Hyndman D, Cooper A, Pruzinsky S, Coad D, Mitsuhashi M
Advanced Gene Computing Technologies, Inc., Irvine, CA, USA.
Biotechniques. 1996 Jun;20(6):1090-4, 1096-7. doi: 10.2144/96206pf01.
In the design of oligonucleotide sequences for targeting DNA or RNA sequences, it can be difficult to identify sequences that will hybridize only to the intended target. The term "sequence-specific" or "sequence-nonspecific" is often used to describe the interactions of an oligonucleotide with a mixture of DNA or RNA. Our new computer program, HYBsimulator (formerly OligoProbe DesignStation), creates a set of candidate oligonucleotides from a target gene. For each of the candidate oligonucleotides, a large sequence database is searched for sequences that will hybridize to the oligonucleotide. This is referred to as computer hybridization simulation (CHS). Using the nearest-neighbor model, the HYBsimulator takes into account mismatches in hybridization and calculates the melting temperature (Tm) or free energy for hybridization to all sequences in a database. The specificity of each oligonucleotide is then quantified by the number of genes that may hybridize and the predicted Tms or free energies of hybridization to those genes. The CHS data are used to select oligonucleotides based on their specificity with respect to a database.
在设计用于靶向DNA或RNA序列的寡核苷酸序列时，很难识别仅与预期靶标杂交的序列。术语“序列特异性”或“序列非特异性”常被用于描述寡核苷酸与DNA或RNA混合物的相互作用。我们的新计算机程序HYBsimulator（以前称为OligoProbe DesignStation）从靶基因创建一组候选寡核苷酸。对于每个候选寡核苷酸，在一个大型序列数据库中搜索将与该寡核苷酸杂交的序列。这被称为计算机杂交模拟（CHS）。使用最近邻模型，HYBsimulator考虑杂交中的错配，并计算与数据库中所有序列杂交的解链温度（Tm）或自由能。然后通过可能杂交的基因数量以及与这些基因杂交的预测Tm值或自由能来量化每个寡核苷酸的特异性。CHS数据用于根据寡核苷酸相对于数据库的特异性来选择寡核苷酸。
