Quantum sensing of microRNAs with nitrogen-vacancy centers in diamond

At a Glance

Metadata	Details
Publication Date	2024-05-06
Journal	Communications Chemistry
Authors	Justas Zalieckas, Martin Greve, Luca Bellucci, Giuseppe Sacco, Verner Håkonsen
Institutions	Norwegian University of Science and Technology, Scuola Internazionale Superiore di Studi Avanzati
Citations	11
Analysis	Full AI Review Included

Quantum Sensing of microRNAs using NV Centers in Diamond: Engineering Analysis

Executive Summary

This research demonstrates a novel quantum sensing modality using Nitrogen-Vacancy (NV) centers in diamond for the label-free, ultrasensitive detection of microRNAs (miR-21), overcoming the fundamental limitations of Debye screening.

Core Innovation: The method senses the intrinsic magnetic noise generated by paramagnetic Mn²⁺ counter ions that accumulate near the negatively charged miR-21, rather than attempting to measure the screened electric charge.
Sensor Platform: Shallow NV centers (7 ± 3 nm depth) in single-crystal diamond are used as quantum magnetometers via T₁ relaxometry (longitudinal spin-lattice relaxation time).
Ultrasensitive Performance: A Limit of Detection (LOD) of 10 pM was achieved for miR-21, translating to an absolute detection of 120 attomoles within the microfluidic channel volume.
Mechanism Validation: Molecular Dynamics (MD) simulations confirmed that the adsorption of a single miR-21 molecule onto the oxygen-terminated diamond surface recruits an average of 8-9 Mn²⁺ ions, significantly increasing local magnetic noise.
Material Engineering: The diamond surface was functionalized using Piranha solution, resulting in oxygen termination (1.6% carboxyl groups) necessary for charge control and Mn²⁺/miR-21 interaction mediation.
Broad Applicability: This technique is extendable beyond diagnostics to sense any charged polyelectrolytes (natural or synthetic), applicable in fields like water treatment and filtering.

Technical Specifications

Parameter	Value	Unit	Context
NV Center Depth	7 ± 3	nm	Below {100} surface (estimated via SRIM)
NV Zero-Field Splitting (D)	2.87	GHz	Triplet ground state
Excitation Wavelength	532	nm	CW Green Laser
Excitation Power Density	9	kW cm^-2	Used for NV initialization/readout
Limit of Detection (LOD)	10	pM	miR-21 concentration
Absolute LOD	120	attomoles	In 12 mm³ microfluidic channel
Measured Relaxation Rate Change (ΔΓ₁)	~1.5	kHz	Observed enhancement for 1 µM miR-21
Mn²⁺ Bulk Concentration	5	mM	Used in stock solutions
Diamond Surface Roughness (Ra)	< 1	nm	Polished {100} face
N₂ Implantation Fluence	10¹³	cm^-2	For NV creation (4 keV energy)
Carboxyl (COOH) Surface Coverage	1.6	%	Estimated via XPS after Piranha treatment
Adsorbed Mn²⁺ Ions (MD)	8-9	ions/miR-21	Accumulated within 4 nm of surface
Microfluidic Channel Volume	~12	mm³	PDMS device
T₁ Relaxometry Pulse Times	τ₁ = 10, τ₂ = 400	µs	Used for spin contrast estimation

Key Methodologies

The experimental procedure integrates advanced material preparation, surface characterization, and quantum sensing techniques:

Diamond Preparation:
- Electronic grade single-crystal diamond (2 x 2 x 0.5 mm) was polished to 100 µm thickness (Ra < 1 nm).
- Diatomic nitrogen (N₂) was implanted at 4 keV energy with a fluence of 10¹³ cm^-2 to create a shallow NV layer (7 ± 3 nm depth).
- Annealing was performed in vacuum at 800 °C for 4 hours to activate the NV centers.
Surface Functionalization (Oxygen Termination):
- The diamond was treated for 30 minutes in Piranha solution (7:3 H₂SO₄(97%):H₂O₂(31%)) to achieve oxygen termination.
- XPS confirmed the presence of hydroxyl/epoxy (64.5%), carbonyl (20.2%), ether (13.7%), and carboxyl (1.6%) functional groups.
Microfluidic Setup:
- The diamond was bonded to a coverslip using UV curing adhesive and mounted into a custom PDMS microfluidic device (~12 mm³ volume).
- A flow control system (controller, distributor valve, flow sensor) ensured precise sequential liquid injection.
Quantum Sensing (T₁ Relaxometry):
- An in-house wide-field microscope was used, exciting the NV ensemble with a 532 nm laser (9 kW cm^-2).
- The longitudinal spin-lattice relaxation time (T₁) was measured using a two-point pulse sequence (τ₁ = 10 µs, τ₂ = 400 µs) to estimate spin contrast.
- Prior to sensing, the surface was flushed with 1 mM EDTA (pH 2.0) to neutralize the negative surface charge and chelate residual paramagnetic ions.
Adsorption and Noise Measurement:
- miR-21 solutions (10 pM to 10 nM) were injected in a 5 mM MnCl₂ / 10 mM NaCl buffer.
- An increase in spin relaxation contrast was observed upon miR-21 injection, directly correlating to the enhanced magnetic noise from accumulated Mn²⁺ ions.
Verification (AFM/XPS):
- AFM confirmed the presence of miR-21 adsorbates by observing increased surface granularity and a larger diameter halo in the 2D Fourier Transform (2DFFT).
- XPS confirmed miR-21 adsorption via the clear appearance of the P 2p peak originating from the nucleic acid phosphate groups.

Commercial Applications

This quantum sensing technology offers significant advantages in fields requiring ultrasensitive, label-free detection of charged macromolecules.

Biomedical Diagnostics:
- Early Cancer Detection: Ultrasensitive, label-free detection of circulating microRNAs (e.g., miR-21) for early diagnosis and monitoring of breast, colorectal, and prostate cancers.
- Neurodegenerative/Autoimmune Disease Monitoring: Sensing of specific RNA biomarkers associated with disease progression.
Quantum Sensing Hardware & Platforms:
- Next-Generation Biosensors: Development of robust, ambient-condition quantum biosensors based on shallow NV ensembles for magnetic noise sensing.
- Microarray Technology: Enabling label-free microRNA microarrays by sensing counter ions, simplifying sample preparation and eliminating fluorescent labeling steps.
Materials Science and Polyelectrolyte Analysis:
- Polymer Characterization: Sensing and analyzing the interaction of synthetic and natural polyelectrolytes (polyanions) with surfaces and counter ions.
Environmental and Industrial Applications:
- Water Treatment and Filtering: Ultrasensitive detection of charged contaminants, polymers, or biological agents in non-transparent liquid media.
- Enhanced Oil Recovery (EOR): Monitoring the behavior and interaction of charged polymers used in EOR processes.

Tech Support

Original Source

DOI: https://doi.org/10.1038/s42004-024-01182-7