Seeman N C, Liu F, Mao C, Yang X, Wenzler L A, Sha R, Sun W, Shen Z, Li X, Qi J, Zhang Y, Fu T J, Chen J, Winfree E
a Department of Chemistry , New York University , New York , NY , 10003.
J Biomol Struct Dyn. 2000;17 Suppl 1:253-62. doi: 10.1080/07391102.2000.10506629.
Abstract The construction of periodic matter and nanomechanical devices are central goals of DNA nanotechnology. The minimal requirements for components of designed crystals are [1] programmable interactions, [2] predictable local intermolecular structures and [3] rigidity. The sticky-ended association of DNA molecules fulfills the first two criteria, because it is specific and diverse, and it results in the formation of B-DNA. Stable branched DNA molecules permit the formation of networks, but individual single branches are too flexible. Antiparallel DNA double crossover (DX) molecules can provide the necessary rigidity, so we use these components to tile the plane. It is possible to include DNA hairpins that act as topographic labels for this 2-D crystalline array, because they protrude from its plane. By altering sticky ends, it is possible to change the topographic features formed by these hairpins, and to detect these changes by means of AFM. We can modify arrays by restricting hairpins or by adding them to sticking ends protruding from the array. Although individual branched junctions are unsuitable for use as crystalline components, parallelograms of four 4-arm junction molecules are sufficiently rigid that they can be used to produce 2D arrays. The arrays contain cavities whose dimensions are readily tuned by changing the edges of their parallelogram components. We have used these arrays to measure directly the angle between the helices of the Holliday junction. The rigidity of the DX motif can also be exploited to produce a nanomechanical device predicated on the B-Z transition. Two DNA double crossover molecules have been joined by a segment of DNAcapable of undergoing the B-Z transition. In the B-conformation, the unconnected helices of the two molecules are on the same side of the connecting helix, whereas in the Z conformation they are on opposite sides, leading to movements of as much as 60Å. This effect is shown by fluorescence resonance energy transfer, because dyes attached to the unconnected helices have different separations in the two states.
构建周期性物质和纳米机械设备是DNA纳米技术的核心目标。设计晶体组件的最低要求是：[1]可编程相互作用，[2]可预测的局部分子间结构，以及[3]刚性。DNA分子的粘性末端结合满足了前两个标准，因为它具有特异性和多样性，并导致B-DNA的形成。稳定的分支DNA分子允许形成网络，但单个单分支过于灵活。反平行DNA双交叉（DX）分子可以提供必要的刚性，因此我们使用这些组件来平铺平面。可以纳入DNA发夹，作为这种二维晶体阵列的形貌标签，因为它们从其平面突出。通过改变粘性末端，可以改变这些发夹形成的形貌特征，并通过原子力显微镜检测这些变化。我们可以通过限制发夹或将它们添加到从阵列突出的粘性末端来修改阵列。尽管单个分支连接点不适合用作晶体组件，但四个4臂连接分子组成的平行四边形具有足够的刚性，可用于生产二维阵列。这些阵列包含一些腔，其尺寸可通过改变平行四边形组件的边缘轻松调整。我们已使用这些阵列直接测量霍利迪连接点螺旋之间的角度。DX基序的刚性还可用于制造基于B-Z转变的纳米机械设备。两个DNA双交叉分子已通过一段能够进行B-Z转变的DNA连接在一起。在B构象中，两个分子未连接的螺旋位于连接螺旋的同一侧，而在Z构象中，它们位于相对侧，导致移动多达60埃。这种效应通过荧光共振能量转移得以体现，因为附着在未连接螺旋上的染料在两种状态下具有不同的间距。
