ＤＮＡ計(jì)算中編碼序列的優(yōu)化設(shè)計(jì)方案

摘要：提出了一種優(yōu)化設(shè)計(jì)方案。該方案的各項(xiàng)評價(jià)指標(biāo)均優(yōu)于根據(jù)以往文獻(xiàn)提供的方法所能得到的最好結(jié)果。尤其是所提出的海明距離測度方法，進(jìn)一步保證了特異性雜交產(chǎn)生的自由能遠(yuǎn)大于非特異性雜交所產(chǎn)生的自由能，便于進(jìn)行DNA編碼序列的設(shè)計(jì)與選擇，為可控的DNA計(jì)算提供可靠有效的編碼序列。

關(guān)鍵詞：DNA計(jì)算;編碼序列;熱力學(xué)參數(shù);物理特性

中圖分類號：TP301．5文獻(xiàn)標(biāo)志碼：A

文章編號：1001－3695(2007)07－0195－04

DNA(Deoxyribo Nucleic Acid)計(jì)算中的序列編碼問題可簡單地定義為:系統(tǒng)地將一個(gè)算法問題的實(shí)例映射為特殊的DNA分子序列。這樣的DNA分子序列應(yīng)能夠確保隨后進(jìn)行的生化反應(yīng)不出現(xiàn)任何錯(cuò)誤，而且反應(yīng)產(chǎn)物中需包含有足夠多的、穩(wěn)定可靠的、能被成功提取的原始算例的解[1]。只有滿足上述兩個(gè)條件的DNA序列才能稱為好的DNA編碼序列。由此可見，編碼問題幾乎涵蓋了DNA計(jì)算研究領(lǐng)域內(nèi)所有的重點(diǎn)和難點(diǎn)。事實(shí)上，為了實(shí)現(xiàn)理想的生化反應(yīng)以及解的檢測，DNA計(jì)算的每一成功算例均離不開設(shè)計(jì)或選擇合適的DNA序列。所以，自DNA計(jì)算誕生以來編碼問題就一直是該研究領(lǐng)域的核心問題之一。隨著研究的進(jìn)一步深入，其重要性愈加突顯，因?yàn)樗谝欢ǔ潭壬蠜Q定著DNA計(jì)算模式的未來。

4結(jié)束語

在DNA計(jì)算中，根據(jù)相關(guān)約束條件建立一套通用的DNA編碼序列設(shè)計(jì)方案是一件非常困難的事情。一些約束條件之間存在著相互制約，并且不同的約束條件所要求的生物實(shí)驗(yàn)條件和方法不同。由于生化反應(yīng)受多種條件的影響，在分子生物學(xué)中，微小的條件變化可能不會影響整體實(shí)驗(yàn)效果及定性分析，但對于DNA計(jì)算來說，這種變化卻可能是致命的。選擇標(biāo)準(zhǔn)時(shí)應(yīng)特別小心。可能的解決方案之一是建立一套多目標(biāo)評價(jià)體系，根據(jù)所要解決實(shí)際問題的需求，通過賦予不同目標(biāo)函數(shù)不同的權(quán)值來實(shí)現(xiàn)針對具體問題的DNA計(jì)算的編碼序列的優(yōu)化設(shè)計(jì)與選擇。另外，從本質(zhì)上來講，DNA計(jì)算是以犧牲空間來換取時(shí)間的一種計(jì)算模式。當(dāng)計(jì)算規(guī)模比較大時(shí)，所需DNA編碼序列的長度和數(shù)目隨之增長。在進(jìn)行編碼序列設(shè)計(jì)與選擇時(shí)，計(jì)算規(guī)模就會隨之增長，為節(jié)省計(jì)算機(jī)處理時(shí)間，還需針對具體約束條件(如ΔG)進(jìn)行算法優(yōu)化。

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