Acta Phys. -Chim. Sin. ›› 2010, Vol. 26 ›› Issue (07): 2007-2014.doi: 10.3866/PKU.WHXB20100701

• BIOPHYSICAL CHEMISTRY • Previous Articles     Next Articles

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


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


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