The Controversial Orientation of Adenine on Gold and Silver

Abstract

In which orientation does adenine adsorb on gold and silver surfaces? This question has been a matter of debate for over 30 years. Since the dawn of surface-enhanced Raman spectroscopy (SERS); it and other techniques such as tip-enhanced Raman spectroscopy (TERS), surface-enhanced infrared absorption spectroscopy (SEIRAS), scanning tunneling microscopy (STM), density functional theory (DFT) simulations, and more, have been used in many attempts to answer this seemingly straightforward, yet controversial, question. Herein, the timeline and recent advances on this topic are explored, and the frequently contradictory findings are put into context and discussed.

Detection of Biological Bricks in Space. The Case of Adenine in Silica Aerogel

“…Adenine has been the subject of numerous SERS studies since the early 2000s. However, there are some debates about how adenine adsorbs on a silver or gold surface, as well as its orientation, which are crucial parameters for the exaltation of the SERS signal [21][22][23][24][25]. There is also uncertainty about the exact assignments of some bands [16,17,[26][27][28].…”

Surface enhancement Raman spectroscopy and density functional theory study of silver nanoparticles synthetized with d‐glucose

“…Harrounhas carried out a thorough analysis of the adenine adsorption sites on gold and silver surfaces, using results obtained by different variants of Raman spectroscopy and computational calculation methods, finding that the experimental conditions are determinant in the nature of union of this molecule. [17] Using methodologies similar to those previously mentioned, Yao and Huang studied the possible conformations of absorption of cysteine on AuNPs, finding a preference in the interaction of this amino acid with the surface through its sulfur and oxygen atoms. [18] On the other hand, Maiti et al measured the absorption of amino polycarboxylic acid ligands on AgNPs using SERS and DFT methods.…”

The effect of DNA bases permutation on surface-enhanced Raman scattering spectrum

“…The latter include DNA characterization with a reduced number of thermocycling steps in polymerase chain reaction (PCR) amplification [25], mutation detection due to molecular conformation change [26] or employing branched DNA technique which relies on the signal amplification of the probe that binds to a specific nucleotide sequence [27], which are typically more sensitive than conventional fluorescent labeling (see for instance a recent work [28]). Nevertheless, the extreme sensitivity of SERS with respect to numerous factors such as substrate quality, dielectric environment, as well as unknown molecule orientation, occasionally leads to controversial results on gold [29] and silver [30] substrates, indicating that further research is needed to understand the basic physical mechanisms of plasmon-DNA interaction and how to leverage them in order to enhance present capabilities, eventually leading to bio-medical applications which require higher precision than achieved today [31]. In particular, considering increasingly complex DNA sequences, where each nucleotide in turn is composed of additional subunits, is expected to introduce novel mechanisms that affect the corresponding Raman and SERS spectra; it is reasonable to assume that incorporating these effects might improve the accuracy of future plasmonic-based detection schemes.…”

“…For simplicity, our computational model studies single orientation of DNA bases relative to the metal, and therefore it is not used for quantitative comparison against experimental results. In fact, predicting the binding sites of ssDNA molecules with the metal and the resultant orientation of these molecules is still somewhat controversial; e.g., adenine binding orientation [29] or orientation dependence due to interaction with magnesium cations [34] (which are used in our experiments), is expected to lead to considerable variation in the corresponding spectra. This work is structured as follows.…”