DNA计算中核酸序列设计方法比较研究(英文)  

Research on Nucleic Acid Sequence Design Methods for DNA Computing

作　　者：张凯[1] 耿修堂[2] 肖建华[3] 赵东明[1] 

机构地区：[1]北京大学信息科学技术学院,北京100871 [2]中国兵器工业集团公司,陕西咸阳712099 [3]南开大学现代物流研究中心,天津300071

出　　处：《计算机学报》2008年第12期2149-2154,共6页Chinese Journal of Computers

基　　金：国家自然科学基金(60533010,30670540,60874036,60503002);国家“八六三”高技术研究发展计划项目基金(2006AA01Z104);中国教育部博士点基金(20070001020);中国博士后科学基金(20060400344)资助

摘　　要：DNA计算是将现实问题进行编码,映射到DNA分子上,然后通过分子生物实验产生出代表问题解的DNA分子,最后通过检测技术提取出该DNA分子.高质量的DNA编码可以尽可能避免或减少计算过程中出现的错误,并使检测阶段易于提取出代表问题解的DNA分子.文中对基于汉明距离和基于自由能的DNA核酸编码方法进行研究,分析了两类方法的约束条件对DNA编码质量的影响,比较了两类方法排除非特异性杂交的完备性和计算量,进一步分析了两类方法编码DNA序列的效率.通过分析和比较得到,两类DNA计算编码方法都能有效地限制DNA分子间的非特异性杂交,其中基于汉明距离的DNA编码方法的计算量比较小,但是它仅能近似地估计DNA分子间杂交的热力学稳定性,不能完全替代最小自由能的编码方法.在满足DNA计算试验精度要求的条件下,采用基于汉明距离的DNA编码设计方法不仅能有效地的挑选出特异性杂交和非特异性杂交的DNA序列,还能有效地减少计算量,从而提高DNA序列设计的效率.DNA computing maps the instances of a reality problem onto specific nucleic acid molecules and protocols so that the result contains the answers to the problem＇s instances to enable successful extraction. Good DNA sequences prevent unwanted hybridization errors during the computation and enable easy retrieval the answers in the extraction phase. At first, the paper introduces two typical nucleic acid sequence methods, free energy based method and Hamming distance based method, and analyzes the influence of constraints on the quality of DNA sequences. In addition, the paper has compared the integrity and computational cost of two methods for excluding the non-specific hybridization sequence. At last, the paper analyzes the efficiency of two nucleic acid sequence design methods. Through the comparison we can see that the Hamming distance based DNA sequence design method can only approximately estimate the thermodynamic stability of DNA hybridization, and can not be a perfect substitute for the minimum free energy method. Further analysis shows that when only consider the free energy of Watson-crick base pairs, the calculation of free energy will be equal to the Hamming distance method. So, if the precision satisfied the requirement of experiment, Hamming distance based DNA seouence design method, not only can effectively distinguish between specific and non-specific hybridization, and effectively reduce the amount of calculation, improve the efficiency of the DNA sequence designing.

关 键 词：DNA计算 自由能 汉明距离 DNA序列设计 

分 类 号：TP301[自动化与计算机技术—计算机系统结构]