據(jù)國外媒體報道,，近期,，在英國國家網(wǎng)格計算(computing grid)平臺和美國TeraGrid系統(tǒng)的幫助下,，倫敦大學學院(UCL)科學家有望揭示地球早期生命起源之謎,。
長期以來科學家認為深海熱液噴口可以孕育核糖核酸(RNA)和脫氧核糖核酸(DNA)有機生物分子,，但他們卻不清楚這些生物分子是如何幸存于熱液噴口的高溫高壓環(huán)境中,。倫敦大學學院計算科學中心彼得·科文伊教授和他的同事們使用世界上最先進的計算網(wǎng)格系統(tǒng)實現(xiàn)計算機模擬,，進而探測DNA分子植入分層礦物后的結構性和穩(wěn)定性。迄今為止,，計算機模擬技術很少用于探測理解早期生物分子形成的化學途徑,。
科文伊解釋說，“‘計算網(wǎng)格’是目前科學家能夠很容易地操控的頂尖計算平臺系統(tǒng),，它可以充分地模擬生物分子和礦石系統(tǒng)模型,。”之前的實驗研究表明像DNA這樣的有機分子可以植入到一種叫做分層雙氫氧(LDHs)的礦石中，然而至今卻沒有研究人員展示這種等級的有機分子和原子如何與礦石發(fā)生交互作用，以及有機分子如何進入到礦石分層中,。據(jù)悉,，分層雙氫氧礦石普遍存在于25億年前的地球早期階段。
計算網(wǎng)格系統(tǒng)模擬形成在熱液噴口附近的高溫和高壓環(huán)境,，這將顯示DNA分子植入分層礦石后所表現(xiàn)的穩(wěn)定性,，以及接觸礦石和處于熱降解作用下所形成的保護狀態(tài)?？莆囊练Q,，計算網(wǎng)格系統(tǒng)非常適合于此類研究基礎上，它片刻時間的運算相當于普通電腦數(shù)年的運算能力,，計算網(wǎng)格將不同地理位置空閑的數(shù)千臺計算機進行聯(lián)網(wǎng),，提供執(zhí)行計算密集應用。
科文伊研究小組對地球生命起源的進化路線已研究了多年,，他們使用遺傳基因信息方法試圖復制和生成早期生命,，就像這項研究中的微小有機分子的形成和早期地球環(huán)境的交互作用。目前,，他們的這項研究發(fā)表在3月18日出版的《美國化學學會期刊》上,。
生物谷推薦原始出處：
J. Am. Chem. Soc., ASAP Article 10.1021/ja077679s S0002-7863(07)07679-2
Web Release Date: March 18, 2008
Computer Simulation Study of the Structural Stability and Materials Properties of DNA-Intercalated Layered Double Hydroxides
Mary-Ann Thyveetil, Peter V. Coveney,* H. Chris Greenwell, and James L. Suter
Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
Received October 5, 2007
Abstract:
The intercalation of DNA into layered double hydroxides (LDHs) has various applications, including drug delivery for gene therapy and origins of life studies. The nanoscale dimensions of the interlayer region make the exact conformation of the intercalated DNA difficult to elucidate experimentally. We use molecular dynamics techniques, performed on high performance supercomputing grids, to carry out large-scale simulations of double stranded, linear and plasmid DNA up to 480 base pairs in length intercalated within a magnesium-aluminum LDH. Currently only limited experimental data have been reported for these systems. Our models are found to be in agreement with experimental observations, according to which hydration is a crucial factor in determining the structural stability of DNA. Phosphate backbone groups are found to align with aluminum lattice positions. At elevated temperatures and pressures, relevant to origins of life studies which maintain that the earliest life forms originated around deep ocean hydrothermal vents, the structural stability of LDH-intercalated DNA is substantially enhanced as compared to DNA in bulk water. We also discuss how the materials properties of the LDH are modified due to DNA intercalation.
