach, however, must relay the recognition event across the intact lipid bilayer, a step that has long been considered impossible because hydrophilic, massively charged DNA/RNA is incompatible with the hydrophobic membrane interior. Here, we show that DNA branch migration can be driven across a lipid bilayer, converting an intracellular nucleic-acid sequence into an amplified, extracellular optical signal while preserving cell viability and compartmentalization, a synthetic transmembrane signal transduction analogous to natural receptors, such as G-protein-coupled receptors (GPCRs), but operating in reverse. We demonstrate this principle with Hybridization Across Lipid for Oligonucleotide Sensing (HALOS), an amphiphilic DNA hairpin comprising a toehold for recognition, a stem for stability, a loop, and cholesterols for transmembrane anchoring. Upon binding to a sequence-specific nucleic acid target, toehold-mediated strand invasion drives DNA branch migration across the bilayer, switching HALOS from a closed to an open conformation that relays the signal to the opposite face. Molecular dynamics simulations revealed that a cholesterol belt stabilizes the DNA stem within the membrane, preserving the hairpin structure necessary for transmembrane signaling. Notably, this branch migration proceeds despite the kinetic barrier of hybridization through the hydrophobic bilayer interior. By combining HALOS with an isothermal hybridization chain reaction (HCR), we established a platform that enables intracellular nucleic acid target detection and amplified fluorescent reporting from outside synthetic vesicles and live mammalian cells, achieving nanomolar-range sensitivity. These results establish DNA branch migration across lipid membranes as a design principle for programmable lysis-free molecular sensing in intact cells.

biophysics↗

bioRxiv2025

Bayesian Nonparametrics for FRET using Realistic Integrative Detectors

Biomolecular dynamics are often strikingly heterogeneous, with individual molecules sampling different states and kinetics--violating the "average molecule" assumption. Yet FRET analyses cannot resolve such variability or distinguish states differing mainly in kinetics, rather than FRET efficiency, as molecular configurations are projected onto 1D FRET signals. Here we introduce BNP-FRET-Bin, inferring state numbers and their kinetics directly from FRET data. In doing so, we eliminate user-specified parameters and expose molecule-to-molecule heterogeneity revealing new biologically relevant Holliday junction states with near identical FRET efficiencies.

biophysics↗

bioRxiv2025

DNA origami-based platform for multi-axial single-molecule force spectroscopy reveals hidden dynamics in Holliday junctions

Biomolecules in living cells experience complex multi-directional mechanical forces that regulate their structure, dynamics, and function. However, most single-molecule techniques primarily exert force along a single axis, thereby failing to emulate the mechanical environment of cells. Here, we demonstrate that single-axis force application fundamentally restricts conformational dynamics by kinetically trapping molecules within distinct dynamic classes, preventing interconversion and exploration of the full conformational landscape. We developed MAESTRO (Multi-Axial Entropic Spring Tweezer along a Rigid Origami), a molecular platform that applies up to 9 pN forces from up to 4 directions simultaneously using programmable ssDNA entropic springs anchored to a DNA origami scaffold. We applied MAESTRO to Holliday junctions (HJs), 4-way DNA intermediates that experience multi-directional tension during homologous recombination. Counterintuitively, we discovered >5x slower kinetics of the HJ conformations under multi-axial tension than under tension-free conditions, enabling direct observations of previously hidden HJ conformational intermediates. Most remarkably, we discovered that multi-axial forces unlock conformational dynamics, enabling interconversion between 5 distinct kinetic classes that remain kinetically inaccessible under zero force or single-axial tension. Furthermore, we demonstrated that tension regulates T7 endonuclease I cleavage site selection, directly linking mechanical environments and molecular mechanics to enzymatic function. By overcoming single-axis limitations, MAESTRO opens new frontiers in molecular mechanobiology, revealing how multi-directional cellular force environments are essential for unlocking the full conformational landscape of biomolecules, and that these complex force patterns serve as master regulators of biological function through mechanisms hidden from conventional approaches.

biophysics↗

bioRxiv2023

High-speed 3D DNA-PAINT and unsupervised clustering for unlocking 3D DNA origami cryptography

DNA origami information storage is a promising alternative to silicon-based data storage, offering a secure molecular cryptography technique that conceals information within arbitrarily folded DNA origami nanostructures. Routing, sliding, and interlacing staple strands lead to the creation of a large 700-bit key size. The realization of practical DNA data storage requires high information density, robust security, and accurate and rapid information retrieval. To meet these requirements, advanced readout techniques and large encryption key sizes are essential. In this study, we report an enhanced DNA origami cryptography protocol to encrypt information in 2D and 3D DNA origami structures, increasing the number of possible scaffold routings and increasing the encryption key size. We employed all-DNA-based steganography with fast readout through high-speed 2D and 3D DNA-PAINT super-resolution imaging, which enables higher information density. By combining 2D and 3D DNA-PAINT data with unsupervised clustering, we achieved an accuracy of up to 89% and high ratios of correct-to-wrong readout, despite the significant flexibility in the 3D DNA origami structure shown by oxDNA simulation. Furthermore, we propose design criteria that ensure complete information retrieval for the DNA origami cryptography protocol. Our findings demonstrate that DNA-based cryptography is a highly secure and versatile solution for transmitting and storing information, making it an attractive choice for the post-silicon era.

biophysics↗