Tandem GA Residues on Opposite Sides of the Loop in Molecular Beacon-like DNA Hairpins Compact the Loop and Increase Hairpin Stability
Tandem GA Residues on Opposite Sides of the Loop in Molecular Beacon-like DNA Hairpins Compact the Loop and Increase Hairpin Stability
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DOI：
10.1021/bi201263n
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发表时间：
2011-10-25
期刊：
影响因子：
2.9
通讯作者：
Stellwagen, Nancy C.
中科院分区：
文献类型：
--
作者：
Chang, Chun Yaw (Joel);Stellwagen, Nancy C.
用毛细管电泳法测定了两个互补的26-核苷酸寡聚体形成的发夹结构的自由溶液电泳迁移率和热稳定性。预测寡聚物形成具有5 bp茎和环中的16个核苷酸的分子信标样发夹。一个发夹，称为发夹2（hp 2），迁移与一个相对较快的自由溶液的流动性，并表现出合理的熔融温度，以及预测流行的结构预测程序Mfold。它的互补物，称为发夹1（hp 1），以较慢的自由溶液迁移率迁移，并仅在含有>= 200 mM Na+的溶液中形成稳定的发夹。观察到hp 1的熔解温度比hp 2的熔解温度低18 ℃，比Mfold预测的熔解温度低20 ℃。hp 2的更高的热稳定性是由于在环的相对侧上存在串联GA残基。如果hp 1环中相应的TC残基被串联GA残基取代，则修饰的发夹的解链温度接近于hp 2中观察到的解链温度。消除hp 2环中的串联GA残基显著降低hp 2的热稳定性。如果环被16个胸腺嘧啶残基的环所取代，则T环发夹的自由溶液迁移率和热稳定性与hp 1所观察到的相同。因此，hp 1的环似乎是相对非结构化的，几乎没有碱基-碱基堆积相互作用。hp 2环相对两侧的串联GA残基之间的相互作用似乎使环紧凑并增加发夹稳定性。
The free solution electrophoretic mobilities and thermal stabilities of hairpins formed by two complementary 26-nucleotide oligomers have been measured by capillary electrophoresis. The oligomers are predicted to form molecular beacon-like hairpins with 5 bp stems and 16 nucleotides in the loop. One hairpin, called hairpin2 (hp2), migrates with a relatively fast free solution mobility and exhibits melting temperatures that are reasonably well predicted by the popular structure-prediction program Mfold. Its complement, called hairpin1 (hp1), migrates with a slower free solution mobility and forms a stable hairpin only in solutions containing >= 200 mM Na+ The melting temperatures observed for hp1 are similar to 18 degrees C lower than those observed for hp2 and similar to 20 degrees C lower than those predicted by Mfold. The greater thermal stability of hp2 is due to the presence of tandem GA residues on opposite sides of the loop. If the corresponding TC residues in the hp1 loop are replaced by tandem GA residues, the melting temperatures of the modified hairpin are close to those observed for hp2. Eliminating the tandem GA residues in the hp2 loop significantly decreases the thermal stability of hp2. If the loops are replaced by a loop of 16 thymine residues, the free solution mobilities and thermal stabilities of the T-loop hairpin are equal to those observed for hp1. Hence, the loop of hp1 appears to be relatively unstructured, with few base-base stacking interactions. Interactions between tandem GA residues on opposite sides of the hp2 loop appear to compact the loop and increase hairpin stability.