Schroth G P, Ho P S
Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331, USA.
Nucleic Acids Res. 1995 Jun 11;23(11):1977-83. doi: 10.1093/nar/23.11.1977.
We have used computer-assisted methods to search large amounts of the human, yeast and Escherichia coli genomes for inverted repeat (IR) and mirror repeat (MR) DNA sequence patterns. In highly supercoiled DNA some IRs can form cruciforms, while some MRs can form intramolecular triplexes, or H-DNA. We find that total IR and MR sequences are highly enriched in both eukaryotic genomes. In E. coli, however, only total IRs are enriched, while total MRs only occur as frequently as in random sequence DNA. We then used a set of experimentally derived criteria to predict which of the total IRs and MRs are most likely to form cruciforms or H-DNA in supercoiled DNA. We show that strong cruciform forming sequences occur at a relatively high frequency in yeast (1/19 700 bp) and humans (1/41 800 bp), but that H-DNA forming sequences are abundant only in humans (1/49 400 bp). Strong cruciform and H-DNA forming sequences are not abundant in the E.coli genome. These results suggest that cruciforms and H-DNA may have a functional role in eukaryotes, but probably not prokaryotes.
我们利用计算机辅助方法在人类、酵母和大肠杆菌的大量基因组中搜索反向重复（IR）和镜像重复（MR）DNA序列模式。在高度超螺旋的DNA中，一些IR可以形成十字形结构，而一些MR可以形成分子内三链体或H-DNA。我们发现，IR和MR序列在两个真核生物基因组中都高度富集。然而，在大肠杆菌中，只有总的IR序列是富集的，而总的MR序列出现的频率与随机序列DNA中的频率相同。然后，我们使用一组实验得出的标准来预测哪些总的IR和MR最有可能在超螺旋DNA中形成十字形结构或H-DNA。我们表明，强十字形形成序列在酵母（1/19700bp）和人类（1/41800bp）中以相对较高的频率出现，但H-DNA形成序列仅在人类中丰富（1/49400bp）。强十字形和H-DNA形成序列在大肠杆菌基因组中并不丰富。这些结果表明，十字形结构和H-DNA可能在真核生物中具有功能作用，但在原核生物中可能没有。
