Herzel H, Weiss O, Trifonov E N
Institute for Theoretical Biology, Humboldt University, Berlin, Germany.
J Biomol Struct Dyn. 1998 Oct;16(2):341-5. doi: 10.1080/07391102.1998.10508251.
The topological state of genomic DNA is of importance for its replication, recombination and transcription. The wrapping of the DNA around nucleosomes is associated with sequence periodicities (Trifonov and Sussman, Proc. Natl. Acad. Sci. USA, 77, pp. 3816-20). Recently, also the negative supercoiling of eubacterial DNA was related to 11 base pair (bp) periodicity (Herzel et al. Physica A, 249, pp. 449-59). Archaeal plasmids and a virus-like particle from Sulfolobus are positively supercoiled, but the superhelical conformation of archaeal genomic DNA is still uncertain. The problem of superhelicity can now be addressed via a comparative statistical analysis of the available complete genomes. For this purpose one has to look for periodicities which are in phase with the helical repeat of 10-11 bp. Similar periodicities are induced, however, by the amphipatic character of alpha-helices of encoded proteins (Zhurkin, Nucl. Acids Res., 9, pp. 1963-71). We show that these protein-induced periodicities are extended over a few periods only. The periods of additional long-ranging oscillations deviate significantly from the value for free DNA. A period of 11 bp in Eubacteria reflects negative supercoiling, whereas the significantly different period of thermophilic Archaea close to 10 bp suggests positive supercoiling of archaeal genomes.
基因组DNA的拓扑状态对其复制、重组和转录至关重要。DNA围绕核小体的缠绕与序列周期性相关（特里福诺夫和苏斯曼，《美国国家科学院院刊》，77卷，第3816 - 3820页）。最近，真细菌DNA的负超螺旋也与11个碱基对（bp）的周期性有关（赫泽尔等人，《物理A》，249卷，第449 - 459页）。古细菌质粒和来自硫化叶菌的病毒样颗粒是正超螺旋的，但古细菌基因组DNA的超螺旋构象仍不确定。现在可以通过对现有完整基因组进行比较统计分析来解决超螺旋问题。为此，必须寻找与10 - 11 bp螺旋重复相位一致的周期性。然而，编码蛋白质的α - 螺旋的两亲性也会诱导出类似的周期性（朱尔金，《核酸研究》，9卷，第1963 - 1971页）。我们表明，这些蛋白质诱导的周期性仅在几个周期内延伸。额外的长程振荡周期与游离DNA的值有显著偏差。真细菌中11 bp的周期反映负超螺旋，而嗜热古细菌中接近10 bp的显著不同的周期表明古细菌基因组是正超螺旋。
