Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates

Abstract

Design and formation of the linker complex. Oligos were purchased in lyophilized form from IDT DNA. Sequences are below. LNA nucleotides are written as +C+G+A, etc. All other nucleotide are DNA. Labeling domain sequences were computer-optimized (31) to minimize sequence complementarity, homology, and melting temperature differences with programs written in MATLAB available at:http://www.dna.caltech.edu/DNAdesign/ Red linker main strand:Red linker protection strand:Blue linker main strand: 5ʼ TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATACGGGGCTGGTTA+G+G+A+T+G 3ʼBlue linker protection strand: 5ʼ TAACCAGCCCCGTAT 3ʼStrands are separately dissolved in water purified by a Milli-Q unit (Millipore) to form stock solutions at ∼300 µM. A 2 M NaCl stock solution is created and filtered using 0.22 µm filters. For the red (blue) linker complex, the main strand and the protection strand are mixed with NaCl stock solution and Milli-Q purified water to obtain 600 µL of dispersal solution with ∼ 33 µM of the main strand, ∼ 36 µM of the protection strand, and 0.1 M NaCl; the concentrations of the main and protection strands were chosen to give a 10% excess of protection strand. This solution is put in a 0.6 mL PCR tube and annealed in an Eppendorf Mastercycler from 95• C to 20• C at 1 • C per minute. The protection strand/main strand partial duplex has a melting temperature T melting ∼50• C in our buffers. Dispersal of SWNTs.To create the red (blue) NL-SWNTs, ∼1 mg of dry HiPco SWNTs are added to 400-600 µL of the dispersal solution in a 1.7 mL PCR tube. The tube is then placed in an ice-water bath and sonicated for ∼90 minutes in a Branson 2510 sonicator (100 W). The water level inside the sonication chamber and the position of the PCR tube is adjusted to apply maximum sonication power to the sample. The temperature of the water bath is maintained at ∼15• C. The SWNTs are sonicated until the solution turns a uniform gray color and all the SWNTs are completely solubilized. The solution is then centrifuged at 16,000 g for 90 min at 15• C. Following this step, the supernatant is retained while the insoluble condensate is discarded. This process yields a high concentration of well-dispersed NL-SWNTs as determined by AFM and TEM images.1

DNA‐Origami‐Driven Lithography for Patterning on Gold Surfaces with Sub‐10 nm Resolution

“…[14] Future studies could lead to the integration of this methodology within multiplexed microfluidic [11] and more multipurpose read out systems, [10a] For example, the integration of modular addressability with biological processes can be utilized for the high throughput analysis of biochemical reactions and biomolecular interactions that require control over proximity and special distribution. Thereby, the DNA origami stamp method presented here brings the opportunity for a more versatile and robust functionalization and patterning of surfaces for the creation of metamaterials [12a] with applications in nanoelectronics [7] and photonics [2c] . Furthermore we show that the immobilization process can be visualized by SPR opening the possibility for the development of highly organized sensing surfaces.…”

“…[2] DNA origami allows the folding of DNA into twodimensional [3] and three-dimensional [4] structures, and has been used to organize biomolecules, [2b, e, 5] nanophotonic [2a, c, f, 6] and electronic [7] components with a resolution of 6 nm / pixel. [8] Two-dimensional DNA origami has been also used as a platform to organize other chemical [9] species that can then be placed on technologically relevant substrates.…”

ssDNA Binding Reveals the Atomic Structure of Graphene

“…In this novel hybrid system graphene could be used as the electrical interconnect and as an e-beam tailored substrate, while origami can be used as template for material growth, 26,27 sensor, 28,29 or even as a template for specific single-molecule chemical reactions. 30 …”

Molecular logic computing model based on DNA self-assembly strand branch migration

“…In fact, since the end of last century, it has made a great progress, both in theoretical models and experimental operations of DNA computing. In addition, it has developed greatly in the interdisciplinary fields of information processing, molecular encoding, nanomachines and so on [6][7][8][9][10][11].…”