Spatially Addressable Multiprotein Nanoarrays Templated by Aptamer-Tagged DNA Nanoarchitectures

Abstract

Experimental MethodsMaterials. The DNA sequences were designed using the SEQUIN program (Seeman, N. C. J. Biomol. Struct. Dyn. 1990, 8, 573-581). DNA strands were commercially synthesized by Integrated DNA Technologies, Inc. (IDT). All unmodified helper strands were purchased from IDT in the format of 96-well plates at 6 nmole synthesis scale and used without further purification. Helper strands modified with aptamer sequences, control sequences and index sequences were purchased from IDT in the format of individual vials and purified by denaturing polyacrylamide gel electrophoresis (PAGE) before use. Strands used in the DX arrays were also purchased from IDT in the format of individual vials and purified by denaturing PAGE. Concentration of purified DNA strands was calculated by measuring optical density at 260 nm wavelengh. Microcon Centrifugal Filter Devices (100,000 MWCO) was purchased from Millipore Corporation. Thrombin was from Haematologic Technologies, Inc., recombinant human PDGF-BB was from BioVision, Inc., and stains all was purchased from Sigma-Aldrich. Both the proteins were reconstituted into aqueous solutions by adding ultrapure water (18 MΩ). M13 viral DNA was purchased from New England Biolabs, Inc. (NEB). (Catalog number: #N4040S. The sequence of the product was confirmed by NEB before they ship to the customers).Assembly of 2-D DNA scaffold. The ABCD arrays were formed by mixing equimolar quantities of all the constituting strands (see Figure S1) at a concentration of 1 µM (as estimated by OD 260 ) in 1 x TAE-Mg 2+ buffer (Tris, 40 mM; Acetic acid, 20 mM; EDTA, 2 mM; and Magnesium acetate, 12.5 mM; pH 8.0). The mixture was cooled slowly from 90 °C to room temperature over 48 hours. Individual DX-B and DX-D tiles were also assembled following the same procedure.

A polycatenated DNA scaffold for the one-step assembly of hierarchical nanostructures

“…2F). These regularly spaced bumps are most likely the thrombin on the DNA backbone (41), and cross sections of these bumps show a small valley between two peaks. These valleys are likely the distance between two thrombin units on the same link, and the spaces between bumps are the result of the empty links that were programmed between thrombinaptamer-containing rings.…”

Assembly of Two‐Dimensional DNA Crystals Carrying N4‐[2‐(tert‐Butyldisulfanyl)ethyl]cytosine Residues

“…There is a wide range of literature that describes a large variety of periodic arrays and their specific patterns [1][2][3][4][5][6][7][8][9][10][11][12][13][14]. The results of this study demonstrate that DNA lattices carrying a single protected thiol group at specific internal DNA sites can be assembled in aqueous buffers and then deposited onto gold surfaces …”

“…For example, large DNA lattices have been transformed into highly regular two-dimensional DNA networks on surfaces that provide templates for the deposition of gold nanoparticles in a regular square network by using biotin-streptoavidin recognition system [7,8]. Fullerene arrays have been assembled on DNA templates [9] as well as gold nanoparticle arrays [10,11] and proteins [12][13][14]. Recently, two-dimensional arrays of quantum dots with controlled periodicity have been prepared using DNA-tile arrays [15].…”

“…But, these ends are usually needed for the assembly of the DNA nanostructure. And we do not want to increase the number of oligonucleotides as described [11,12,14]. For these reasons, we plan to insert reactive thiol groups at the nucleobase.…”

Pore Size Variability of DNA Nanomeshes by Polymerase Chain Reaction

“…Recent advances in this field include the use of self-assembled DNA nanostructures as scaffolds for the construction of hierarchical, multi-component structures, which would promise more functionalizability and applicability. 6,8 Most, if not all, of the previously reported structures have been derived from the tightly controlled self-assembly of sophisticatedly but intricately designed DNA building blocks. One set of building blocks intrinsically produces one predetermined, final structure, although some attempts have been reported to tune final structures by combining several building blocks differently.…”