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首页> 外文期刊>Biochemistry >Thermodynamic parameters for an expanded nearest-neighbor model for the formation of RNA duplexes with single nucleotide bulges.
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Thermodynamic parameters for an expanded nearest-neighbor model for the formation of RNA duplexes with single nucleotide bulges.

机译：具有单核苷酸凸起形成RNA双链体的扩展最近邻模型的热力学参数。

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Thirty-four RNA duplexes containing single nucleotide bulges were optically melted, and the thermodynamic parameters deltaH degrees, deltaS degrees, deltaG degrees (37), and T(M) for each sequence were determined. Data from this study were combined with data from previous thermodynamic data [Longfellow, C. E., Kierzek, R., and Turner, D. H. (1990) Biochemistry 29, 278-85] to develop a model that will more accurately predict the free energy of an RNA duplex containing a single nucleotide bulge. Differences between purine and pyrimidine bulges as well as differences between Group I duplexes, those in which the bulge is not identical to either neighboring nucleotide, and Group II duplexes, those in which the bulge is identical to at least one neighboring nucleotide, were considered. The length of the duplex, non-nearest-neighbor effects, and bulge location were also examined. A model was developed which divides sequences into two groups: those with pyrimidine bulges and those with purine bulges. The proposed model for pyrimidine bulges predicts deltaG degrees (37,bulge) = 3.9 kcal/mol + 0.10deltaG degrees (37,nn) + beta, while the model for purine bulges predicts deltaG degrees (37,bulge) = 3.3 kcal/mol - 0.30deltaG degrees (37,nn) + beta, where beta has a value of 0.0 and -0.8 kcal/mol for Group I and Group II sequences, respectively, and deltaG degrees (37,nn) is the nearest-neighbor free energy of the base pairs surrounding the bulge. The conformation of bulge loops present in rRNA was examined. Three distinct families of structures were identified. The bulge loop was either extrahelical, intercalated, or in a "side-step" conformation.
机译：含有单核苷酸凸起的三十四个RNA双链体是光学熔化的，并且测定热力学参数Dertah度，δ度量，Δδ度（37）和T（m）的每种序列。本研究的数据与来自先前热力学数据的数据相结合[朗福尔，CE，Kierzek，R.和特纳，DH（1990）生物化学29,278-85]开发一个更准确地预测自由能的模型RNA双链体含有单个核苷酸凸起。嘌呤和嘧啶凸起的差异以及I基团的双链体之间的差异，凸起与相邻核苷酸的那些与相邻的核苷酸和II族双链体相同的那些，其中凸起与至少一个相邻核苷酸相同的那些。还检查了双工，非最近邻效应和凸起位置的长度。开发了一种模型，其将序列分成两组：嘧啶凸起的那些和嘌呤凸起的那些。嘧啶凸起的所提出的模型预测ΔTreg度（37，凸起）= 3.9kcal / mol + 0.10deltag度（37，Nn）+β，而嘌呤凸起的模型预测ΔTreg度（37，凸起）= 3.3 kcal / mol - 0.30deltag度（37，Nn）+β，其中β具有0.0和-0.8kcal / mol的I和-2 kcal / mol，分别和序列度（37，nn）是最接近的自由能围墙周围的底部对。检查RRNA中存在的凸起环的构象。确定了三个不同的结构系列。凸起环是呈纤维形式的，嵌入的或“侧面”构象。

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