RNA interactions in the 5′ region of the HIV-1 genome
RNA interactions in the 5′ region of the HIV-1 genome
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DOI：
10.1016/j.jmb.2003.12.010
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发表时间：
2004-02-13
影响因子：
5.6
通讯作者：
Kjems, J
中科院分区：
文献类型：
--
作者：
Damgaard, CK;Andersen, ES;Kjems, J
HIV-1RNA二聚体基因组的未翻译的前导被折叠成一个复杂的结构，在病毒复制周期中发挥着多重和重要的作用。在这里，我们使用生物信息学、酶探针、天然凝胶电泳和紫外光交联实验相结合的方法，研究了HIV-1基因组5‘744个核苷酸中的二级和三级结构元件。我们使用最近开发的RNA折叠算法(Pold)预测了20个不同的HIV-1序列比对的共同二级结构。结合这一分析和生化数据，我们提出了整个744核苷酸片段的二级结构模型，它包含了以前识别的和新的结构元素。特别是，我们的数据为包含Aug Gag起始密码子的区域和上游区域之间的远程相互作用提供了强有力的证据，我们证明这一特征在远亲关系较远的人和动物逆转录病毒中高度保守。为了获得关于三级相互作用的信息，我们应用了分子内紫外光交联策略，并在PBS发夹结构中确定了一种新的三级相互作用。(C)2003爱思唯尔有限公司。保留所有权利。
The untranslated leader of the dimeric HIV-1 RNA genome is folded into a complex structure that plays multiple and essential roles in the viral replication cycle. Here, we have investigated secondary and tertiary structural elements within the 5' 744 nucleotides of the HIV-1 genome using a combination of bioinformatics, enzymatic probing, native gel electrophoresis, and UV-crosslinking experiments. We used a recently developed RNA folding algorithm (Pfold) to predict the common secondary structure of an alignment of 20 divergent HIV-1 sequences. Combining this analysis with biochemical data, we present a secondary structure model for the entire 744 nucleotide fragment, which incorporates previously recognized and novel structural elements. In particular, our data provided strong evidence for a long-distance interaction between the region encompassing the AUG Gag initiation codon and an upstream region and we demonstrate that this feature is highly conserved in distantly related human and animal retroviruses. To obtain information about tertiary interactions we applied an intramolecular UV-crosslinking strategy and identified a novel tertiary interaction within the PBS hairpin structure. (C) 2003 Elsevier Ltd. All rights reserved.