Entropy-driven collective interactions in DNA brushes on a biochip
Entropy-driven collective interactions in DNA brushes on a biochip
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DOI：
10.1073/pnas.1220076110
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发表时间：
2013-03-19
影响因子：
11.1
通讯作者：
Bar-Ziv, Roy H.
中科院分区：
文献类型：
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作者：
Bracha, Dan;Karzbrun, Eyal;Bar-Ziv, Roy H.
生物芯片上的DNA刷中的无细胞基因表达依赖于基因密度和方向，这表明刷形成具有分区条件的隔室。在高密度下，DNA熵弹性、静电和排除体积相互作用的相互作用导致集体构象，影响DNA相关蛋白的功能。因此，在没有蛋白质的致密DNA中测量集体相互作用，对于理解拥挤的细胞环境和设计无细胞合成生物芯片至关重要。在这里，我们沿着密度梯度在生物芯片上组装密集的DNA聚合物刷，并使用倏逝荧光直接测量DNA的集体延伸。1 kbp的DNA在刷子中经历了主要的构象变化，从松弛的随机线圈到拉伸的结构，遵循密度与离子强度比的通用函数，标度指数为1/3。DNA的延伸是由于离子的渗透压引起的膨胀力，这些离子被困在刷子中以保持局部电荷中性，与DNA熵弹性的恢复力竞争。测量结果揭示了渗透、盐渍、蘑菇和准中性刷染制度之间的DNA交叉。令人惊讶的是，在生理离子强度下，DNA密度不会诱导集体拉伸，尽管有显著的链重叠，这意味着DNA中排除的体积相互作用很弱。
Cell-free gene expression in localized DNA brushes on a biochip has been shown to depend on gene density and orientation, suggesting that brushes form compartments with partitioned conditions. At high density, the interplay of DNA entropic elasticity, electrostatics, and excluded volume interactions leads to collective conformations that affect the function of DNA-associated proteins. Hence, measuring the collective interactions in dense DNA, free of proteins, is essential for understanding crowded cellular environments and for the design of cell-free synthetic biochips. Here, we assembled dense DNA polymer brushes on a biochip along a density gradient and directly measured the collective extension of DNA using evanescent fluorescence. DNA of 1 kbp in a brush undergoes major conformational changes, from a relaxed random coil to a stretched configuration, following a universal function of density to ionic strength ratio with scaling exponent of 1/3. DNA extends because of the swelling force induced by the osmotic pressure of ions, which are trapped in the brush to maintain local charge neutrality, in competition with the restoring force of DNA entropic elasticity. The measurements reveal in DNA crossover between regimes of osmotic, salted, mushroom, and quasineutral brush. It is surprising to note that, at physiological ionic strength, DNA density does not induce collective stretch despite significant chain overlap, which implies that excluded volume interactions in DNA are weak.