A mathematical model and a computerized simulation of PCR using complex templates
A mathematical model and a computerized simulation of PCR using complex templates
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DOI：
10.1093/nar/24.18.3538
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发表时间：
1996-09-15
影响因子：
14.9
通讯作者：
Levy, AA
中科院分区：
文献类型：
--
作者：
Rubin, E;Levy, AA
采用数学模型和计算机模拟方法研究PCR特异性。该模型描述了通过随机引物-模板相互作用形成的非靶向PCR产物的发生率。PCR模拟用引物对扫描DNA序列数据库。根据模型预测，在典型的反应条件下，具有复杂模板的PCR应该很少产生非靶向产物。这是令人惊讶的，因为这样的产物通常是在严格优化的条件下在真正的PCR中扩增的。通过比较模型预测和模拟结果，研究了这种“PCR悖论”的原因。我们发现真实基因组序列的随机性偏差不能解释真实PCR中频繁出现的非靶向产物。对“PCR悖论”最可能的解释是PCR对错配的相对较高的耐受性。该模型还预测错配容忍度对非目标产物数量的影响最大，其次是引物长度、模板尺寸和产物尺寸限制。该模型和模拟可用于PCR研究、引物设计和检测DNA的独特性和随机性。
A mathematical model and a computer simulation were used to study PCR specificity. The model describes the occurrences of non-targeted PCR products formed through random primer-template interactions. The PCR simulation scans DNA sequence databases with primers pairs. According to the model prediction, PCR with complex templates should rarely yield non-targeted products under typical reaction conditions. This is surprising as such products are often amplified in real PCR under conditions optimized for stringency. The causes for this 'PCR paradox' were investigated by comparing the model predictions with simulation results. We found that deviations from randomness in sequences from real genomes could not explain the frequent occurrence of non-targeted products in real PCR. The most likely explanation to the 'PCR paradox' is a relatively high tolerance of PCR to mismatches. The model also predicts that mismatch tolerance has the strongest effect on the number of non-targeted products, followed by primer length, template size and product size limit. The model and the simulation can be utilized for PCR studies, primer design and probing DNA uniqueness and randomness.