Albert F G, Bronson E C, Fitzgerald D J, Anderson J N
Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.
J Biol Chem. 1995 Oct 6;270(40):23570-81. doi: 10.1074/jbc.270.40.23570.
A computer program for predicting DNA bending from nucleotide sequence was used to identify circular structures in retroviral and cellular genomes. An 830-base pair circular structure was located in a control region near the center of the genome of the human immunodeficiency virus type I (HIV-I). This unusual structure displayed relatively smooth planar bending throughout its length. The structure is conserved in diverse isolates of HIV-I, HIV-II, and simian immunodeficiency viruses, which implies that it is under selective constraints. A search of all sequences in the GenBank data base was carried out in order to identify similar circular structures in cellular DNA. The results revealed that the structures are associated with a wide range of sequences that undergo recombination, including most known examples of DNA inversion and subtelomeric translocation systems. Circular structures were also associated with replication and transposition systems where DNA looping has been implicated in the generation of large protein-DNA complexes. Experimental evidence for the structures was provided by studies which demonstrated that two sequences detected as circular by computer preferentially formed covalently closed circles during ligation reactions in vitro when compared to nonbent fragments, bent fragments with noncircular shapes, and total genomic DNA. In addition, a single T-->C substitution in one of these sequences rendered it less planar as seen by computer analysis and significantly reduced its rate of ligase-catalyzed cyclization. These results permit us to speculate that intrinsically circular structures facilitate DNA looping during formation of the large protein-DNA complexes that are involved in site- and region-specific recombination and in other genomic processes.
利用一个根据核苷酸序列预测DNA弯曲的计算机程序，来识别逆转录病毒和细胞基因组中的环状结构。在人类免疫缺陷病毒I型（HIV-I）基因组中心附近的一个调控区域内，定位到了一个830个碱基对的环状结构。这种不同寻常的结构在其全长范围内呈现出相对平滑的平面弯曲。该结构在HIV-I、HIV-II和猿猴免疫缺陷病毒的不同分离株中都保守存在，这意味着它受到选择性限制。为了在细胞DNA中识别类似的环状结构，对GenBank数据库中的所有序列进行了搜索。结果显示，这些结构与经历重组的广泛序列相关，包括大多数已知的DNA倒位和亚端粒易位系统实例。环状结构还与复制和转座系统相关，在这些系统中，DNA环化被认为与大蛋白质-DNA复合物的形成有关。对这些结构的实验证据由一些研究提供，这些研究表明，与非弯曲片段、非圆形弯曲片段和总基因组DNA相比，计算机检测为环状的两个序列在体外连接反应过程中优先形成共价闭合环。此外，这些序列之一中的单个T→C替换使其在计算机分析中看起来平面度降低，并显著降低了其连接酶催化环化的速率。这些结果使我们推测，内在的环状结构在涉及位点和区域特异性重组以及其他基因组过程的大蛋白质-DNA复合物形成过程中促进了DNA环化。
