Flanking A·T basepairs destabilize the B(∗) conformation of DNA A-tracts.
Flanking A·T basepairs destabilize the B(∗) conformation of DNA A-tracts.
复制标题
侧翼 A·T 碱基对会破坏 DNA A 束的 B(→) 构象的稳定性。
DOI：
10.1016/j.bpj.2015.01.044
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发表时间：
2015
影响因子：
3.4
通讯作者：
Stellwagen,NancyC
中科院分区：
文献类型：
--
作者：
Stellwagen,Earle;Dong,Qian;Stellwagen,NancyC
毛细管电泳已用于表征单价阳离子与 26 碱基对 DNA 寡聚物的相互作用，该寡聚物包含嵌入具有不同碱基对组成的侧翼序列中的 A 束。使用 26 碱基对随机序列寡聚物作为参考；锂离子和四丁基铵 (TBA+) 离子用作探针离子。在含有 <∼100 mM 阳离子的溶液中，A-tract 和随机序列寡聚物的自由溶液迁移率是相同的。在较高的阳离子浓度下，A-tract 低聚物在 TBA+ 中比参考低聚物迁移得更快，在 Li+ 中比参考低聚物迁移得更慢。因此，不同大小的阳离子与 DNA A 束的相互作用差异很大。在 TBA+ 中观察到的增加的迁移率表明，大的疏水性 TBA+ 离子优先被排除在 A-tract 小沟附近，增加了 A-tract 低聚物的有效净电荷并增加了迁移率。相比之下，Li+离子会降低A-tract低聚物的迁移率，因为Li+离子优先定位在狭窄的A-tract小沟中。将 A 束嵌入富含 AT 的侧翼序列中，显着改变了单价阳离子与 B* 构象的优先相互作用。因此，嵌入基因组 DNA 中的 A 束可能会或可能不会优先与单价阳离子相互作用，具体取决于侧翼序列中 A·T 碱基对的相对数量。
Capillary electrophoresis has been used to characterize the interaction of monovalent cations with 26-basepair DNA oligomers containing A-tracts embedded in flanking sequences with different basepair compositions. A 26-basepair random-sequence oligomer was used as the reference; lithium and tetrabutylammonium (TBA+) ions were used as the probe ions. The free solution mobilities of the A-tract and random-sequence oligomers were identical in solutions containing <∼100 mM cation. At higher cation concentrations, the A-tract oligomers migrated faster than the reference oligomer in TBA+and slower than the reference in Li+. Hence, cations of different sizes can interact very differently with DNA A-tracts. The increased mobilities observed in TBA+suggest that the large hydrophobic TBA+ions are preferentially excluded from the vicinity of the A-tract minor groove, increasing the effective net charge of the A-tract oligomers and increasing the mobility. By contrast, Li+ions decrease the mobility of A-tract oligomers because of the preferential localization of Li+ions in the narrow A-tract minor groove. Embedding the A-tracts in AT-rich flanking sequences markedly alters preferential interactions of monovalent cations with the B∗conformation. Hence, A-tracts embedded in genomic DNA may or may not interact preferentially with monovalent cations, depending on the relative number of A·T basepairs in the flanking sequences.