Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom.
J Am Chem Soc. 2011 Feb 23;133(7):2177-82. doi: 10.1021/ja1073239. Epub 2011 Jan 26.
Hybridization of DNA strands can be used to build molecular devices, and control of the kinetics of DNA hybridization is a crucial element in the design and construction of functional and autonomous devices. Toehold-mediated strand displacement has proved to be a powerful mechanism that allows programmable control of DNA hybridization. So far, attempts to control hybridization kinetics have mainly focused on the length and binding strength of toehold sequences. Here we show that insertion of a spacer between the toehold and displacement domains provides additional control: modulation of the nature and length of the spacer can be used to control strand-displacement rates over at least 3 orders of magnitude. We apply this mechanism to operate displacement reactions in potentially useful kinetic regimes: the kinetic proofreading and concentration-robust regimes.
DNA 链的杂交可用于构建分子器件，而 DNA 杂交动力学的控制是设计和构建功能和自主器件的关键要素。引发链置换已被证明是一种强大的机制，可实现 DNA 杂交的可编程控制。到目前为止，控制杂交动力学的尝试主要集中在引发序列的长度和结合强度上。在这里，我们表明在引发和置换结构域之间插入间隔物可以提供额外的控制：通过调节间隔物的性质和长度，可以控制链置换速率，其范围至少跨越 3 个数量级。我们将该机制应用于在潜在有用的动力学范围内操作置换反应：动力学校验和浓度稳健范围。
