Structure and surface dynamics of genomic DNA as probed with surface-enhanced Raman spectroscopy: Trace level sensing of nucleic acids extracted from plants.

In this work surface-enhanced Raman spectra of nucleic acids from in vitro grown Solanum tuberosum L. cultivars and populations (Buzau population, Lazarea population, Patraque d'Auvergne, RFA Roclas Clone 2.6 Ferma, Vitelotte Negresse, Roclas Clone C, Blue Congo) were measured with 532 nm laser line. Main surface-enhanced Raman modes of these DNAs have been analyzed. Also, DNA from two grapevine (Vitis vinifera L.) varieties were studied at acidic pHs by surface-enhanced Raman spectroscopy. Modified SERS intensities and wavenumber shifts of nucleic acids bands were observed upon lowering the pH, being a proof of binding affinity changes of DNA with silver nanoparticles (AgNPs) and of structural modifications induced at acidic pHs in DNA molecular groups. Furthermore, the (sub)picosecond surface dynamics of DNA extracted from leaf tissues of grapevine (Vitis vinifera L.) varieties was investigated. In this work, the bands full widths at half-maximum (FWHMs) have values in the wavenumber range from 8 to 34 cm-1. (Sub)picosecond molecular dynamics of DNA groups with global relaxation times between 0.31 ps - 1.33 ps has been found.

Acidic pH-responsive changes of DNA structure and surface dynamics as probed with ultrasensitive Raman spectroscopy.

In this work structural and (sub)picosecond surface dynamical changes of genomic DNA isolated from different medicinal plants (Hyssopus officinalis, Majorana hortensis, Melissa officinalis, Mentha piperita, Mentha piperita cv "Cristal", Monarda didyma and Matricaria chamomilla), as probed with surface-enhanced Raman spectroscopy (SERS), are discussed upon modifying the acidic pH of mixtures consisting of silver colloidal suspension and DNA samples, respectively. Binding affinity changes of DNA with silver NPs and nucleic acids protonation are supposed to take place upon lowering the pH. A small percentage of Hoogsteen GC basepairs was found in Mentha piperita cv "Cristal" DNA, at low acidic pH. As a general observation, the global relaxation times corresponding to different functional groups of the investigated genomic DNAs, respectively, show a decrease of their values upon lowering the pH.

Surface dynamics of genomic DNAs upon lowering the pH, in the presence of graphene/AgNPs-based SERS detection platform.

Graphene/AgNPs-based surface dynamics of native DNA functional groups at different acidic pH values was discussed using surface-enhanced Raman spectroscopy (SERS). Also, ab initio dynamics of Verlet type was investigated for nucleic acid nitrogenous bases adsorbed on a graphene surface, respectively. The experimental dynamical parameters were given in terms of full widths at half-maximum (FWHMs) and (sub)picosecond global relaxation times, associated with SERS bands. Furthermore, using density functional theory (DFT) as implemented in SIESTA and the velocity autocorrelation function (VACF), we have obtained the vibrational density of states (VDOS) for each of the four DNA bases placed on a pristine graphene layer. Graphical abstract Top: computed VbDOS for guanine. Bottom: Verlet temperature as a function of time.