Probing Allostery through DNA

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Probing Allostery through DNA

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Title: Probing Allostery through DNA
Author: Kim, Sangjin; Broströmer, Erik; Jin, Jianshi; Chong, Shasha; Ge, Hao; Wang, Siyuan; Gu, Chan; Yang, Lijiang; Gao, Yi Qin; Su, Xiao-dong; Sun, Yujie; Xie, Xiaoliang Sunney; Xing, Dong

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Citation: Kim, Sangjin, Erik Broströmer, Dong Xing, Jianshi Jin, Shasha Chong, Hao Ge, Siyuan Wang, et al. 2013. Probing allostery through DNA. Science 339(6121): 816-819.
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Abstract: Allostery is well documented for proteins but less recognized for DNA-protein interactions. Here, we report that specific binding of a protein on DNA is substantially stabilized or destabilized by another protein bound nearby. The ternary complex's free energy oscillates as a function of the separation between the two proteins with a periodicity of ~10 base pairs, the helical pitch of B-form DNA, and a decay length of ~15 base pairs. The binding affinity of a protein near a DNA hairpin is similarly dependent on their separation, which—together with molecular dynamics simulations—suggests that deformation of the double-helical structure is the origin of DNA allostery. The physiological relevance of this phenomenon is illustrated by its effect on gene expression in live bacteria and on a transcription factor's affinity near nucleosomes.
Published Version: doi:10.1126/science.1229223
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