{"title":"Accurate curve fitting procedure for UV melting analysis of highly thermostable RNA hairpins.","authors":"Junji Kawakami, Yuko Tanaka, Kae Kishimoto","doi":"10.1093/nass/nrp114","DOIUrl":null,"url":null,"abstract":"<p><p>Thermostable RNA hairpins with specific loop sequences are critically important structural elements for proper folding of functional RNAs. Thermodynamic parameters of the structural elements are indispensable for secondary structure prediction. However when RNA folds into highly thermostable hairpin-loop structures, it is difficult to determine the melting temperature and other thermodynamic parameters from the normal UV melting analysis. In this study, we demonstrate a procedure to solve the problem using our software, Jfit. UV absorbance in the higher temperature region above 95 degrees C and the upper baseline were estimated using this analytical procedure. The ideal lines of -RlnK vs. 1/T were generated from the predicted thermodynamic parameters and the solution candidates were compared with the van't Hoff plot generated from the measured melting curve to judge their self-consistency. As a result, our analysis was able to reduce the number of the possible solution and to specify the best set of thermodynamic parameters for the stable hairpin formation.</p>","PeriodicalId":87448,"journal":{"name":"Nucleic acids symposium series (2004)","volume":" 53","pages":"227-8"},"PeriodicalIF":0.0000,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/nass/nrp114","citationCount":"5","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Nucleic acids symposium series (2004)","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/nass/nrp114","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 5
Abstract
Thermostable RNA hairpins with specific loop sequences are critically important structural elements for proper folding of functional RNAs. Thermodynamic parameters of the structural elements are indispensable for secondary structure prediction. However when RNA folds into highly thermostable hairpin-loop structures, it is difficult to determine the melting temperature and other thermodynamic parameters from the normal UV melting analysis. In this study, we demonstrate a procedure to solve the problem using our software, Jfit. UV absorbance in the higher temperature region above 95 degrees C and the upper baseline were estimated using this analytical procedure. The ideal lines of -RlnK vs. 1/T were generated from the predicted thermodynamic parameters and the solution candidates were compared with the van't Hoff plot generated from the measured melting curve to judge their self-consistency. As a result, our analysis was able to reduce the number of the possible solution and to specify the best set of thermodynamic parameters for the stable hairpin formation.
具有特定环序列的耐热性RNA发夹是功能RNA正确折叠的关键结构元件。结构单元的热力学参数是二级结构预测不可缺少的参数。然而,当RNA折叠成高度耐热的发夹环结构时,很难从常规的紫外熔化分析中确定熔化温度和其他热力学参数。在这项研究中,我们展示了一个程序来解决这个问题,使用我们的软件,Jfit。使用此分析程序估计了95℃以上较高温度区域的紫外线吸收度和上基线。根据预测的热力学参数生成-RlnK vs. 1/T的理想曲线,并将候选溶液与实测熔化曲线生成的范霍夫图进行比较,判断其自洽性。结果,我们的分析能够减少可能解的数量,并指定稳定发夹形成的最佳热力学参数集。