On the Structure and Desorption Dynamics of DNA Bases Adsorbed on Gold:  A Temperature-Programmed Study

Abstract

The structure and desorption dynamics of mono- and multilayer samples of adenine, cytosine, guanine, and thymine on polycrystalline gold thin films are studied using temperature-programmed desorption-infrared reflection absorption spectroscopy (TPD-IRAS) and temperature-programmed desorption-mass spectroscopy (TPD-MS). It is shown that the pyrimidines, adenine and guanine, adsorb to gold in a complex manner and that both adhesive (adenine) and cohesive (guanine) interactions contribute the apparent binding energies to the substrate surface. Adenine displays at least two adsorption sites, including a high-energy site (210 degrees C, approximately 136 kJ/mol), wherein the molecule coordinates to the gold substrate via the NH2 group in an sp3-like, strongly perturbed, nonplanar configuration. The purines, cytosine and thymine, display a less complicated adsorption/desorption behavior. The desorption energy for cytosine (160 degrees C, approximately 122 kJ/mol) is similar to those obtained for adenine and guanine, but desorption occurs from a single site of dispersed, nonaggregated cytosine. Thymine desorbs also from a single site but at a significantly lower energy (100 degrees C, approximately 104 kJ/mol). Infrared data reveal that the monolayer architectures discussed herein are structurally very different from those observed for the bases in the bulk crystalline state. It is also evident that both pyrimidines and purines adsorb on gold with the plane of the molecule in a nonparallel orientation with respect to the substrate surface. The results of this work are discussed in the context of improving the understanding of the design of capturing oligonucleotides or DNA strands for bioanalytical applications, in particular, for gold nanoparticle-based assays.

Distinct Adsorbed States of DNA and RNA Bases Investigated by Flocculation-Assisted Surface Enhanced Raman Scattering

“…Thus, bases of A, G and C with a primary amino group (-NH 2 ) showed much lower critical concentrations than those of T and U without an -NH 2 group. Higher ccf values for A, G and C suggest much stronger interaction of these bases with Au surfaces compared with T and U, which is consistent with former reports on thermal stability of DNA bases adsorbed on gold [27]. Preferential adsorption of A, G and C is presumably due to coordination of a lone pair electrons located in purine and pyrimidine rings.…”

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.…”

Instantaneous Attachment of an Ultrahigh Density of Nonthiolated DNA to Gold Nanoparticles and Its Applications

“…over 100 kJ/mol) with thymine adsorption being the weakest. [45][46][47] While this energy is weaker than alkylthiol binding to gold (e.g. 120-160 kJ/mol), high stability could still be achieved.…”