Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):6106-11. doi: 10.1073/pnas.1113532109. Epub 2012 Apr 2.
B-DNA becomes unstable under superhelical stress and is able to adopt a wide range of alternative conformations including strand-separated DNA and Z-DNA. Localized sequence-dependent structural transitions are important for the regulation of biological processes such as DNA replication and transcription. To directly probe the effect of sequence on structural transitions driven by torque, we have measured the torsional response of a panel of DNA sequences using single molecule assays that employ nanosphere rotational probes to achieve high torque resolution. The responses of Z-forming d(pGpC)(n) sequences match our predictions based on a theoretical treatment of cooperative transitions in helical polymers. "Bubble" templates containing 50-100 bp mismatch regions show cooperative structural transitions similar to B-DNA, although less torque is required to disrupt strand-strand interactions. Our mechanical measurements, including direct characterization of the torsional rigidity of strand-separated DNA, establish a framework for quantitative predictions of the complex torsional response of arbitrary sequences in their biological context.
B-DNA 在超螺旋压力下变得不稳定，能够采用多种替代构象，包括链分离 DNA 和 Z-DNA。局部序列依赖性结构转变对于 DNA 复制和转录等生物过程的调控非常重要。为了直接研究序列对由扭矩驱动的结构转变的影响，我们使用单分子测定法测量了一组 DNA 序列的扭转响应，该测定法采用纳米球旋转探针来实现高扭矩分辨率。Z 形成的 d(pGpC)(n)序列的响应与我们基于螺旋聚合物中协同转变的理论处理的预测相符。含有 50-100bp 错配区域的“泡”模板显示出类似于 B-DNA 的协同结构转变，尽管破坏链间相互作用所需的扭矩较小。我们的力学测量，包括对链分离 DNA 的扭转刚度的直接表征，为在其生物环境中对任意序列的复杂扭转响应进行定量预测建立了框架。
