Demonstration of a word design strategy for DNA computing on surfaces
Demonstration of a word design strategy for DNA computing on surfaces
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DOI：
10.1093/nar/25.23.4748
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发表时间：
1997-12-01
影响因子：
14.9
通讯作者：
Corn, RM
中科院分区：
文献类型：
--
作者：
Frutos, AG;Liu, QH;Corn, RM
本文提出了一种利用短寡核苷酸（16聚体）“DNA字”的连接集在表面上进行DNA计算的策略。16聚体字的格式为5 ′-FFFFvvvvvvFFFF-3 ′，其中4-8位数据存储在8个可变（“v”）碱基位置中，其余的固定（“F”）碱基位置用作字标签。使用模板和图谱策略，识别出一组108个8聚体，其中每个8聚体与该集合所有其他成员的互补序列（4 bm互补序列）具有至少4个碱基错配，以用作可变碱基序列集。此外，4和12个单词标签的集合形式为ABCD.分别鉴定了8bm和6 bm互补的DCBA。选择具有50%的G/C含量的16聚体，以使完全匹配的杂交DNA双链体的热力学稳定性相似;使用简单的成对相加法来估计完全匹配和错配杂交热力学。提出了一系列的初步实验，使用小阵列的18聚体连接到化学修饰的金表面和荧光标记的互补研究的杂交吸附和酶操作的寡核苷酸。
A strategy for DNA Computing on surfaces using linked sets of 'DNA words' that are short oligonucleotide's (16mers) is proposed. The 16mer words have the format 5'-FFFFvvvvvvvvFFFF-3' in which 4-8 bits of data are stored in 8 variable ('v') base locations, and the remaining fixed ('F') base locations are used as a word label. Using a template and map strategy, a set of 108 8mers each of which possesses at least a 4 base mismatch with the complements to all the other members of the set (4bm complements) are identified for use as a variable base sequence set, In addition, sets of 4 and 12 word labels of the form ABCD....DCBA that are respectively 8bm and 6bm complements with each other are identified. The 16mers are chosen to have a G/C content of 50% in order to make the thermodynamic stability of the perfectly matched hybridized DNA duplexes similar; a simple pairwise additive method is used to estimate the perfect match and mismatch hybridization thermodynamics. A series of preliminary experiments are presented that use small arrays of 18mers attached to chemically modified gold surfaces and fluorescently labeled complements to study the hybridization adsorption and enzymatic manipulation of the oligonucleotides.