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Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops

机译：对称2×2核苷酸RNA内环顾闭合的令人惊讶的序列效果

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摘要

GU base pairs are important RNA structural motifs and often close loops. Accurate prediction of RNA structures relies upon understanding the interactions determining structure. The thermodynamics of some 2 × 2 nucleotide internal loops closed by GU pairs are not well understood. Here, several self-complementary oligonucleotide sequences expected to form duplexes with 2 × 2 nucleotide internal loops closed by GU pairs were investigated. Surprisingly, nuclear magnetic resonance revealed that many of the sequences exist in equilibrium between hairpin and duplex conformations. This equilibrium is not observed with loops closed by Watson–Crick pairs. To measure the thermodynamics of some 2 × 2 nucleotide internal loops closed by GU pairs, non-self-complementary sequences that preclude formation of hairpins were designed. The measured thermodynamics indicate that some internal loops closed by GU pairs are unusually unstable. This instability accounts for the observed equilibria between duplex and hairpin conformations. Moreover, it suggests that future three-dimensional structures of loops closed by GU pairs may reveal interactions that unexpectedly destabilize folding.
机译：GU碱基对是重要的RNA结构主题和经常关闭环。对RNA结构的精确预测依赖于理解相互作用确定结构。由GU对封闭的一些2×2核苷酸内部环的热力学不太了解。这里，研究了预期的几种自互补的寡核苷酸序列，其预期形成双链体的双链体通过GU对封闭的2×2核苷酸内环。令人惊讶的是，核磁共振揭示了许多序列存在于发夹和双相构象之间的平衡。没有由Watson-Crick对封闭的环路未观察到这种平衡。为了测量由GU对闭合的约2×2核苷酸内环的热力学，设计了设计妨碍形成发夹的非自互补序列。测量的热力学表明GU对封闭的一些内部环路异常不稳定。这种不稳定占双相和发夹构象之间观察到的均衡。此外，它表明，GU对关闭的未来的循环三维结构可能会揭示意外地稳定折叠的相互作用。

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  • 来源
    《Biochemistry》 |2018年第14期|共11页
  • 作者

    Kyle D. Berger; Scott D. Kennedy; Susan J. Schroeder; Brent M. Znosko; Hongying Sun; David H. Mathews; Douglas H. Turner;

  • 作者单位

    Department of Biochemistry and Biophysics University of Rochester School of Medicine and Dentistry Rochester New York 14642 United States;

    Department of Biochemistry and Biophysics University of Rochester School of Medicine and Dentistry Rochester New York 14642 United States;

    Department of Chemistry University of Oklahoma Norman Oklahoma 73019 United States;

    Department of Chemistry Saint Louis University St. Louis Missouri 63103 United States;

    Department of Biochemistry and Biophysics University of Rochester School of Medicine and Dentistry Rochester New York 14642 United States;

    Department of Biochemistry and Biophysics University of Rochester School of Medicine and Dentistry Rochester New York 14642 United States;

    Center for RNA Biology University of Rochester School of Medicine and Dentistry Rochester New York 14642 United States;

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  • 正文语种 eng
  • 中图分类 生物化学;
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