FREE-ENERGY OF IMPERFECT NUCLEIC-ACID HELICES .2. SMALL HAIRPIN LOOPS
FREE-ENERGY OF IMPERFECT NUCLEIC-ACID HELICES .2. SMALL HAIRPIN LOOPS
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DOI：
10.1016/0022-2836(73)90096-x
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发表时间：
1973-01-01
影响因子：
5.6
通讯作者：
CROTHERS, DM
中科院分区：
文献类型：
--
作者：
GRALLA, J;CROTHERS, DM
用酶法合成的确定序列的寡核苷酸的物理研究用于定量评估小RNA发夹环和螺旋的稳定性。系列(AP)4G(PC)N(PU)4，N=4，5或6，当N≥5时以单分子发夹螺旋形式存在，而当N≤4时以不完全二聚体螺旋形式存在。在这个尺寸范围内，当未结合核苷酸的尺寸从3个增加到4个到5个时，发夹环变得更有利(热力学上不那么不稳定)。非常小的发夹环特别不稳定；其碱基序列暗示有三个核苷酸的发夹环的分子通常会存在一个五个的环，包括一个断裂的末端碱基对。碱基对和环形成的热力学参数是通过一种方法计算的，该方法不需要使用测量的多核苷酸熔化热。关于寡核苷酸双螺旋的文献数据估计了三个可能的相邻碱基对之间的六种类型的堆积相互作用中的每一种对自由能的贡献。这种方法的优点是利用寡核苷酸的性质来预测小RNA螺旋的稳定性，避免了从高聚物的性质进行长时间的外推。我们提供了随温度变化的自由能表，使人们能够预测许多简单的RNA二级结构的稳定性和热转变温度(适用于~1M-Na+浓度)。作为一个例子，我们将规则应用于tRNASer(酵母)的分离片段(Coutts，1971)，其性质未被用于计算自由能参数。预测了88℃的实验熔化温度，误差为5°。C。
Physical studies of enzymically synthesized oligonucleotides of defined sequence are used to evaluate quantitatively the stability of small RNA hairpin loops and helices. The series (Ap)4G(pC)N(pU)4,N= 4, 5 or 6, exists as monomolecular hairpin helices whenN≥ 5, and as imperfect dimer helices whenN≤ 4. In this size range, hairpin loops become more favorable (less destabilizing thermodynamically) as they increase in size from 3 to 4 to 5 unbonded nucleotides. Very small hairpin loops are particularly destabilizing; molecules whose base sequence would imply a hairpin loop of three nucleotides will generally exist with a loop of five, including a broken terminal base pair.Thermodynamic parameters for base pair and loop formation are calculated by a method which makes unnecessary the use of measured enthalpies of polynucleotide melting. Literature data on oligonucleotide double helices yield estimates of the free energy contribution from each of the six types of stacking interactions between three possible neighboring base pairs. The advantage of this approach is that the properties of oligonucleotides are used in predicting the stability of small RNA helices, avoiding the long extrapolation from the properties of high polymers.We provide Tables of temperature-dependent free energies that allow one to predict the stability and thermal transition temperature of many simple RNA secondary structures (applicable to ~1m-Na+concentration). As an example, we apply the rules to an isolated fragment of tRNASer(yeast) (Coutts, 1971), whose properties were not used in calculating the free-energy parameters. The experimental melting temperature of 88 °C is predicted with an error margin of 5 deg. C.