Polarity Control for Nonthiolated DNA Adsorption onto Gold Nanoparticles

Abstract

Gold nanoparticles (AuNPs) functionalized with thiolated DNA have enabled many studies in nanoscience. The strong thiol/gold affinity and the nanoscale curvature of AuNPs allow the attached DNA to adapt an upright conformation favourable for hybridization. Recently, it has been shown that non-thiolated DNA can also be attached via DNA base adsorption. Without a thiol label, both ends of the DNA and even internal bases could be adsorbed, decreasing the specificity of subsequent molecular recognition reactions. In this work, we employed a modular sequence design approach to systematically study the effect of DNA sequence on adsorption polarity. A block of poly-adenine (poly-A) could be used to achieve a high density of DNA attachment. When the poly-A block length is short (e.g. below 5-7), the loading was independent of the block length and the conjugate cannot hybridize to its cDNA effectively, suggesting a random attachment controlled by adsorption kinetics.Increasing the block length leads to reduced capacity but improved hybridization, suggesting that more DNA with the desired conformation was adsorbed due to the thermodynamic effects of poly-A binding.The design can be further improved by including capping sequences rich in T or G. Finally, a more general double-stranded DNA approach was described to be suitable for DNA that cannot satisfy the abovementioned design requirements.

eMethylsorb: rapid quantification of DNA methylation in cancer cells on screen-printed gold electrodes

“…Adenine-rich oligonucleotides have been observed to display the highest binding affinity to gold surfaces over other oligonucleotide sequences. [15][16][17][18][19] Due to adenine-gold adsorption affinity being higher than that of guanine-gold, a higher amount of adenine-enriched ss-DNA will adsorb onto the working surface of the SPE-Au. The amount of adsorbed DNA is detected electrochemically by measuring the interfacial electron transfer reaction of [Fe(CN) 6 To demonstrate the eMethylsorb assay, we detected methylation levels in synthetic DNA samples which were designed to be similar to bisulte-treated and asymmetric PCR-amplied target sequences of the EN1 gene.…”

Parallel Polyadenine Duplex Formation at Low pH Facilitates DNA Conjugation onto Gold Nanoparticles

“…>60 poly-A DNA per 13 nm AuNP). 25,26 Without a thiol group, DNA is expected to wrap around AuNPs, 27-31 which should limit its density.…”

“…19 After observing the interesting effect of low pH, we initially attributed it to a simple electrostatic model. In this work, we emphasized also on the effect of DNA conformation, which allowed us to explain the difference between poly-A and poly-C spacer, 26 and also the adsorption of non-thiolated DNA. Now that the importance of the parallel poly-A is confirmed, we can intentionally design sequences to contain poly-A instead of poly-C.…”

Tandem Phosphorothioate Modifications for DNA Adsorption Strength and Polarity Control on Gold Nanoparticles

“…The first limitation is the lack of sequence generality. 21 For example, if a DNA is rich in adenine or cytosine in the whole sequence, it is unlikely that it can be attached only via the intended poly-A anchor. 21 If the other end is also 4 adsorbed on gold, subsequent hybridization may be hindered.…”