物理化学学报 >> 2010, Vol. 26 >> Issue (07): 2007-2014.doi: 10.3866/PKU.WHXB20100701

生物物理化学 上一篇    下一篇

蛋白质与线性DNA片断结合过程中的末端效应

杨晓静, 刘曦励, 娄春波, 欧阳颀   

  1. 北京大学理论生物学中心, 物理学院, 北京 100871
  • 收稿日期:2010-02-12 修回日期:2010-03-29 发布日期:2010-07-02
  • 通讯作者: 欧阳颀 E-mail:qi@pku.edu.cn

End Effects during the Binding of Protein to Linear DNA Fragments

YANG Xiao-Jing, LIU Xi-Li, LOU Chun-Bo, OUYANG Qi   

  1. Center for Theoretical Biology, School of Physics, Peking University, Beijing 100871, P. R. China
  • Received:2010-02-12 Revised:2010-03-29 Published:2010-07-02
  • Contact: OUYANG Qi E-mail:qi@pku.edu.cn

摘要:

各种体外实验技术被广泛地用来研究DNA-蛋白质之间的相互作用, 但体外和体内实验一个最明显的区别是实验使用的DNA片段远远短于基因组DNA, 因而多出了大量线性DNA分子末端. 末端问题曾倍受关注, 若干研究小组在不同系统中对其进行了研究, 但结果却并不一致, 甚至完全相反. 本文利用表面等离子共振技术(SPR)对一系列不同长度非特异DNA和Mnt阻遏蛋白结合和解离过程进行实时监测, 结果表明该蛋白在线性DNA分子末端有比内部位点更高的解离速率. 通过考察在不同位点含有特异序列的DNA与Mnt阻遏蛋白的结合过程, 发现线性DNA分子末端在一定距离内会直接影响DNA与该蛋白的特异性结合.

关键词: 末端效应, DNA-转录因子相互作用, Mnt阻遏蛋白, 表面等离子共振

Abstract:

Many in vitro techniques have been employed to elucidate the interaction between DNA and protein. However, one of the most significant differences between in vitro and in vivo studies is that DNA fragments used for in vitro experiments are usually much shorter than genomic DNA. Therefore, several investigators have sought to examine the effects of linear DNA ends on DNA-protein interactions in different systems. Surprisingly, the various efforts have led to contradictory results. Here, we revisit this issue using the DNA-Mnt repressor interaction system. Using surface plasmon resonance (SPR), we monitor both the association and dissociation of the Mnt repressor with a series of DNA fragments. We conclude that Mnt repressor dissociation from DNA near the ends occurs faster than that frominternal positions. In addition, we find that proximity to the end can directly influence protein-specific binding for binding sites near the end.

Key words: End effect, DNA-transcription factor interaction, Mnt repressor, Surface plasmon resonance

MSC2000: 

  • O643