Most DNA scanning proteins uniquely recognize their cognate sequence motif and slide on DNA assisted by some sort of clamping interface. The pioneer transcription factors that control cell fate in eukaryotes must forgo both elements to gain access to DNA in naked and chromatin forms; thus, whether or how these factors scan naked DNA is unknown. Here, we use single-molecule techniques to investigate naked DNA scanning by the Engrailed homeodomain (enHD) as paradigm of highly promiscuous recognition and open DNA binding interface. We find that enHD scans naked DNA quite effectively, and about 200000-fold faster than expected for a continuous promiscuous slide. To do so, enHD scans about 675 bp of DNA in 100 ms and then redeploys stochastically to another location 530 bp afar in just 10 ms. During the scanning phase enHD alternates between slow- and medium-paced modes every 3 and 40 ms, respectively. We also find that enHD binds nucleosomes and does so with enhanced affinity relative to naked DNA. Our results demonstrate that pioneer-like transcription factors can in principle do both, target nucleosomes and scan active DNA efficiently. The hybrid scanning mechanism used by enHD appears particularly well suited for the highly complex genomic signals of eukaryotic cells.

中文翻译：

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如何使用混杂识别和无钳位扫描裸 DNA：先锋转录因子模型


大多数 DNA 扫描蛋白唯一地识别它们的同源序列基序，并在某种夹紧界面的辅助下滑到 DNA 上。控制真核生物细胞命运的先驱转录因子必须放弃这两种元素才能获得裸露和染色质形式的 DNA;因此，这些因素是否或如何扫描裸 DNA 尚不清楚。在这里，我们使用单分子技术研究 Engrailed 同源域 （enHD） 的裸 DNA 扫描，作为高度混杂识别和开放 DNA 结合界面的范式。我们发现 enHD 可以非常有效地扫描裸 DNA，并且比连续混杂玻片的预期快约 200000 倍。为此，enHD 在 100 毫秒内扫描了大约 675 bp 的 DNA，然后在短短 10 毫秒内随机重新部署到 530 bp 远的另一个位置。在扫描阶段，enHD 分别每 3 毫秒和 40 毫秒在慢速和中速模式之间交替。我们还发现 enHD 结合核小体，并且相对于裸 DNA 具有增强的亲和力。我们的结果表明，先锋样转录因子原则上可以同时做这两件事，靶向核小体并有效地扫描活性 DNA。enHD 使用的混合扫描机制似乎特别适合真核细胞高度复杂的基因组信号。