Le S Y, Chen J H, Maizel J V
Laboratory of Mathematical Biology, National Cancer Institute, Frederick, MD 21701.
Nucleic Acids Res. 1989 Aug 11;17(15):6143-52. doi: 10.1093/nar/17.15.6143.
RNA stem-loop structures situated just 3' to the frameshift sites of the retroviral gag-pol or gag-pro and pro-pol regions may make important contributions to frame-shifting in retroviruses. In this study, the thermodynamic stability and statistical significance of such secondary structural features relative to others in the sequence have been assessed using a newly developed method that combines calculations of the lowest free energy of formation of RNA secondary structures and the Monte Carlo simulations. Our results show that stem-loop structures situated just 3' to the frameshift sites are both highly stable and statistically significant relative to others in the gag-pol or gag-pro and pro-pol junction domains (both 300 nucleotides upstream and downstream from the possible frameshift sites are included) of Rous sarcoma virus (RSV), human immunodeficiency virus (HIV-1), bovine leukemia virus (BLV), human T-cell leukemia virus type II (HTLV-II), and mouse mammary tumor virus (MMTV). No other more stable, or significant folding regions are predicted in these domains.
位于逆转录病毒gag-pol或gag-pro以及pro-pol区域移码位点下游3'端的RNA茎环结构可能对逆转录病毒的移码过程起到重要作用。在本研究中，使用一种新开发的方法评估了此类二级结构特征相对于序列中其他结构的热力学稳定性和统计学意义，该方法结合了RNA二级结构形成的最低自由能计算和蒙特卡罗模拟。我们的结果表明，位于移码位点下游3'端的茎环结构在劳氏肉瘤病毒（RSV）、人类免疫缺陷病毒1型（HIV-1）、牛白血病病毒（BLV）、人类T细胞白血病病毒II型（HTLV-II）和小鼠乳腺肿瘤病毒（MMTV）的gag-pol或gag-pro以及pro-pol连接域（包括可能移码位点上游和下游各300个核苷酸）中，相对于其他结构既高度稳定又具有统计学意义。在这些区域中未预测到其他更稳定或更显著的折叠区域。
