| Summary: | 碩士 === 國立成功大學 === 化學工程學系碩博士班 === 98 === In this thesis, we seek a fundamental understanding of molecular combing of DNA as well as to apply it to develop an addressable one-dimensional nanowire for molecular probing and functional recognition. In addition, we develop a new optoelectronic platform for particle manipulation. This thesis consists of four parts.
In Chapter 3, we examine how the interface motion affects the DNA combing on an untreated hydrophilic or hydrophobic substrate to see if DNA molecules can be stretched and immobilized onto the substrate in the absence of specific binding effects. Two methods are employed to conduct the combing: lid lifting and evaporation. For the combing using the lid lifting method, we find that more DNA molecules can be immobilized and stretched on a hydrophilic substrate compared with a hydrophobic substrate. In addition, combed DNA molecules on a hydrophilic substrate than on a hydrophilic surface appear longer than those on a hydrophobic substrate. Why combing is more efficient on a hydrophilic substrate is that the shear stress and the surface velocity on such a substrate is increased in the direction toward the contact line, giving rise to pre-stretching and pre-concentration effects on DNA molecules near the contact line. As for combing driven by evaporation, we are able to directly observe unraveling of single DNA molecule by the retreating interface and successive combing of DNA molecules. A successful combing by this method seems to hinge on if sufficient DNA molecules can be built up at the contact line and on if these DNAs can be confined within the corner to undergo constant unraveling and combing actions without being swept out by the local flow. We also observed that the combing here does not necessarily require specific binding between DNA and the underlying substrate, which is different from the commonly accepted molecular combing mechanism proposed by Bensimon.
In Chapter 4, we put forth to design a microfluidic platform having the ability to adjust the dewetting speed for examining how molecular combing is influenced by the dewetting speed. We also modify the surface with silane groups having different numbers of alkyls to reveal how specific binding and the hydrophicity of a surface play roles in the combing.We find that for a hydrophilic surface, there exists a maximum combing efficiency in the range of the applied dewetting speed. This result can be attributed to two opposite actions produced by the retreating interface on a DNA: forward unraveling by the interface and backward dragging by the surface. At low dewetting speeds, these two effects work to assist in unfolding stretching, and anchoring of DNA molecules. If the dewetting speed is high, the coil end of a stretched and anchored DNA could shrink so fast that the DNA would lose its contact to the interface. In this case, the DNA would only undergo unfavorable compression by the backward dragging. As for a hydrophobic surface, in addition to the maximam mentioned above, the combing efficiency declines and then rises up when the dewetting speed is further increased. The phenomenon could be attributed to the decrease of the dynamic contact angle to an acute angle at a high dewetting speed. The results found in this Chapter suggest that plausible combing mechanisms should include sweeping/trapping of DNA toward/at the contact line, unfolding of DNA by the moving interface, and binding of DNA onto the underlying substrate.
In Chapter 5, we apply our setup in Chapter 4 to prepare an addressable one-dimensional nanosensor by first combing DNA molecules onto a substrate following by conjugating these DNAs with functionalized quantum-dot nanocolloids. With the aid of fluorescence resonance energy transfer (FRET), we demonsrate that targeted molecules can be captured by the prepared quantum-dot-DNA molecular combs. Such a one-dimensional FRET sensor could be applied to molecular docking or developed into a structured molecular device for transfering or detecting signals arising from specific molecular interactions.
In the last part (Chapter 6) of this thesis, we develop a new optoelectronic microfluidic platform for manipulating suspended particles through combined effects of optical trapping and light-induced AC electrokinetics. We find that the optical trapping effect is actually opposed by the induced electrokinetic effects at both low and high frequencies.
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