Siegmund Karsten, Ahlborn Carolin, Richert Clemens
Institute for Organic Chemistry, University of Karlsruhe, Karlsruhe, Germany.
Nucleosides Nucleotides Nucleic Acids. 2008 Apr;27(4):376-88. doi: 10.1080/15257770801944147.
Incomplete binding, saturation, and cross-hybridization between partially complementary strands complicate the parallel detection of nucleic acids via DNA microarrays. Treating the competing equilibria governing binding to microarrays requires computational tools. We have developed the web-based program ChipCheckII that calculates total hybridization matrices for target strands interacting with probes on small DNA microarrays. The program can be used to compute the extent of cross-hybridization and other phenomena affecting fidelity of detection based on sequences, quantities of strands, and hybridization conditions as inputs. Enthalpy and entropy of duplex formation are generated locally with UNAfold, including those for complexes that are partially matched. Simulated binding versus temperature curves for portions of a commercial genome chip demonstrate the extent to which cross-hybridization can complicate DNA detection. ChipCheckII is expected to aid nucleic acid chemists in developing high fidelity DNA microarrays.
部分互补链之间的不完全结合、饱和以及交叉杂交使得通过DNA微阵列对核酸进行平行检测变得复杂。处理与微阵列结合相关的竞争平衡需要计算工具。我们开发了基于网络的程序ChipCheckII，它可以计算与小型DNA微阵列上的探针相互作用的目标链的总杂交矩阵。该程序可用于根据作为输入的序列、链的数量和杂交条件，计算交叉杂交的程度以及影响检测保真度的其他现象。双链形成的焓和熵由UNAfold局部生成，包括部分匹配的复合物的焓和熵。商业基因组芯片部分区域的模拟结合与温度曲线表明，交叉杂交会使DNA检测变得多么复杂。预计ChipCheckII将有助于核酸化学家开发高保真DNA微阵列。
