核小体中组蛋白与DNA相互作用自由能的测量。

Measurement of histone-DNA interaction free energy in nucleosomes.

作者信息

Thåström A, Lowary P T, Widom J

机构信息

Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, 2153 Sheridan Road, Evanston, IL 60208-3500, USA.

出版信息

Methods. 2004 May;33(1):33-44. doi: 10.1016/j.ymeth.2003.10.018.

DOI:10.1016/j.ymeth.2003.10.018

PMID:15039085

Abstract

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.

摘要

核小体定位DNA序列正日益受到关注，这是因为它们在体内基因调控和其他染色体功能中所起的作用，还因为它们揭示了有关DNA自身序列依赖性结构和力学的新见解。在此，我们描述了定量核小体中组蛋白-DNA相互作用相对亲和力的方法，即不同DNA序列的核小体定位能力。我们回顾了其他人开发的方法，然后详细讨论了我们自己测量组蛋白-DNA相互作用自由能的方法。与早期方法相比，我们基于透析的方法降低了获得非平衡或不可重复结果的可能性。它便于同时直接比较许多序列的自由能，并且允许分析具有广泛相对亲和力的DNA。