Quantum magnetic imaging for DNA biophysical measurements

Abstract

An outstanding challenge in biophysics is sensing the relative bio-mechanical orienta-tion of single-molecule biological systems. Prior approaches used to study single-molecule biophysics rely on attaching fluorescent or otherwise optically detectable probes to bio- mechanical systems, and inferring the underlying bio-dynamics from the imaged position of the probe. This approach is limited as distinct bio-mechanical configurations may result in the same imaged position dependence of the probe. Additionally, if a flourescent probe is chosen, measurements can only be performed for time scales on the order of seconds due to photobleaching. In this thesis, a new imaging modality is developed that relies on ferro- magnetic probes of bio-mechanical orientation. Because a ferromagnet has an unchanging magnetic moment, imaging the re-orientation of a ferromagnetic probe attached to a single- molecule bio-mechanical system can directly provide information about bio-mechanical ori- entation. Additionally, a ferromagnetic probe will never photobleach, enabling long-time scale orientation tracking. A high-sensitivity magnetic imaging platform based on the diamond nitrogen-vacancy (NV) center is developed to image the ferromagnetic probe moment direction. The NV center is a quantum defect whose electron spin has long spin coherence times, spin-coupled optical transitions and is photostable, allowing for optical probing of the ground state spin transitions, which couple strongly to external fields including magnetic field. Additionally, NV sensors can be fabricated near the surface of the biocompatible solid-state diamond host material, and can operate at room temperature under ambient conditions. This thesis details significant progress in the application of the diamond NV quantum sensor to study single-molecule DNA bio-mechanical orientation. A wide-field vector mag- netic field imaging platform based on a near-surface ensemble of diamond NV defects is constructed. This wide-field magnetic imager enables nanotesla scale magnetic sensitivity with optical-diffraction-limited spatial resolution. Single DNA molecules are attached to ferromagnetic nanoparticles at one end and the diamond sensor at the other. DNA bio- physical quantities are measured by imaging the ferromagnetic particle orientation. The sensor fabrication, optical and microwave measurement system, fundamental and practical sensitivity limitations are presented. Two types of magnetic moment orientation imaging are advanced: dynamic magnetic orientation sensing and static magnetic orientation sensing. In the dynamic imaging modality, a novel quantum control technique for high sensi- tivity dynamic imaging is developed and applied to image the dynamic reorientation of a DNA-tethered ferromagnetic particle for the first time. In the state-of-the-art diamond sensor constructed for this bio-mechanical orientation sensing platform, microscopic inho- mogeneities due to diamond crystal strain were found to limit magnetic sensitivity and magnetic particle imaging frame rate. A novel quantum protocol was developed which ex- ploits the symmetry of the NV defect ground state structure to mitigate the contribution of microscopic inhomogeneities in non-magnetic fields, and double the contribution of magnetic fields to the imaging signal. A DNA-tethered ferromagnetic particle was reoriented by an applied fluid flow, and the quantum control protocol enabled imaging of this reorientation at video rates. This proof-of-principle experiment is a concrete demonstration of unbleaching, high-frame-rate dynamic bio-mechanical orientation tracking using ferromagnetic particles. In the static imaging modality, the quantum imaging platform is used to directly probe the bend stiffness of nuclesome-scale DNA fragments. In previous experiments, the bend stiffness of short, nucleosome-scale DNA molecules appears to disagree with the standard polymer bending model which is compatible with longer DNA length scales. However, prior experiments have relied on either indirect inference measurements or measurements of ensembles of DNA molecules to quantify short-DNA bending. In this thesis, DNA- tethered ferromagnetic probes are used in a magnetic tweezer assay to construct a nano- mechanical torque balance that can directly measure the bend stiffness of individual DNA molecules. The quantum imaging platform is used to measure the ferromagnetic probe moment direction and applied magnetic tweezer field direction simultaneously. Deviations between the probe moment vector and the applied field vector provide a measure of the torque exerted by the DNA molecule on the ferromagnetic probe. The direct measurement of the bend stiffness of individual DNA molecules is performed for a first time. This collection of work represents a significant development in quantum-enabled bio- sensing to address fundamental questions in biophysics and inspires further biophysical measurements and quantum sensor development.