NSF-BSF: Synchronous electro-optical DNA detection using low-noise dielectric nanopores on sapphire

纳米孔DNA传感是一项新兴的技术，近年来被开发用于检测DNA一级序列和表观遗传信息(如甲基化)，这对基础生物学和精密医学都是至关重要的。然而，纳米孔中快速、准确的DNA甲基化检测仍然滞后。这是由于导电硅(Si)固有的大电容性噪声以及DNA与纳米孔表面复杂的动态相互作用造成的信噪比(SNR)不足。该项目提出了一项多学科研究计划，以解决固态纳米孔设备中高速和低噪声生物分子传感的根本挑战。新的设计将电和光传感结合在一个传感器平台上，以提高传感精度。它采用晶体蓝宝石作为绝缘衬底，集成了大带隙二氧化钛薄膜作为传感元件，最大限度地降低了电子和光学噪声。DNA甲基化检测的演示将证明我们的二氧化钛/蓝宝石纳米孔传感器在检测复杂分子结构方面的可行性，这些结构将对分子标记检测和分子-分子相互作用产生广泛影响。教育目标是向本科生和研究生推广与电子纳米传感器相关的工程教育，并更好地培养他们成为未来的创新者，以转化纳米生物技术。推广的目标是提高公众对纳米传感器在医疗保健中的重要性的认识，并吸引K-12学生和未被充分代表的个人参与STEM职业生涯。这项研究旨在通过创建一个显著改进的纳米孔传感器平台来填补纳米孔传感研究的知识空白，该平台将低光学背景氧化钛薄膜集成在低电容从而低电气噪声的蓝宝石上。研究团队将在蓝宝石上制造细小而薄的二氧化钛薄膜，建立薄膜形成和纳米孔钻孔的高通量制造方法，进行单分子DNA移位，研究DNA与纳米孔的相互作用，并分析数据进行甲基化检测。建议的传感器平台具有许多关键功能，以支持各种新兴生物分子诊断技术的发展。首先，在绝缘蓝宝石上形成超小(10μm)电介质膜消除了衬底电导，即使对于高介电常数和超薄(5 Nm)的二氧化钛设备，也能将芯片电容大幅降至几皮法拉德，从而显著降低背景高频电噪声，显著改善高带宽传感。此外，薄膜形成和纳米孔钻孔都将通过高通量制造方法实现，即晶片规模和批量处理兼容的蓝宝石蚀刻和直接激光打孔，从而实现低成本和可重复生产。这种可伸缩制造、低噪音、高灵敏度的纳米孔将促进高分辨率基因识别和甲基化状态的量化，并大大降低成本。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Nanopore DNA sensing is an emerging technology, and has recently been developed to detect both the DNA primary sequence and epi-genetic information (such as methylation), which is crucial to both fundamental biology and precision medicine.. However, high-speed and accurate DNA methylation detection in nanopores still lags behind. This is attributed to an insufficient signal-to-noise ratio (SNR) resulting from the inherent large electrical capacitive noise from the conductive silicon (Si) and also the complex DNA dynamic interaction with nanopore surface. This project proposes a multidisciplinary research plan to address the fundamental challenges in high-speed and low-noise biomolecular sensing in a solid-state nanopore device. The new design combines electrical and optical sensing on a single sensor platform to improve the sensing accuracy. It utilizes crystalline sapphire as an insulating substrate and integrates large-bandgap titanium oxide thin film as the sensing element to minimize both the electronic and optical noise. The demonstration of DNA methylation detection will prove the feasibility of our TiO2/sapphire nanopore sensors in detecting complex molecular structures that will have broad impact on molecular marker detection and molecule-molecule interactions. The educational objectives are to promote electronic nanosensors related engineering education to undergraduate and graduate students, and to better prepare them as future innovators to transform nanobiotechnologies. The outreach objectives are to promote public awareness of the importance of nanosensors in health care and to attract the participation of K-12 students and underrepresented individuals in STEM careers.This research is to fill the knowledge gap in nanopore sensing research by creating a significantly improved nanopore sensor platform that integrates low-optical background titanium oxide membranes on low-capacitance and hence low-electrical-noise sapphire. The research team will fabricate small and thin TiO2 membranes on sapphire, establish high-throughput manufacturing methods for both membrane formation and nanopore drilling, perform single-molecule DNA translocation, study the DNA-nanopore interaction, and analyze the data for methylation detection. The proposed sensor platform has a number of key features to support the development of a wide variety of emerging biomolecular diagnostic technologies. First, the creation of ultrasmall (10 μm) dielectric membranes on insulating sapphire eliminates substrate conductance, and drastically minimizes the chip capacitance to a few picoFarads even for high-dielectric-constant and ultrathin (5 nm) TiO2 devices, thus significantly reducing the background high-frequency electrical noise and markedly improving high-bandwidth sensing. Further, both membrane formation and nanopore drilling will be achieved by high-throughput manufacturing methods, i.e. wafer-scale and batch-processing compatible sapphire etching and direct laser drilling, thus enabling low-cost and repeatable production. The scalably manufactured, low-noise, high-sensitivity nanopores will facilitate high-resolution gene identification and quantitation of their methylation status in a single measurement and at a greatly reduced cost.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.