Design of nucleic acid sequences for DNA computing based on a thermodynamic approach.
Design of nucleic acid sequences for DNA computing based on a thermodynamic approach.
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DOI：
10.1093/nar/gki235
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发表时间：
2005
影响因子：
14.9
通讯作者：
Ohuchi A
中科院分区：
文献类型：
--
作者：
Tanaka F;Kameda A;Yamamoto M;Ohuchi A
我们已经开发了一种用于设计多个核酸序列的算法，所述多个核酸序列在序列与其互补序列之间具有均匀的解链温度，并且基于最小自由能（ΔGmin）彼此不非特异性杂交。满足这些约束的序列可以用于计算、各种工程应用，如微阵列和纳米制造。我们的算法是一个随机生成和测试算法：它随机生成一个候选序列，并测试该序列是否满足约束。该算法的新奇在于滤波方法使用贪婪搜索来计算ΔGmin。这在计算ΔGmin之前有效地排除了不适当的序列，从而与没有滤波的算法相比，大大减少了计算时间。计算机实验结果表明，贪婪搜索优于传统的基于汉明距离的方法。此外，体外实验结果表明，126个序列的实验自由能（ΔGexp）与ΔGmin（|R| 0.90），而不是汉明距离（|R| = 0.80）。这些结果验证了热力学方法的合理性。我们实现了我们的算法在一个图形用户界面为基础的程序用Java编写的。
We have developed an algorithm for designing multiple sequences of nucleic acids that have a uniform melting temperature between the sequence and its complement and that do not hybridize non-specifically with each other based on the minimum free energy (ΔGmin). Sequences that satisfy these constraints can be utilized in computations, various engineering applications such as microarrays, and nano-fabrications. Our algorithm is a random generate-and-test algorithm: it generates a candidate sequence randomly and tests whether the sequence satisfies the constraints. The novelty of our algorithm is that the filtering method uses a greedy search to calculate ΔGmin. This effectively excludes inappropriate sequences before ΔGmin is calculated, thereby reducing computation time drastically when compared with an algorithm without the filtering. Experimental results in silico showed the superiority of the greedy search over the traditional approach based on the hamming distance. In addition, experimental results in vitro demonstrated that the experimental free energy (ΔGexp) of 126 sequences correlated well with ΔGmin (|R| = 0.90) than with the hamming distance (|R| = 0.80). These results validate the rationality of a thermodynamic approach. We implemented our algorithm in a graphic user interface-based program written in Java.
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影响因子：
14.9
作者：
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通讯作者：
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作者：
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