Xia T, SantaLucia J, Burkard M E, Kierzek R, Schroeder S J, Jiao X, Cox C, Turner D H
Department of Chemistry, University of Rochester, New York 14627-0216, USA.
Biochemistry. 1998 Oct 20;37(42):14719-35. doi: 10.1021/bi9809425.
Improved thermodynamic parameters for prediction of RNA duplex formation are derived from optical melting studies of 90 oligoribonucleotide duplexes containing only Watson-Crick base pairs. To test end or base composition effects, new sets of duplexes are included that have identical nearest neighbors, but different base compositions and therefore different ends. Duplexes with terminal GC pairs are more stable than duplexes with the same nearest neighbors but terminal AU pairs. Penalizing terminal AU base pairs by 0.45 kcal/mol relative to terminal GC base pairs significantly improves predictions of DeltaG degrees37 from a nearest-neighbor model. A physical model is suggested in which the differential treatment of AU and GC ends accounts for the dependence of the total number of Watson-Crick hydrogen bonds on the base composition of a duplex. On average, the new parameters predict DeltaG degrees37, DeltaH degrees, DeltaS degrees, and TM within 3.2%, 6.0%, 6.8%, and 1.3 degreesC, respectively. These predictions are within the limit of the model, based on experimental results for duplexes predicted to have identical thermodynamic parameters.
用于预测RNA双链体形成的改进热力学参数源自对90个仅含沃森-克里克碱基对的寡核糖核苷酸双链体的光学熔解研究。为了测试末端或碱基组成的影响，纳入了新的双链体集合，这些双链体具有相同的紧邻碱基，但碱基组成不同，因此末端也不同。具有末端GC对的双链体比具有相同紧邻碱基但末端为AU对的双链体更稳定。相对于末端GC对，将末端AU碱基对的能量罚分设为0.45千卡/摩尔，可显著改善从紧邻碱基模型对ΔG°37的预测。提出了一个物理模型，其中对AU和GC末端的不同处理解释了沃森-克里克氢键总数对双链体碱基组成的依赖性。新参数平均预测的ΔG°37、ΔH°、ΔS°和熔解温度（TM）分别在3.2%、6.0%、6.8%和1.3摄氏度的范围内。基于对预测具有相同热力学参数的双链体的实验结果，这些预测在模型的限度内。
