| ¡¡ | Chinese Journal of Computers Full Text |
| Title | Research on Nucleic Acid Sequence Design Methods for DNA Computing |
| Authors | ZHANG Kai1) GENG Xiu-Tang2) XIAO Jian-Hua3) ZHAO Dong-Ming1) |
| Address | 1)(School of Electronics Engineering and Computer Science, Peking University, Beijing 100871) 2)(China North Industries Group Corporation, Xianyang, Shaanxi 712099) 3)(Research Center of Logistics, Nankai University, Tianjin 300071) |
| Year | 2008 |
| Issue | No.12(2149¡ª2154) |
| Abstract & Background | Abstract 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 sequence 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. Keywords DNA computing; free energy; Hamming distance; DNA sequence design |