Measurement of histone-DNA interaction free energy in nucleosomes
Measurement of histone-DNA interaction free energy in nucleosomes
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DOI：
10.1016/j.ymeth.2003.10.018
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发表时间：
2004-05-01
期刊：
影响因子：
4.8
通讯作者：
Widom, J
中科院分区：
文献类型：
--
作者：
Thåström, A;Lowary, PT;Widom, J
核小体定位DNA序列越来越受到人们的关注，因为它们在体内基因调控和其他染色体功能中的作用，并且因为它们揭示了DNA本身的序列依赖性结构和机制的新见解。在这里，我们描述了定量核小体中组蛋白-DNA相互作用的相对亲和力的方法，即，不同DNA序列的核小体定位能力。我们回顾别人开发的方法，然后详细讨论我们自己的方法来测量组蛋白-DNA相互作用的自由能。与早期的方法相比，我们基于透析的方法降低了获得非平衡或不可重现结果的可能性。它便于同时直接比较许多序列的自由能，并且它允许分析具有宽范围相对亲和力的DNA。(C)2003年爱思唯尔公司All rights reserved.
Nucleosome positioning DNA sequences are of increasing interest because of their proposed roles in gene regulation and other chromosome functions in vivo, and because they have revealed new insights into the sequence-dependent structures and mechanics of DNA itself. Here, we describe methods to quantify the relative affinities of histone-DNA interactions in nucleosomes, i.e., the nucleosome positioning power of differing DNA sequences. We review methods developed by others and then discuss in detail our own approach to measurement of histone-DNA interaction free energies. Compared to earlier methods, our dialysis-based approach reduces the possibility that non-equilibrium or irreproducible results could be obtained. It facilitates a direct comparison of free energies for many sequences at the same time and it allows analysis of DNAs having a wide range of relative affinities. (C) 2003 Elsevier Inc. All rights reserved.