DNA Polymerization on Gold Nanoparticles through Rolling Circle Amplification: Towards Novel Scaffolds for Three‐Dimensional Periodic Nanoassemblies

Abstract

Recent years have witnessed an explosion of interest in the use of DNA-nanoparticle bioconjugates for programmed nanostructures, 1D or 2D nanoparticle arrays, nanoelectronics, and biosensing and biodiagnostics. [1][2][3][4][5][6][7][8][9] DNA was chosen as a polymeric material in these studies owing mainly to the specificity of DNA base-pairing, the predictability of inter-or intramolecular interactions, its physicochemical stability, and mechanical rigidity. In addition, DNA can be manipulated and modified by a wide range of enzymes, including DNA polymerase, ligase, and restriction endonucleases. The powerful, convenient, and specific enzymatic manipulations make DNA a highly desirable building block for the construction of various nanostructures. In the current study, we set out to investigate whether we can perform rolling circle amplification (RCA) between a DNA oligonucleotide tethered to gold nanoparticles (AuNPs) as the primer and a single-stranded circular DNA as a template, catalyzed by a special DNA polymerase known as f29 DNA polymerase (f29DNAP). RCA is a powerful but simple biochemical method that can be used to generate long single-stranded DNA (ssDNA) with a repeating sequence unit. [10][11] In a typical RCA process, a DNA polymerase, such as f29DNAP, which has a strong ability to displace newly synthesized DNA strands, makes continuous nucleotide additions to a growing DNA chain over a short circular single-stranded DNA as the template under isothermal conditions. As a result, long, linear tandemly repetitive single strands of DNA are produced. As the synthesized long DNA molecules contain many repeating sequence motifs, RCA coupled with ensuing hybridization with fluorescent DNA probes has been used as an on-chip signal-amplification tool for sensitive biosensing. [12][13][14][15][16] Recently, it has been shown that long DNA molecules from RCA can be used as scaffolds for assembling nanoparticles to form 1D nanoparticle arrays. [17][18] However, to our knowledge, performing the RCA reaction on gold nanoparticles and using the resultant special DNA-AuNP assemblies to form 3D nanoparticle array have not been demonstrated. Figure 1 schematically illustrates the RCA process on gold nanoparticles and its scaffolding for 3D periodical nanoassemblies. Gold nanoparticles of 15 nm diameter were first prepared by the classical citrate reduction route. Thiolmodified DNA primers (41 nucleotides) were then functionalized onto the nanoparticles following Mirkins approach. [5] The concentration of DNA primers on the gold nanoparticles, referred to hereafter as primer-Au, was determined using UV/Vis spectroscopy by measuring the amount of DNA in solution before and after coupling; each primer-Au contained approximately 230 DNA primer strands. A 63-nucleotidelong circular DNA template was then annealed with the DNA-functionalized gold nanoparticles. The hybridization efficiency, as examined by measuring the radioactivity on the gold nanoparticles and in solution after annealing with a radiolabeled circular DNA ...

Cell-surface sensors for real-time probing of cellular environments

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DNA‐based plasmonic nanoarchitectures: from structural design to emerging applications

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Colorimetric Sensing by Using Allosteric‐DNAzyme‐Coupled Rolling Circle Amplification and a Peptide Nucleic Acid–Organic Dye Probe

“…[12] RCA-T and the matching primer, "RCA-P", were used to perform the RCA reaction as described previously. [13] The details of this reaction and subsequent color-development procedures are provided in the Supporting Information. We found that DiSC2(5) retained the blue color in the hybridization buffer (50 mm Tris-HCl (Tris = 2-amino-2-hydroxymethylpropane-1,3-diol), pH 7.5, and 100 mm NaCl; Figure 2 b, tube 1).…”