Nagel J H A, Flamm C, Hofacker I L, Franke K, de Smit M H, Schuster P, Pleij C W A
Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands.
Nucleic Acids Res. 2006 Jul 19;34(12):3568-76. doi: 10.1093/nar/gkl445. Print 2006.
There is little experimental knowledge on the sequence dependent rate of hairpin formation in RNA. We have therefore designed RNA sequences that can fold into either of two mutually exclusive hairpins and have determined the ratio of folding of the two conformations, using structure probing. This folding ratio reflects their respective folding rates. Changing one of the two loop sequences from a purine- to a pyrimidine-rich loop did increase its folding rate, which corresponds well with similar observations in DNA hairpins. However, neither changing one of the loops from a regular non-GNRA tetra-loop into a stable GNRA tetra-loop, nor increasing the loop size from 4 to 6 nt did affect the folding rate. The folding kinetics of these RNAs have also been simulated with the program 'Kinfold'. These simulations were in agreement with the experimental results if the additional stabilization energies for stable tetra-loops were not taken into account. Despite the high stability of the stable tetra-loops, they apparently do not affect folding kinetics of these RNA hairpins. These results show that it is possible to experimentally determine relative folding rates of hairpins and to use these data to improve the computer-assisted simulation of the folding kinetics of stem-loop structures.
关于RNA中发夹形成的序列依赖性速率，实验知识很少。因此，我们设计了可以折叠成两种互斥发夹之一的RNA序列，并使用结构探测确定了两种构象的折叠比例。这种折叠比例反映了它们各自的折叠速率。将两个环序列之一从富含嘌呤的环变为富含嘧啶的环确实提高了其折叠速率，这与DNA发夹中的类似观察结果非常吻合。然而，将其中一个环从常规的非GNRA四环变为稳定的GNRA四环，或将环大小从4 nt增加到6 nt，均未影响折叠速率。这些RNA的折叠动力学也已用“Kinfold”程序进行了模拟。如果不考虑稳定四环的额外稳定能，这些模拟与实验结果一致。尽管稳定四环具有高稳定性，但它们显然不影响这些RNA发夹的折叠动力学。这些结果表明，可以通过实验确定发夹的相对折叠速率，并利用这些数据改进茎环结构折叠动力学的计算机辅助模拟。
