Zhang Jingyun, McCauley Micah J, Maher L James, Williams Mark C, Israeloff N E
Department of Physics, Northeastern University, Boston, MA 02115, USA.
Nucleic Acids Res. 2009 Mar;37(4):1107-14. doi: 10.1093/nar/gkn1011. Epub 2009 Jan 7.
The mechanism by which sequence non-specific DNA-binding proteins enhance DNA flexibility is studied by examining complexes of double-stranded DNA with the high mobility group type B proteins HMGB2 (Box A) and HMGB1 (Box A+B) using atomic force microscopy. DNA end-to-end distances and local DNA bend angle distributions are analyzed for protein complexes deposited on a mica surface. For HMGB2 (Box A) binding we find a mean induced DNA bend angle of 78 degrees, with a standard error of 1.3 degrees and a SD of 23 degrees, while HMGB1 (Box A+B) binding gives a mean bend angle of 67 degrees, with a standard error of 1.3 degrees and a SD of 21 degrees. These results are consistent with analysis of the observed global persistence length changes derived from end-to-end distance measurements, and with results of DNA-stretching experiments. The moderately broad distributions of bend angles induced by both proteins are inconsistent with either a static kink model, or a purely flexible hinge model for DNA distortion by protein binding. Therefore, the mechanism by which HMGB proteins enhance the flexibility of DNA must differ from that of the Escherichia coli HU protein, which in previous studies showed a flat angle distribution consistent with a flexible hinge model.
通过原子力显微镜检查双链DNA与高迁移率族B型蛋白HMGB2（A盒）和HMGB1（A + B盒）的复合物，研究了序列非特异性DNA结合蛋白增强DNA柔韧性的机制。分析沉积在云母表面的蛋白质复合物的DNA端到端距离和局部DNA弯曲角度分布。对于HMGB2（A盒）结合，我们发现平均诱导DNA弯曲角度为78度，标准误差为1.3度，标准差为23度，而HMGB1（A + B盒）结合给出的平均弯曲角度为67度，标准误差为1.3度，标准差为21度。这些结果与从端到端距离测量得出的观察到的全局持久长度变化的分析一致，并且与DNA拉伸实验的结果一致。两种蛋白质诱导的弯曲角度的适度广泛分布与静态扭结模型或蛋白质结合导致的DNA扭曲的纯柔性铰链模型均不一致。因此，HMGB蛋白增强DNA柔韧性的机制必须不同于大肠杆菌HU蛋白的机制，在先前的研究中，HU蛋白显示出与柔性铰链模型一致的平角分布。
