Quantum biosensing on a multiplexed functionalized diamond microarray

At a Glance

Metadata	Details
Publication Date	2025-08-15
Journal	arXiv (Cornell University)
Authors	Ignacio Chi-Durán, Ernest Villafranca, David Dang, Rachelle Rosiles, Chi Fai Cheung
Analysis	Full AI Review Included

Technical Documentation & Analysis: Quantum Biosensing on Functionalized Diamond Microarrays

Executive Summary

This research demonstrates a significant advancement in high-throughput quantum biosensing by successfully integrating a multiplexed DNA microarray directly onto a single-crystal diamond (SCD) chip utilizing Nitrogen-Vacancy (NV) centers.

Scalable Quantum Platform: Established a scalable platform for multiplexed molecular recognition using NV centers, overcoming barriers related to surface functionalization and high-density spatial multiplexing.
High-Density Array: Demonstrated a 7×7 DNA microarray, enabling simultaneous detection of 49 distinct biomolecular features on a compact 2×2 mm² SCD chip.
Rapid Surface Engineering: Developed a rapid, single-step silanization protocol (15 minutes at 95 °C) to create a subnanometer (0.28 ± 0.08 nm) antifouling Biotin-PEG monolayer.
Minimized NV-Target Separation: The subnanometer functionalization layer minimizes the distance between near-surface NV centers (7 ± 2 nm depth) and the target molecules, maximizing quantum coupling efficiency.
Label-Free Quantum Readout: Introduced a novel transduction mechanism based on target-induced displacement of paramagnetic Gd³⁺-DOTA spin labels.
Robust Quantum Signal: Target binding resulted in the removal of the magnetic noise source, restoring the NV T₁ relaxation time by 93% to 95%, providing a robust, binary quantum readout signal.
Generalizability: The displacement assay is inherently generalizable for detecting nucleic acids, proteins, and small metabolites using DNA aptamers, paving the way for integrated quantum diagnostics.

Technical Specifications

Parameter	Value	Unit	Context
Diamond Material Used	Single Crystal Diamond (SCD)	N/A	Electronic grade slab (Element Six).
Chip Dimensions	2 × 2 × 0.5	mm³	Compact size for microarray integration.
NV Center Depth	7 ± 2	nm	Optimized shallow depth for strong surface spin coupling.
DNA Microarray Density	7 × 7 (49)	Spots	High-density multiplexing capability.
DNA Spot Diameter	150	µm	Spot size patterned using non-contact dispensing robot.
Functionalization Time (Silanization)	15	minutes	Rapid, single-step Biotin-PEG-Silane process.
Silanization Temperature	95	°C	Reaction temperature in anhydrous DMSO.
Biotin-PEG Layer Thickness	0.28 ± 0.08	nm	Subnanometer antifouling layer thickness (AFM measured).
SA-ssDNA Layer Thickness	2.5	nm	Thickness of the immobilized streptavidin-DNA complex.
T₁ Reduction (Gd³⁺ Labeling)	47% to 70%	%	Reduction relative to control, dependent on Gd³⁺ density.
T₁ Restoration (Target Displacement)	93% to 95%	%	Recovery of T₁ time, confirming successful label removal.
Excitation Wavelength (Quantum Sensing)	515	nm	Laser used for NV ensemble interrogation (T₁ relaxometry).

Key Methodologies

The successful integration of the DNA microarray relied on precise diamond preparation and a highly efficient, single-step functionalization process:

Diamond Substrate Cleaning: Single-crystalline diamond slabs were cleaned using sonication in water (5 min) followed by Nanostrip solution at 60 °C for 15 minutes to ensure an oxygen-terminated surface rich in hydroxyl groups.
Surface Dehydration: Diamonds were thoroughly rinsed and dried, followed by soaking in anhydrous acetone (≥ 5 minutes) to prepare the surface for silane reaction.
Rapid Silanization/PEGylation: A single-step reaction was performed using a 15% (m/m) solution of Biotin-PEG-Silane in anhydrous DMSO at 95 °C for 15 minutes, covalently attaching the antifouling layer to the diamond surface hydroxyl groups.
ssDNA-Streptavidin Complexation: Biotinylated ssDNA was mixed with streptavidin (ratio 1.5:1) to form a 1 µM solution, which was then incubated with the PEGylated diamond surface for 20 minutes.
Microarray Fabrication: A non-contact picoliter dispensing robot was used to pattern 300-picoliter droplets of the DNA-streptavidin solution onto the 2×2 mm² surface, creating the 7×7 array of 150 µm spots.
Quantum Readout (T₁ Relaxometry): NV ensembles were interrogated using a custom epifluorescence inverted microscope and a 515 nm laser. T₁ measurements were performed sequentially after each functionalization step to monitor the magnetic noise introduced or removed by the Gd³⁺ spin labels.

6CCVD Solutions & Capabilities

This research highlights the critical need for high-quality, precisely engineered diamond substrates for next-generation quantum biosensors. 6CCVD is uniquely positioned to supply the foundational materials required to replicate, scale, and advance this work.

Research Requirement	6CCVD Solution & Value Proposition
High-Purity SCD Substrates	Electronic Grade Single Crystal Diamond (SCD): We provide high-purity SCD wafers (up to 500 µm thickness) essential for creating stable, shallow NV ensembles (like the 7 ± 2 nm depth used here). Our material ensures minimal intrinsic defects, maximizing NV coherence and sensitivity.
Ultra-Smooth Surface Finish	Precision Polishing (Ra < 1 nm): The success of subnanometer functionalization relies on an atomically flat surface. 6CCVD guarantees SCD polishing to an industry-leading roughness of Ra < 1 nm, crucial for minimizing NV-target distance and ensuring homogeneous chemical grafting.
Custom Chip Dimensions (2x2 mm² chiplets)	Custom Dicing and Laser Cutting: While the researchers used small chiplets, 6CCVD can process plates up to 125 mm (PCD) or large SCD wafers. We provide precision laser cutting and dicing services to deliver custom dimensions compatible with high-throughput microarray dispensing robots.
Surface Termination Control	Tailored Surface Chemistry: The silanization protocol requires a specific oxygen-terminated surface rich in hydroxyl groups. 6CCVD supplies SCD substrates with controlled surface terminations (O-terminated, H-terminated) to ensure optimal chemical reactivity for protocols like Biotin-PEG-Silane grafting.
Scaling and Parallelization	Large-Area Polycrystalline Diamond (PCD): For scaling multiplexed biosensing arrays beyond the current 49-spot limit, 6CCVD offers large-area Polycrystalline Diamond (PCD) wafers up to 125 mm in diameter, polished to Ra < 5 nm, enabling massive parallelization of quantum sensor networks.
Advanced Integration	Custom Metalization Services: Should future iterations of this quantum biosensor require integrated microwave delivery structures (e.g., coplanar waveguides used for T₁ measurements), 6CCVD offers in-house metalization capabilities (Au, Pt, Ti, Cu) directly onto the diamond surface.

Engineering Support

6CCVD’s in-house team of PhD material scientists and engineers specializes in optimizing diamond properties for quantum applications. We offer consultation services to assist researchers in selecting the ideal SCD grade, surface orientation (e.g., (100) used in this study), and surface termination required for advanced NV-based biosensing projects.

For custom specifications or material consultation, visit 6ccvd.com or contact our engineering team directly.

View Original Abstract

Quantum sensing with nitrogen-vacancy (NV) centers in diamond promises to revolutionize biological research and medical diagnostics. Thanks to their high sensitivity, NV sensors could, in principle, detect specific binding events with metabolites and proteins in a massively parallel and label-free way, avoiding the complexity of mass spectrometry. Realizing this vision has been hindered by the lack of quantum sensor arrays that unite high-density spatial multiplexing with uncompromising biochemical specificity. Here, we introduce a scalable quantum biosensing platform that overcomes these barriers by integrating the first multiplexed DNA microarray directly onto a subnanometer antifouling diamond surface. The 7x7 DNA array, patterned onto a diamond chip, enables simultaneous detection of 49 distinct biomolecular features with high spatial resolution and reproducibility, as verified by fluorescence microscopy. Molecular recognition is converted into a quantum signal via a target-induced displacement mechanism in which hybridization removes a Gd$^{3+}$-tagged DNA strand, restoring NV center spin relaxation times (T$_1$) and producing a binary quantum readout. This platform establishes a new paradigm for high-throughput, multiplexed quantum biosensing and opens the door to advanced molecular diagnostics and large-scale quantum sensor networks operable in complex biological environments.

Tech Support

Original Source

DOI: None