Department of Chemistry, Single Molecule Analysis Group, 930 N. University Avenue, University of Michigan, Ann Arbor, Michigan 48109-1055, USA.
Nano Lett. 2013 Jun 12;13(6):2754-9. doi: 10.1021/nl400976s. Epub 2013 May 28.
We use single-particle fluorescence resonance energy transfer (FRET) to show that organizing oligonucleotide probes into patterned two-dimensional arrays on DNA origami nanopegboards significantly alters the kinetics and thermodynamics of their hybridization with complementary targets in solution. By systematically varying the spacing of probes, we demonstrate that the rate of dissociation of a target is reduced by an order of magnitude in the densest probe arrays. The rate of target binding is reduced less dramatically, but to a greater extent than reported previously for one-dimensional probe arrays. By additionally varying target sequence and buffer composition, we provide evidence for two distinct mechanisms for the markedly slowed dissociation: direct hopping of targets between adjacent sequence-matched probes and nonsequence-specific, salt-bridged, and thus attractive electrostatic interactions with the DNA origami pegboard. This kinetic behavior varies little between individual copies of a given array design and will have significant impact on hybridization measurements and overall performance of DNA nanodevices as well as microarrays.
我们利用单粒子荧光共振能量转移（FRET）技术表明，将寡核苷酸探针组织成 DNA 折纸纳米棒上的图案二维阵列，会显著改变它们在溶液中与互补靶标杂交的动力学和热力学性质。通过系统地改变探针的间距，我们证明在最密集的探针阵列中，靶标解离的速率降低了一个数量级。靶标结合的速率降低的幅度较小，但比以前报道的一维探针阵列的降低幅度更大。通过进一步改变靶序列和缓冲组成，我们为明显减缓的解离提供了两种不同机制的证据：靶标在相邻序列匹配的探针之间的直接跳跃，以及非序列特异性、盐桥连接的、因此与 DNA 折纸 peg 板有吸引力的静电相互作用。这种动力学行为在给定阵列设计的各个副本之间变化很小，这将对杂交测量和 DNA 纳米器件以及微阵列的整体性能产生重大影响。
