Nonlinear Electrical and Optical Properties of Nano Sensor Array for Stochastic Molecular Interactions

生物晶片的應用中，分子診斷的基礎在於專一性的分子辨識機制，傳統上此一生物分子的交互作用行為多是基於巨觀量測方式下的時間與空間平均訊號而得到分子動靜態行為的分析，但對於平衡係數所表示的分子動態訊息與結構組成的分析，理論上在微觀環境中應可由小至單一分子的組合觀測而獲得相同的預測。本論文研究之目的即在於發展一奈米陣列(每點直徑50奈米)檢測平台，利用時間與空間的加總方式，進行單一分子隨機動態反應之統計行為的量測，並據以進行定量分析，作為高度創新數位式奈米生物晶片的理論基礎與可行性驗證。據此本論文之三項重要架構分別為(1)奈米製造：零維的仿生數位奈米陣列平台發展與一維導電高分子奈米導線製作；(2)觀測奈米解析尺度之多功能光學顯微系統，並使用一維週期性奈米結構驗證解析度及其光學性質；(3) 模擬與分析一維與二維分子交互作用的統計行為模型。們使用沾筆式奈微影系統(Dip-Pen Nanolithography, DPN)製作零維奈米圖案(點陣列)與一維奈米圖案(線陣列)。在點陣列中，最小的反應區為50奈米，用來同時取得一維/二維的訊號 (時空的訊號加總)。目前已做到靜態反應偵測無須標定螢光探針之生物分子結合，並正確地量測streptavidin的高度為4奈米。在改善奈米陣列晶片的鈍化層方面，我們提出有別於以往使用化學修飾產生鈍化層的方式，使用原子層沉積技術(Atomic Layer Deposition，ALD)產生2奈米氧化鋁表面薄膜於矽與鍺晶片上，並在其上製作奈米點陣列進行評估。在一維奈米圖案(線陣列)，我們使用DPN製作導電高分子的奈米導線，線寬為68奈米與300奈米，並精確排列奈米導線研究室溫之電氣特性與串並聯性質，探討其非線性的電性質，並將整個感測器應用於一氧化氮(NO)的感測，目前可測得10 ppm的濃度。 為觀察一維與二維奈米陣列晶片上發生的分子辨識事件，我們著手發展一套高解析度的暗場顯微鏡並結合光譜的多功能影像系統，以提供奈米解析能力之遠場影像與定性定量的光譜訊號。解析度的評估是使用多種光碟片的一維奈米結構進行確認，目前推算的解析度為40奈米。另外，我們在碟片的軌道上鍍上一層50奈米的金膜，討論不同碟片的吸收光譜因表面電漿受到不同週期結構的影響，並在其上固定上一層薄生物分子，觀察其吸收峰值的變化。此結果未來可發展整合式碟片式奈米陣列晶片的光學診斷系統。 建立分子隨機交互作用的統計行為是基於離子通道開關的機率分佈進行拓展。首先利用亂數產生兩階層(bi-state)之訊號，模擬奈米尺度下一維與二維之分子交互作用的訊號，以驗證檢定模型的可行性，並根據此模型的標準差變化決定奈米陣列的維度大小。利用文獻中一維作用訊號的驗證驗證分析顯示此概念的可行性。期待將來應用驗於證微巨觀的生物分子隨機行為的統計模型，並推廣到不同分子系統的應用， 例如: multi-states system (鉀離子通道)。In the biochip applications, the mechanism of specific molecular recognition plays a fundamental role for molecular diagnosis. Traditionally, the dynamics of such an interaction are obtained by spatial and temporal summations of measured signals at macroscopic scale. However, it should be feasible to acquire such information in microscopic environment at single molecule level. The goal of this research is to develop platform technologies for a novel "digital nanoarray", with feature size down to 50 nm, to explore the microscopic measurement of stochastic behaviour at single molecule level and the feasibility studies of acquiring molecular dynamics by spatial-temporal summations of non-labelling biomolecules. These platform technologies include (1) nanofabrication of zero dimensional (0 D) nanodot array for developing a biomimicking platform and one-dimensional (1 D) nanowire array of conducting polymer for NO gas sensing; (2) a multi-functional dark-field microscopy (DFM) with nano-resolution down to 40 nm and spectroscopic function for characterizing observed nanostructure; and (3) a theoretical model for simulation and analysis of one and two dimensional of stochastic molecular interaction. First of all, we have used dip-pen nanotechnology (DPN) to fabricate nanoarray and nanowires for the studies of their nonlinear optical and electrical properties at large scale. With the fabricated nanodot array of 50 nm in diameter, we were able to immobilize bio-molecules on to prepared surface and acquire both 1 D and 2 D signals for further calculation of the spatial-temporal summations. The non-labeling detection of biomolecular recognition has been done by scanning images of AFM, and the resultant height of streptavidin is about 4 nm, which is close to the theoretical value. To improve the quality of surface preparation, we have used the atomic layer deposition (ALD) to deposit a 2 nm thickness of alumina oxide as a passivation layer to minimize non-specific binding to the native glass surface. We have compared the performance of both oxide surface of germanium and silicon substrate with the bare silicon surface. In the prepared 1 Dnanowire of both 68 nm and 300nm in line width, we are able to precisely align the nanowires across the gap of two microelectrodes. The nonlinear I-V curves of single nanowire were measured and analyzed at room temperature for practical applications. Several parallel and series circuitries of nanowire are measured for the verification of theoretical calculation. Finally, the nanowire array is applied for NO detection. In order to observe the stochastic behavior of single molecule on the digital nanoarray, it is essential to develop an optical microscopy beyond the diffraction limits. Herein, we reported a multifunctional optical microscopic system that combined the features of dark-field microscopy (DFM) with a spectrophotometric function to characterize the nanoarray for both qualitative and quantitative analysis. We have used various formats of optical storage discs, which have different feature sizes in the pitch of track patterns, to demonstrate the resolving power of this system. The calculated resolution is down to 40 nm. Moreover, a thin gold layer is deposited on the disc to study the optical enhancement of pit features and the change of absorption peaks due to surface Plasmon resonance (SPR) effect. A significant change of absorption peak is obtained by depositing a thin film of biolmolecules on the gold film. These results indicate the possible use of this nanoarray platform on medical diagnosis. The stochastic model of behavior of biomolecular interactions is similar to the bi-state (on-off) of channel proteins. Our simulation results show that 100 of molecular interactions are the same in both 1 D and 2 D signals. After this simulation process, we are able to determine the proper size of nanoarray by evaluating the reasonable errors of possibility. We have used deposited 1 D data from internet for our own purposes. This model can be applied to the multi-state systems in the future.致謝 Ibstract in Chinese IIbstract in English IVontent VIIigure caption VIIIable caption XII Introduction 1.1 Behavior of single molecular interaction 1.2 Literature review 3.3 Motivation for developing a biomimicking platform 6.4 Dissertation organization 9 Nanofabrication: dip-pen nanolithography 13.1 Background of nanofabrication 13.2 Sensing phenomena of sensor at nanometer scale 14.3 Tip-based nanolithography 15.4 Zero-dimensional nanofabrication 17.5 One-dimension nanofabrication 44 Observation : Ultrahigh resolution of dark-field microscopy 73.1 Prolong: dark-field microscopy for nanostructure 73.2 Introduction of optical nanoscopy 73.3 Motivation to develop high-resolution DFM 75.4 Materials and methods for 1D nanostructure and DFM system 75.5 Results and discussions of optical properties of 1-D nanostructure 78.6 Short summary 86 Analysis of stochastic single of biomolecular interaction 94.1 Stochastic behavior of biomolecular interaction 94.2 Nanoarray size 95.3 Simulation by presented data 96 Conclusion and future work 100.1 The future works for biomimicking platform 100.2 Development of a fast-response gas sensor using SET-based CP nanowire 101eference 10