Phosphorothioate DNA Mediated Sequence-Insensitive Etching and Ripening of Silver Nanoparticles

Abstract

Many DNA-functionalized nanomaterials and biosensors have been reported, but most have ignored the influence of DNA on the stability of nanoparticles. We observed that cytosine-rich DNA oligonucleotides can etch silver nanoparticles (AgNPs). In this work, we showed that phosphorothioate (PS)-modified DNA (PS-DNA) can etch AgNPs independently of DNA sequence, suggesting that the thio-modifications are playing the major role in etching. Compared to unmodified DNA (e.g., poly-cytosine DNA), the concentration of required PS DNA decreases sharply, and the reaction rate increases. Furthermore, etching by PS-DNA occurs quite independent of pH, which is also different from unmodified DNA. The PS-DNA mediated etching could also be controlled well by varying DNA length and conformation, and the number and location of PS modifications. With a higher activity of PS-DNA, the process of etching, ripening, and further etching was taken place sequentially. The etching ability is inhibited by forming duplex DNA and thus etching can be used to measure the concentration of complementary DNA.

Keywords: biosensors; oligonucleotides; phosphorothioate; plasmonics; silver nanoparticles.

Figure 1

(A) The structure of PO- and PS-DNA linkages for poly-C and poly-T DNA. The potential binding sites of DNA to AgNPs are marked in black and red circles. (B) The dropped extinction at 395 nm induced by 10 μM of 15-mer PO-DNA and PS-DNA. UV-vis spectra of the AgNPs treated with PO- and PS-DNA with the sequences of (C) A₁₅, (D) T₁₅, (E) G₁₅, and (F) C₁₅. The red dash lines represent red shifted spectra, while the black lines are for non-shifted spectra.

Figure 2

TEM micrographs of (A) untreated 20 nm AgNPs, and the AgNPs treated with 10 μM (B) PS₁₄-A₁₅, (C) PS₁₄-T₁₅, (D) PS₁₄-G₁₅, and (E) PS₁₄-C₁₅. (F) The average hydrodynamic diameter of the AgNPs etched by 10 μM of various 15-mer PS-DNA.

Figure 3

(A) PO-C₁₅, (B) PS₁₄-C₁₅, and (C) PS₁₄-T₁₅ concentration-dependent etching of the AgNPs. Relationship between DNA concentration and (D) dropped extinction and (E) wavelength shift of the AgNPs. (F) Comparison of the AgNPs etched by poly-C PO and PS DNA. With a stronger silver binding affinity, the PS DNA achieved the stage III reaction of further etching the larger AgNPs produced from the previous ripening stage.

Figure 4

Effect of pH on the kinetics of (A) PO-C₁₅, (B) PS₁₄-C₁₅, and (C) PS₁₄-T₁₅ mediated AgNPs etching. Citrate buffer was used for pH 4.0, 5.0, and 6.0, and MOPS buffer was used for pH 7.0 and 7.9. (D) Effect of low pH on the structure of some PO and PS DNA.

Figure 5

(A) The PS-DNA sequences used for studying the number of PS modifications. PS-DNA mediated AgNP etching as a function of (B) poly-T DNA length, (C) the number, and (D) the location of PS modifications. The final concentration of PS₄-T₅ was 35 μM, while the concentration of all other PS-DNAs was 10 μM.

Figure 6

(A) Schematics and (B) DNA sequences used for PS-DNA conformation-dependent etching of AgNPs. The mistached base is underlined. (C) UV-vis spectra of the AgNPs mixed with the PS-R DNA in the presence of various concentrations of the cDNA. The spectrum of the AgNPs (no DNA) is in bold with red color. The arrow points increased cDNA concetnration. (D) Dropped extinction of the AgNPs with the PS-R DNA mixed with 25 μM of different DNA sequences.