通过引物设计和提高退火温度提高实时定量PCR检测microRNA的特异性

目的：了解因某些microRNA (miRNA) 家族成员序列相似，以及同一种成熟miRNA的长度不均一对PCR定量检测结果的影响，寻找区分相似miRNA成员和准确定量的方法和条件。方法: 采用RNA加尾和引物延伸实时定量RT-PCR法，设计不同位置错配的引物，以克隆到质粒中的全长成熟miRNA为模板，比较在不同退火温度下各种错配引物与完全匹配引物在扩增miRNA上的效率差异，并根据由此得出的经验设计let-7家族成员引物，以克隆的成熟miRNA为模板，检测其在不同退火温度下区分相似家族成员的能力。此外，设计了10组3′末端碱基位置不同的特异引物，比较了它们在检测小鼠大脑miRNA表达水平上的差异。结果：提高退火温度12 ℃~14 ℃将最大限度增加特异性而不降低敏感性，将引物的3′ 末端置于差异碱基或其附近可以有效区分相似miRNA序列，将引物3′ 末端置于miRNA第18~20个碱基，可避免漏检较短的成熟miRNA，使定量更真实准确。结论：精心设计引物并提高退火温度可提高实时定量PCR检测microRNA的特异性和准确性。

Increasing specificity of real time PCR to detect microRNA through primer design and annealing temperature increase

Objective: To investigate the non-specific and inaccurate amplification in cases of highly similar sequences among family members and the length heterogeneity of mature microRNA ( miRNA) ,and find a condition that discriminates maximally among similar miRNA family members and detects the accurate expression level of miRNAs. Methods: Primers with their mismatches and/or 3' end at different positions were designed. Amplification efficiencies were compared using matched and various mismatched primers by RNA-tailing and primer-extension RT-PCR at different annealing temperatures. Expression levels of several miRNAs in mouse brain were compared using miRNA specific primers with different termini. Results: Raising annealing temperatures 12℃-14℃above the T_m of the primers maximally increased amplification specificity without sacrificing sensitivity. Primers designed with their termini on or near variant positions could efficiently discriminate between miRNA isoforms. Using primers that terminated before the end of the mature miRNA did not miss the detection of shorter mature miRNA and provided accurate expression levels. Conclusion: Careful primer design and higher annealing temperature can increase specificity and accuracy of real time PCR miRNA detection.