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    Please use this identifier to cite or link to this item: http://ir.lib.ncu.edu.tw/handle/987654321/71301

    Title: 探討中性DNA與一般DNA雜交反應熱力學與結合機制之研究;Studies of thermodynamic and mechanism for neutralized DNA (nDNA)/DNA and DNA/DNA duplex formation
    Authors: 陳奕儒;Chen,Yi-Ju
    Contributors: 化學工程與材料工程學系
    Keywords: 恆溫滴定微卡計;圓二色光譜儀;結合機制;焓熵補償效應;核酸分子;isothermal titration calorimetry;circular dichroism;binding mechanism;enthalpy-entropy compensation;nucleic acid
    Date: 2016-07-22
    Issue Date: 2016-10-13 12:41:51 (UTC+8)
    Publisher: 國立中央大學
    Abstract: 在過去的幾十年來,由人體基因表現以作疾病的預防與臨床醫療的研究逐漸蓬勃發展,並朝向精準醫學方向邁進。而為了提升基因晶片檢測目標核酸分子雜交的效率,本研究利用一種核酸類似物,骨幹上磷酸根所帶的負電由甲基化所遮蔽,使核酸分子呈現電中性,與互補股序列DNA雜交時因為靜電排斥力的下降而有更好的穩定性,期待改質過的探針對於序列的辨識性、靈敏性、專一性得到改善。
    ;In the past few decades, detection and recognition of nucleic acid hybridization has been booming. In order to enhance the hybridization efficiency, we try to make a good use of neutralized DNA (nDNA) which is a DNA analogue with the backbone phosphate groups replaced by phosphate methylated groups. To reduce the electrostatic repulsion between the complementary DNA, we modified nDNA into DNA single strand and hope to improve the sensitivity and specificity of the nDNA probe. With the aim to know how the incorporation of nDNA is the optimized design, in this study we discuss a lot of different experimental conditions including nDNA numbers of modification, bases and position effect. We also proved that the nDNA sequences exhibit a stronger hybridization affinity than their corresponding DNA sequences no matter in general or the lower ionic strength buffer condition. In order to understand the hybridization thermodynamics and mechanism information from the combination of the calorimetric techniques, spectroscopic and molecular simulation were used. CD measurements highlight the modified duplexes adopt a B-form conformation that is similar to the unmodified duplexes. An entirely thermodynamic profile for nDNA/DNA hybridization suggested that nDNA-induced stability emanates from a favorable enthalpy change but a less favorable entropic term. Isothermal titration calorimetry (ITC) also showed that an increase in the binding constant between the two strands as we add nDNA while we also need to consider the DNA length. By ITC and melting studies, the modifications of nDNA in the terminal is more stable than that of in the central. And the guanine modification enhanced the thermal stability that was attributed to the stronger base stacking interaction. Our results indicated that the hybridization process of nDNA is more exothermic than the natural DNA resulting from greater hydrogen bonding especially in the lower salt concentration. We also evaluated the hybridization energies from the molecular simulation. The computed energies for the duplex involving nDNA are often larger than those for DNA/DNA due to the lower electrostatic interaction. By the experiment and simulation, we conclude the basic hybridization thermodynamic and mechanism information in order to provide a proper sequence design/modification guideline.
    Appears in Collections:[化學工程與材料工程研究所] 博碩士論文

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