運用限制酶進行基因表現分析之生物資訊解決方案

Bioinformatic solution for the restriction analysis of gene expression

鍾希和(Hsih-Ho Chung)

指導教授 ： 張震東

共同指導教授 ： 林文昌(Wen-Chang Lin)

國立臺灣大學/生命科學院/生化科學研究所/碩士(2004年)

https://doi.org/10.6342/NTU.2004.01651

摘要

在以限制酶分析基因家族表現的實驗中，研究者必須先設計引子去放大目標基因家族。而之前我們實驗室的研究目標是人類的酪胺酸磷酸激活酶(tyrosine kinase)，當時設計引子的方法是：已知在酪胺酸磷酸激活酶的催化功能區塊中，DFG與DVW是這個家族中絕大部分基因都具有的兩個區域，於是便可以把它們轉回相對應的基因密碼，再與當時已知的所有人類的酪胺酸磷酸激活酶作比對並延伸至適合的長度，而這兩段序列就可以拿來作為放大酪胺酸磷酸激活酶基因家族的引子。
現在由於有了功能區塊資料庫﹝Conserved domain database﹞以及其他生物資訊方面的工具及資料，我們可把這種設計引子的程序自動化，使研究者只需執行程式，就可得到適合其目標基因家族的引子。除此之外，在以限制酶切聚合酶鏈反應產物後，要做片段大小的比對工作，也可由這個程式來進行，程式提供的這兩個功能，摒除了人工設計引子及比對片段大小時可能發生的錯誤，因而增進了基因表現分析實驗的精確性與可信度。

關鍵字

基因表現 ； 生物資訊

並列摘要

Many gene families play important roles in medical studies. For example, most of the protein tyrosine kinase (PTK) genes are proto-oncogenes. They are involved in the cell growth, differentiation, development, apoptosis and signal transduction pathways. There are more than ninety different tyrosine kinase genes that have been identified, and cross-talks between different PTKs have been reported. Therefore, it is essential to examine the overall expression profile of PTK family, as well as other gene families.
In performing the experiment of restriction analysis of gene expression (RAGE), researchers should design the degenerate primers to amplify the genes of interest. Previously in our laboratory, the genes of interest are the tyrosine kinase family. The previous method for finding the suitable degenerate primers is based on translating the conserved motif of DFG and DVW into their degenerate genetic codons. Then researchers can use them as the PCR primer to amplify the tyrosine kinase family.
With the release of Conserved Domain Database (CDD) from NCBI and newly developed tools in bioinformatics, we can now automate this procedure. And for the efficacy and reproducibility of computer program, researchers can choose any family of interest and follow the simple steps in our program to do the degenerate primer design and fragments matching after PCR products being cut by restriction enzymes in RAGE experiment. The program is valuable for the automatic process of primer design and restriction analysis. By running this program, researchers can avoid the possible errors resulted from manual design and analysis.

並列關鍵字

bioinformatics ； gene expression

參考文獻

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