Theoretical Studies On Interaction Of Zinc Finger Nuclease With DNA

Because of the highly cutting of metal nuclease to DNA, more and more people begin to pay attention and design these nuclease moleculars. Although with a very high cutting capacity, it always has a great threat to normal DNA while cutting morbid DNA according to its poor specificity of their choice. To end this, there is an urgent need for a nuclease with good select specificity. Zinc finger proteins can solve this problem and bring the dawn, which not only can be able identify the type of the DNA nucleotide sequence,but also incorporate in the DNA major groove stably. With the help of zinc finger protein, the metal nuclease not only achieves a specificity of DNA cutted by the extractionof hydrogen in the vicinity of sugar ring, but also has the function to identify a specific DNA nucleotide sequence, which aroused the interest of the major researchers.In this paper, we mainly do three parts work:Firstly, we take the method of molecular docking to study the main factors in the identification and binding of zinc finger to DNA and examine the zinc finger protein DNA binding strength through changing the DNA sequence. By monitoring the binding energy, we found that the decrease in the binding energy when the first zinc finger DNA binding sites from sequences GUA、CYT、CYT and CYT change into the DNA sequence of second zinc finger identifying CYT、CYT、GUA and CYT or another sequence of third zinc finger recognizing CYT、CYT、CYT and CYT. But contrasting the two mutations in the nucleotide sequence of CCGC and CCCC, the former has a lower binding energy than the latter. So we can conclude that the first zinc finger in the process of identifying focuses on the identification of their naturally occurring sequence of GCCC, and then recognizing others, such as CCGC and CCCC.Secondly, the zinc finger nuclease is the combination of zinc finger protein and the artificial metallonuclease through a linked field, which can recognize special DNA sequences and result in DNA scission. However, since crystal structure of the zinc finger nuclease has not been obtained in experiments, theoretical studies on interactions of zinc finger nuclease with DNA remain very limited. In this work, firstly, the binding modes of the zinc finger nuclease Spl-Cu(BPA) with B-DNA were predicted using the HadDock program, and then,25ns molecular dynamics simulations were performed. The simulated results reveal that the amino acid residues of Spl interact with the major groove of the DNA nucleotide through a hydrogen bond force, and Cu(BPA) can stay in the minor groove steadily, whose orientation is advantageous for extracting hydrogen from adjacent sugar ring, in order to make the nuclease Cu(BPA) deducing DNA strand scission in some certain regions. The results of these calculations illustrate the introduction of zinc finger protein of DNA detection agent to enhance the copper nuclease DNA cleavage specificity.Thirdly, this section consists of two organic reaction mechanism. The first reaction is that the Aryl azide interact with the Bu2BOTf to generate the N-alkylated aniline. There are many methods to synthesis N-alkylated aniline in experiment. But these methods require that the experimental conditions are more stringent,either at higher temperature or using toxic or corrosive alkylating reagent. In this paper, we use the density functional theory to calculate the reaction mechanism, professor Nagula Shankaraiah proposed, to verify its correctness. All structures of the reactants, transition states, intermediates and products were fully optimized at the B3LYP/6-31+G(d,p) level of theory to ensure we have the corrected results. By the calculating the IRC, we can assure that the transition state is the bridge connecting reactant and expected product. The calculating results show that the azide under the effect of dialkyl triflate, not only be able to better obtain the desired product and the restrictions on the reaction conditions are more flexible, such as reacting at room temperature. The calculated results show that it can provide theoretical support and help on the design of a new reaction. The second reaction is a multi-component synthesis of poly-substituted indolizine. The pyrindine derivative have received great attention as they widely occur as key structural subunits of manybioactive natural products, organic fluorescent materials, and pharmaceutical substances. Multi-component reactions (MCRs) have emerged as powerful and bond-forming efficient tools in organic, combinatorial, and medicinal chemistry. Actually, three-component reactions have been demonstrated as a straightforward approach to the synthesis of indolizines. Mao’s seminar began their investigations by treating pyridine and phenacyl bromide with ethyl glyoxalate through concise and efficient four-component tandem approaches to polysubstituted indolizine derivatives involving the formation of pyridinium ylides and α, β-unsaturated ketones with subsequent1,3-dipolar cycloaddition and aromatization reaction. All structures of reactants, transition states, intermediates and products are optimized in the M05/6-31+G (d, p) level. The investigation not only can reveal the reaction mechanism, but also can provide theoretical significance for the design of subsequent reactions.