THERMODYNAMIC PARAMETERS FOR LOOP FORMATION IN RNA AND DNA HAIRPIN TETRALOOPS
THERMODYNAMIC PARAMETERS FOR LOOP FORMATION IN RNA AND DNA HAIRPIN TETRALOOPS
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DOI：
10.1093/nar/20.4.819
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发表时间：
1992-02-25
影响因子：
14.9
通讯作者：
TINOCO, I
中科院分区：
文献类型：
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作者：
ANTAO, VP;TINOCO, I
我们测定了15种RNA和19种DNA发夹在1 M NaCl、0.01 M磷酸钠、0.1 mM EDTA和pH 7下的解链温度（T（m））和热力学参数。所有这些发夹都有四个碱基的环，这是16S和23S核糖体RNA中最常见的环大小。RNA发夹在环序列、环闭合碱基对（A. U、C. G或G. C）、茎的碱基序列和茎大小（4或5个碱基对）方面存在差异。DNA发夹在环序列、闭环碱基对（C. G或G. C）和四碱基对茎的碱基序列上存在差异。发夹的热力学性质可以由茎的最近邻相互作用加上来自环的贡献来表示。由此，我们得到了RNA和DNA四环形成的热力学参数。对于我们研究的四环，环形成的自由能（在37 ℃）约为+3千卡/摩尔，这对于RNA或DNA是最常见的。在+1 kcal/mol附近有额外的稳定环，其Δ G度为37，但RNA和DNA的序列不一定相同。闭合碱基对也很重要;从C. G变为G. C会降低RNA和DNA中几个四环的稳定性。这些值将有助于预测RNA和DNA的二级结构。
We determined the melting temperatures (T(m)) and thermodynamic parameters of 15 RNA and 19 DNA hairpins at 1 M NaCl, 0.01 M sodium phosphate, 0.1 mM EDTA, at pH 7. All these hairpins have loops of four bases, the most common loop size in 16S and 23S ribosomal RNAs. The RNA hairpins varied in loop sequence, loop-closing base pair (A.U, C.G, or G.C), base sequence of the stem, and stem size (four or five base pairs). The DNA hairpins varied in loop sequence, loop-closing base pair (C.G, or G.C), and base sequence of the four base-pair stem. Thermodynamic properties of a hairpin may be represented by nearest-neighbor interactions of the stem plus contributions from the loop. Thus, we obtained thermodynamic parameters for the formation of RNA and DNA tetraloops. For the tetraloops we studied, a free energy of loop formation (at 37-degrees-C) of about +3 kcal/mol is most common for either RNA or DNA. There are extra stable loops with DELTA-G-degrees-37 near +1 kcal/mol, but the sequences are not necessarily the same for RNA and DNA. The closing base pair is also important; changing from C.G to G.C lowered the stability of several tetraloops in both RNA and DNA. These values will be useful in predicting RNA and DNA secondary structures.