The effects of local DNA sequence on the interaction of ligands with their preferred binding sites
The effects of local DNA sequence on the interaction of ligands with their preferred binding sites
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DOI：
10.1016/j.biochi.2008.01.001
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发表时间：
2008-07-01
期刊：
影响因子：
3.9
通讯作者：
Fox, Keith R.
中科院分区：
文献类型：
--
作者：
Hampshire, Andrew J.;Fox, Keith R.
我们研究了局部DNA序列对偏端霉素，Hoechst 33258，棘霉素，放线菌素和光辉霉素与它们的首选结合位点的相互作用的影响，使用了一系列的DNA片段，包含每个对称的六核苷酸序列。在几种情况下，我们发现配体的首选结合位点的亲和力受到它们所处的六核苷酸环境的影响。AT-选择性小沟结合配体Hoechst 33258在与16个不同的X（A/T）4 y位点的结合中显示出200倍的差异;最强的结合是与AAAM的结合，最弱的是与（G/QT`FAA（C/G）的结合。虽然TTAA通常是较差的结合位点，但ATTAAT优于TTTAAA，并且它们都比GTTAAC和CTTAAG好得多。类似地，TTATAA和ATATAT是比GTATAC和CTATAG更好的结合位点。相比之下，偏端霉素在各种X（A/T）4 γ位点之间显示出较少的区分，在最佳[（A/T）AATT（T/A）1和最差[GATATC和（G/C）TrAA（C/G）]位点之间具有20倍的差异。尽管放线菌素与GpC结合，但它与任何GGCC位点几乎没有相互作用，但对其他XYGCXY位点的亲和力仅显示出6倍的变化。棘霉素与CpG结合，但不与TTCGAA、TGCGCA和AGCGCT结合，而最好的结合是与AACGTT结合。四核苷酸CCGG和ACGT产生一贯良好的结合位点，无论周围的序列，而与TCGA和GCGC的相互作用是敏感的六核苷酸上下文。具有中央GCGC的六核苷酸，两侧为A和T，是比两侧为G和C的那些更弱的棘霉素位点，尤其是CGCGCG。光神霉素的最佳X（G）/Q4 Y结合位点位于AGCGCT和GGGCCC，最差的是CCCGGG和TCCGGA。这些足迹片段是用于比较配体与所有潜在的对称六核苷酸的结合的有价值的工具，并提供了对局部DNA序列对配体-DNA相互作用的影响的见解。(c)2008年，Elsevier Masson SAS。All rights reserved.
We have examined the effects of local DNA sequence on the interaction of distamycin, Hoechst 33258, echinomycin, actinomycin and mithramycin with their preferred binding sites using a series of DNA fragments that contain every symmetrical hexanucleotide sequence. In several instances we find that the affinity for the ligands' preferred binding sites is affected by the hexanucleotide context in which they are located. The AT-selective minor groove binding ligand Hoechst 33258 shows a 200-fold difference in binding to the 16 different X(A/T)4y sites; the strongest binding is to AAAM and the weakest is to (G/QT`FAA(C/G). Although TTAA is generally a poor binding site, ATTAAT is better than TTTAAA and they are both much better than GTTAAC and CTTAAG. Similarly, TTATAA and ATATAT are better binding sites than GTATAC and CTATAG. In contrast, distamycin shows less discrimination between the various X(A/T)4y Sites, with a 20-fold difference between the best [(A/T)AATT(T/A)l and worst [GATATC and (G/C)TrAA(C/G)] sites. Although actinomycin binds to GpC it shows little or no interaction with any of the GGCC sites, yet shows only a six-fold variation in affinities for the other XYGCXY sites. Echinomycin binds to CpG yet shows no binding to TTCGAA, TGCGCA and AGCGCT, while the best binding is to AACGTT. The tetranucleotides CCGG and ACGT produce consistently good binding sites, irrespective of the surrounding sequences, while the interaction with TCGA and GCGC is sensitive to the hexanucleotide context. Hexanucleotides with a central GCGC, flanked by A and T are weaker echinomycin sites than those flanked by G and C, especially CGCGCG. The best X(G/Q4Y binding sites for mithramycin were located at AGCGCT and GGGCCC, and the worst at CCCGGG and TCCGGA. These footprinting fragments are valuable tools for comparing the binding of ligands to all the potential symmetrical hexanucleotides and provide insights into the effects of local DNA sequence on ligand-DNA interactions. (c) 2008 Elsevier Masson SAS. All rights reserved.