O'Toole Amanda S, Miller Stacy, Serra Martin J
Department of Chemistry, Allegheny College, 520 N. Main St., Meadville, PA 16335, USA.
RNA. 2005 Apr;11(4):512-6. doi: 10.1261/rna.7254905.
Thermodynamic parameters are reported for duplex formation in 1 M NaCl for 16 RNA sequences, each containing a core tetramer duplex, GGCC, and a 3' overhang consisting of two bases. The results indicate additional double-helical stability is conferred by the double 3' terminal overhang relative to the single 3' terminal overhang. A nearest-neighbor analysis of the data indicates that the free energy contribution at 37 degrees C of the second base in the double 3' terminal overhang varies from 0 to 0.7 kcal/mol. The second base in the 3' double overhang can contribute nearly the same stability to a duplex as a base pair or a 3' dangling overhang. Stability contribution of a dangling base, two nucleotides removed from the 3' end of a duplex, is dependent upon both the identity of the base as well as that of the dangling base that it neighbors. A second dangling base only increases the stability of the duplex when it is neighboring a 3' purine dangling nucleotide. Furthermore, a second dangling pyrimidine provides a greater contribution to duplex stability than a purine. A nearest-neighbor model was developed to predict the influence of 3' double overhang on the stability of duplex formation. The model improves the prediction of free energy and melting temperature when tested against six sequences with different core duplexes.
报道了16个RNA序列在1M NaCl中形成双链体的热力学参数，每个序列都包含一个核心四聚体双链体GGCC和一个由两个碱基组成的3'突出端。结果表明，相对于单个3'末端突出端，双3'末端突出端赋予了额外的双螺旋稳定性。对数据的最近邻分析表明，双3'末端突出端中第二个碱基在37摄氏度时的自由能贡献在0到0.7千卡/摩尔之间变化。3'双突出端中的第二个碱基对双链体的稳定性贡献几乎与一个碱基对或一个3'悬垂突出端相同。从双链体3'末端去除两个核苷酸的悬垂碱基的稳定性贡献取决于该碱基的身份以及与其相邻的悬垂碱基的身份。只有当第二个悬垂碱基与3'嘌呤悬垂核苷酸相邻时，它才会增加双链体的稳定性。此外，第二个悬垂嘧啶对双链体稳定性的贡献比嘌呤更大。开发了一个最近邻模型来预测3'双突出端对双链体形成稳定性的影响。当针对具有不同核心双链体的六个序列进行测试时，该模型改进了对自由能和熔解温度的预测。
