Biology subjects

Chopade, P.

Publications and source records attributed to Chopade, P..

2 recordsLinked to original sources

bioRxiv2026

DNA-templated Chiral Metamaterial Array as Information Bits

The growth of digital information demands physically secure information bits that combine intrinsic randomness with multi-layered optical readout. Digital metamaterials with physical unclonable function characteristics are promising, but nearly all examples operate at microwave or terahertz frequencies. Extending digital metamaterials to the visible range requires a physical property that allows binary (0/1) encoding via nanoscale geometry and is orthogonal to intensity-or color-based imaging. Chiral plasmonic metamaterials satisfy these criteria perfectly: their broken mirror symmetry yields chirality polarity in the visible spectrum whose sign and magnitude directly encode bit values ("0", spin-up; "1", spin-down), while remaining invisible under linear polarization. Here, we realize visible-range digital metamaterials by programming self-assembled DNA origami templates with asymmetrically placed gold nanorods to create discrete 3D chiral metamolecules. Using on-surface DNA origami assembly and the Silica Microsphere-Assisted Patterning by Liquid Elimination (SiMPLE) method, we fabricate large-scale bit arrays on optical active glass substrate in solution with [~]1.33 m lattice spacing, [~]86% site occupancy, and [~]12-month stability after silicification. These bottom-up fabricated digital metamaterial array exhibits two independent security layers: (1) a macroscopic spatial pattern only visible by dark-field microscopy, and (2) hidden binary information stored in the single-particle chiroptical response, read out by position-resolved circular dichroism spectroscopy. Quantitative analysis confirms reliable bit encoding and high optical randomness arising from slight structural variations. By leveraging the polarity of plasmonic chirality to translate molecular-scale handedness into robust visible-range digital signals, this work establishes a scalable nanophotonic platform for secure optical information storage, authentication, and encryption.

bioengineering↗

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↗