pKa shifting in double-stranded RNA is highly dependent upon nearest neighbors and bulge positioning.
pKa shifting in double-stranded RNA is highly dependent upon nearest neighbors and bulge positioning.
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双链 RNA 中的 pKa 变化高度依赖于最近邻居和凸出位置。
DOI：
10.1021/bi400768q
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发表时间：
2013
期刊：
影响因子：
2.9
通讯作者：
P. Bevilacqua
中科院分区：
文献类型：
--
作者：
Jennifer L. Wilcox;P. Bevilacqua
RNA中pKa的改变对于许多生物过程是重要的;然而，负责改变的驱动力还没有被很好地理解。在这里，我们确定如何质子化碱基周围的结构环境影响pKa的双链RNA（dsRNA）的转变。用（31）P NMR测定了不同序列和结构环境下A（+）·C碱基对中腺嘌呤的pKa值。我们发现了一个显着的依赖pKa的最近的邻居和附近的凸起的位置上的碱基配对强度。增加最近邻碱基配对强度使A（+）·C碱基对中腺嘌呤的pKa值从6.5增加到8.1，增加了1.6个pKa单位，远高于中性。在距离质子化的A（+）·C碱基对两个碱基对处增加一个凸起，使pKa仅比完全碱基配对的发夹小约0.5个单位;然而，将凸起定位在距离A（+）·C碱基对仅一个碱基对处，会阻止质子化碱基对以及几个侧翼碱基对的形成。将在25 °C和100 mM KCl下收集的数据与生物温度和Mg（2+）浓度进行比较，发现只有轻微的pKa变化，表明生物系统中相似的序列背景在生物pH下有可能被质子化。我们提出了一个通用模型，以帮助确定质子化碱基在各种dsRNA介导的过程中可能发挥的作用，包括阿达尔编辑，miRNA加工，程序性核糖体移码和核酶中的一般酸碱催化。
Shifting of pKa's in RNA is important for many biological processes; however, the driving forces responsible for shifting are not well understood. Herein, we determine how structural environments surrounding protonated bases affect pKa shifting in double-stranded RNA (dsRNA). Using (31)P NMR, we determined the pKa of the adenine in an A(+)·C base pair in various sequence and structural environments. We found a significant dependence of pKa on the base pairing strength of nearest neighbors and the location of a nearby bulge. Increasing nearest neighbor base pairing strength shifted the pKa of the adenine in an A(+)·C base pair higher by an additional 1.6 pKa units, from 6.5 to 8.1, which is well above neutrality. The addition of a bulge two base pairs away from a protonated A(+)·C base pair shifted the pKa by only ~0.5 units less than a perfectly base paired hairpin; however, positioning the bulge just one base pair away from the A(+)·C base pair prohibited formation of the protonated base pair as well as several flanking base pairs. Comparison of data collected at 25 °C and 100 mM KCl to biological temperature and Mg(2+) concentration revealed only slight pKa changes, suggesting that similar sequence contexts in biological systems have the potential to be protonated at biological pH. We present a general model to aid in the determination of the roles protonated bases may play in various dsRNA-mediated processes including ADAR editing, miRNA processing, programmed ribosomal frameshifting, and general acid-base catalysis in ribozymes.
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影响因子：
4.5
作者：
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通讯作者：
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通讯作者：
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