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

Executive Summary

Core Achievement: Demonstration of a scalable quantum biosensing platform integrating the first multiplexed 7x7 DNA microarray (49 distinct sensing elements) directly onto a functionalized diamond surface.
Novel Surface Chemistry: Introduction of a rapid (15-minute), single-step silanization protocol using biotin-PEG-silane, creating a subnanometer (0.28 ± 0.08 nm) antifouling layer on oxygen-terminated (100)-diamond.
Quantum Transduction Mechanism: Utilizes a target-induced displacement assay where unlabeled target DNA displaces a paramagnetic Gd³⁺-DOTA-labeled incumbent strand.
Binary Quantum Readout: Displacement removes the local magnetic noise source, causing a measurable restoration of the Nitrogen-Vacancy (NV) center spin relaxation time (T₁). T₁ was restored by 93% to 95% of the control value upon successful displacement.
High Specificity and Multiplexing: Achieved high sequence selectivity with minimal cross-reactivity (less than 6% of total signal) across the 49-spot array, demonstrating spatial addressability.
Generalizability: The platform is inherently label-free for the target molecule and can be generalized using DNA aptamers to detect various biomolecules, including proteins and small metabolites, beyond just DNA.

Technical Specifications

Parameter	Value	Unit	Context
Diamond Substrate Size	2 x 2 x 0.5	mm³	Single-crystalline, electronic grade
NV Center Depth	7 ± 2	nm	Obtained from implantation-energy correlations
Functionalization Time (Silanization)	15	minutes	Single-step Biotin-PEG-Silane process
PEG Monolayer Thickness (Dried)	0.28 ± 0.08	nm	Measured via AFM
ssDNA-SA Layer Thickness	2.5	nm	Measured via AFM (reduced due to dehydration)
Streptavidin Surface Coverage	67	%	Estimated over 200 x 200 nm² area
ssDNA Density	27,500	molecules/µm²	Density of ssDNA-conjugated streptavidin
DNA Microarray Size	7 x 7 (49 spots)	Array	Patterned on 2 x 2 mm² chip
DNA Spot Diameter	150	µm	Spot size dispensed by picoliter robot
Hybridization Yield	~26	%	Relative to direct dsDNA immobilization
Cross-Reactivity (Non-specific adsorption)	less than 6	%	Relative to total signal
Gd³⁺ Labels per Strand (Low)	3.4 ± 1.2	Complexes	Gd³⁺-DOTA complexes on incumbent strand
Gd³⁺ Labels per Strand (High)	8.5 ± 1.3	Complexes	Gd³⁺-DOTA complexes on incumbent strand
T₁ Reduction (3.4x Gd³⁺)	47	%	Reduction relative to Gd³⁺-free control
T₁ Restoration (3.4x Gd³⁺)	93	%	Restoration upon strand displacement
T₁ Restoration (8.5x Gd³⁺)	95	%	Restoration upon strand displacement
Correlation Time (τ_c) Range	0.67 to 4.76	ns	Extracted from T₁ fitting

Key Methodologies

Diamond Cleaning: Single-crystalline diamond slabs were sonicated in water (5 min), followed by cleaning in Nanostrip solution at 60°C for 15 minutes, and rinsed with DI water.
Pre-Silanization Preparation: Diamonds were soaked in anhydrous acetone for at least 5 minutes to remove excess surface water.
Single-Step Silanization/PEGylation: Diamonds were incubated in a freshly prepared 15% (m/m) solution of Biotin-PEG-Silane (MW 2k) in anhydrous DMSO at 95°C for 15 minutes.
ssDNA-Streptavidin (SA) Complex Formation: Biotinylated ssDNA was mixed with streptavidin (ratio ssDNA:SA = 1.5:1) to form a 1 µM solution. Diamonds were incubated in this solution for 20 minutes.
Microarray Patterning: A non-contact dispensing robot (SciTEM) applied 300-picoliter droplets of DNA-streptavidin solution onto the PEGylated surface, creating a tightly packed 7x7 array (150 µm spots).
Quantum Readout Preparation: Duplex DNA constructs were immobilized, featuring a long substrate strand and a shorter incumbent strand labeled with 3.4x or 8.5x Gd³⁺-DOTA complexes.
Sensing and Measurement: T₁ relaxometry measurements were performed using a custom epifluorescence inverted microscope setup, interrogating NV ensembles with a 515 nm laser. Static magnetic fields were applied using permanent neodymium magnets.
Target Detection: The diamond was incubated with an unlabeled, fully complementary “invader” strand, which displaced the Gd³⁺-labeled incumbent strand, and the resulting T₁ restoration was measured.

Commercial Applications

This technology establishes a foundation for high-throughput quantum diagnostics and sensor networks, relevant to:

Advanced Molecular Diagnostics: Real-time, parallelized biomolecular analysis for early disease detection (e.g., viral RNA detection, cancer biomarkers).
Therapeutic Drug Monitoring: Label-free detection of small metabolites and proteins using DNA aptamers integrated into the microarray.
Integrated Quantum Sensor Arrays: Development of large-scale quantum sensor networks operable in complex biological environments.
High-Throughput Screening (HTS): Massively parallel detection of specific binding events, avoiding the complexity and time constraints of traditional mass spectrometry.
Diamond Quantum Sensing Platforms: Provides a robust, scalable, and chemically specific surface functionalization architecture for commercial NV-based quantum sensors (e.g., those produced by Quantum Diamond Technologies Inc., listed as an author affiliation).

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