Article pubs.acs.org/Langmuir
Approaching the Limit: Can One DNA Strand Assemble into Defined Nanostructures? Cheng Tian, Chuan Zhang, Xiang Li, Chenhui Hao, Shuaijiang Ye, and Chengde Mao* Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States ABSTRACT: This article reports a simple, symmetrical DNA building block (motif): a bulged DNA duplex consisting of two short, identical strands. Multiple copies of the same motif can interact with each other through T junctions. The resulting superstructures include predesigned 1D and 2D arrays that have been visualized by atomic force microscopy (AFM).
1. INTRODUCTION DNA is an excellent building block1,2 for constructing a wide range of nanostructures,3−19 which can further serve as structural templates to organize guest molecules or nanoparticles.20−25 Most DNA nanostructures are based on Holliday junctionlike motifs. Novel building blocks are expected to enhance the nanoconstruction capability further. For example, a T-shaped junction composed of two different DNA duplexes was proposed.26 The central component of this model is Watson−Crick base pairing between a five- or six-base-long single-stranded internal loop and a complementary singlestranded overhang, resulting in a T-shape structure, dubbed the T junction or T motif. The T motif provides a new geometry for constructing DNA nanostructures.26−28 All reported T motifs are composed of two different single-stranded DNA molecules. It is desirable to reduce the component DNA strands to avoid problems such as the inaccuracy of DNA ratios between different DNA strands, the high cost of DNA synthesis, and the difficulty of introducing DNA component strands into an assembly system (e.g., cells). To ease these problems, herein we apply a sequence symmetry strategy29 to design DNA T junctions that can assemble into 1D and 2D arrays. The current symmetric motif is a DNA complex assembled from two identical DNA strands (Figure 1). Each strand contains five domains: (1) a central palindrome (black), (2) two complementary segments (green), and (3) another two complementary segments (red). Two strands hybridize with each other through the black and green segments to form the two-stranded complex that contains a central black duplex domain, two green duplex domains, and four red singlestranded domains. The two pairs of red segments (one-half turn or five to six bases long) can recognize and hybridize with each other among the motifs, leading to the assembly of individual motifs into even larger architectures. The local structure of the hybridization of each pair of red segments is a T-shaped, three-way junction26 that requires the red segments to have a fixed length of five or six bases, but the length of the © 2013 American Chemical Society
green and black segments can vary, resulting in different motif sizes. Because of the helical nature of the DNA duplex, the length of the black duplex domain also determines the motif shape. It is composed of an even and odd number of half turns for the Z- and C-shaped motifs, respectively. In either case, a 2fold rotational axis goes through the center of the symmetrical motif. However, the axis is in the molecular plane of the Cshaped motif and is perpendicular to the plane of the Z-shaped motif. Note that the structure of the motif (C or Z shape) and how the motif assembles (1D or 2D arrays) are determined by the duplex length because the two strands are in a helical conformation instead of being straight lines. When the duplex length changes, the rotational phase will change as well.
2. EXPERIMENTAL SECTION 2.1. Oligonucleotides. DNA sequences were designed with the SEQUIN computer program (Seeman, N. C. De Novo Design of Sequences for Nucleic-Acid Structural Engineering. J. Biomol. Struct. Dyn. 1990, 8, 573−581). All oligonucleotides were purchased from IDT, Inc. and purified by 15−20% denaturing polyacrylamide gel electrophoresis (PAGE). 2.2. DNA Self-Assembly in Solution. DNA strands (2.0 μM for the Z-shaped tile or 1.2 μM for the C-shaped tile) were dissolved in TAE-Mg2+ buffer and slowly cooled from 95 to 22 °C over 48 h in a water bath. The TAE-Mg2+ buffer consisted of Tris (40 mM, pH 8.0), acetic acid (20 mM), EDTA (2 mM), and magnesium acetate (12.5 mM). 2.3. DNA Self-Assembly on a Mica Surface. DNA strands (2.0 μM for the Z-shaped tile or 1.2 μM for the C-shaped tile) were dissolved in TAE-Mg2+ buffer and incubated at 95 °C for 5 min, at 65 °C for 1 h, at 50 °C for 1 h, at 37 °C for 1 h, at 22 °C for 1 h, at 32 °C for 1 h (Z-shaped tile), or at 48 °C for 1 h (C-shaped tile). Five microliters of annealed solution was transferred onto a preheated mica surface and incubated at 32 °C (Z-shaped tile) or 48 °C (C-shaped tile) in a humidity chamber for 16 h. Received: June 21, 2013 Revised: September 17, 2013 Published: October 2, 2013 5859
dx.doi.org/10.1021/la402326b | Langmuir 2014, 30, 5859−5862
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Figure 2. Atomic force microscopy (AFM) analysis of self-assembled DNA 1D arrays assembled (a) in solution and (b) on a mica surface. In each case, a pair of images at different magnifications is shown.
Figure 1. Self-assembly from symmetric bulged DNA duplex motifs into (a) 1D and (b) 2D arrays. Each motif consists of two identical DNA strands, and each strand contains five segments: a central palindrome (black) whose homodimerization forms the central helical domain, two green complementary sequences whose heterodimerization forms two flanking helical domains, and two red complementary sequences that remain single-stranded in symmetric motifs. The intermotif hybridization of red segments (a half-turn or five to six bases long) forms a T junction (see inset in a) and leads to the assembly of motifs into periodic arrays. The length of the central, black helical domain is an even number of half turns (1 turn here) for the Zshaped motif and an odd number of half turns (1.5 turns here) for the C-shaped motif. Both motifs have 2-fold rotational symmetry, but the 2-fold rotational axis is in the plane for the C-shaped motif and is perpendicular to the plane for the Z-shaped motif.
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