Subpicosecond surface dynamics in genomic DNA from in vitro-grown plant species: a SERS assessment

Abstract

In this work the surface-enhanced Raman total half band widths of seven genomic DNAs from leaves of chrysanthemum (Dendranthema grandiflora Ramat.), common sundew (Drosera rotundifolia L.), edelweiss (Leontopodium alpinum Cass), Epilobium hirsutum L., Hypericum richeri ssp. transsilvanicum (Čelak) Ciocârlan, rose (Rosa x hybrida L.) and redwood (Sequoia sempervirens D. Don. Endl.) have been measured. We have shown that surface-enhanced Raman spectroscopy (SERS) can be used to study the fast subpicosecond dynamics of DNA in the proximity of a metallic surface. The dependencies of the total half band widths and the global relaxation times, on the DNA molecular subgroup structure and on the type of genomic DNA, are reported. In our study, the full widths at half-maximum (FWHMs) for the SERS bands of genomic DNAs from different leaf tissues are typically in the wavenumber range from 15 to 55 cm(-1). Besides, it can be observed that molecular relaxation processes studied in this work have a global relaxation time smaller than 0.71 ps and larger than 0.19 ps. A comparison between different ranges of FT-Raman and SERS band parameters, respectively, corresponding to DNA extracted from leaf tissues is given. It is shown that the interaction between DNA and a metallic surface has the potential to lead to a shortening of the global relaxation times, as compared with molecular dynamics in solution. We have found that the surface dynamics of molecular subgroups in plant DNA is, in some cases, about two times faster than the solution dynamics of nucleic acids. This can be rationalized in a qualitative manner by invoking the complex landscape of the interaction energy between the molecule and the silver surface.

Distinguishing genomicDNAofBrassica junceaandArabidopsis thalianausing surface‐enhanced Raman scattering

“…The observed differences in the SERS results of Muntean et al and the present study are possibly due to the changes in the adsorption pattern of the nucleotide bases on the metal NPs surfaces. In addition, the excitation wavelengths of 514, 633, and 785 nm with the laser powers of 10, 17, and 100 mW were used in the present study, whereas the SERS measurements by Muntean et al were carried out using the frequency‐doubled output of pulsed Nd 3+ :YAG laser emitting at 532 nm with laser power of 45 mW. The use of pulsed laser may lead to higher peak power and local heating of DNA samples.…”

“…The SERS results of gDNA from B. juncea plant observed in the present study were compared with the previous results on SERS of plant DNA, which illustrated that in contrast to the study of Muntean et al where intense peaks were observed around 1600, 1360, and 1300 cm −1 , our results and those of Qiu et al as well as Liu et al found weak peaks in the region 1150–1800 cm −1 and strong peaks at 625, 718, and 1013 cm −1 . The observed differences in the SERS results of Muntean et al and the present study are possibly due to the changes in the adsorption pattern of the nucleotide bases on the metal NPs surfaces. In addition, the excitation wavelengths of 514, 633, and 785 nm with the laser powers of 10, 17, and 100 mW were used in the present study, whereas the SERS measurements by Muntean et al were carried out using the frequency‐doubled output of pulsed Nd 3+ :YAG laser emitting at 532 nm with laser power of 45 mW.…”

“…Due to the increasing interest in sensitive and detailed structural information required in molecular biophysics and medicine, SERS study of genomic DNA (gDNA) from plants has gained importance. The SERS investigation of gDNA from in vitro grown tomato plant showing the structural changes of the DNA upon cryopreservation was reported by Muntean et al They also carried out subpicosecond dynamics of DNA from plant tissues . SERS study of gDNA of different plant tissues was also investigated .…”

Influence of the Au Cluster Enhancer on Vibrational Spectra of Nucleotides in MD Simulation of a SERS Sensor

“…The study of vibrational spectra of the nucleotides in the dynamic interaction with the metallic nanoparticles (NP) [44,45] located close to graphene nanopore can combine translocation localization and nucleotide interaction enhancement or modification due to (1) the graphene LJ interaction and (2) the Au LJ interaction. For the initial interaction of the Au20 nanoparticle with cytosine nucleotide, the Au20 NP was localized close to the cytosine initial position as it is shown in…”

Vibrational Relaxation of the Backbone and Base Modes in LacDNA Complexes by UV Resonance Raman Spectroscopy

“…Previously, monitoring the changes in the normal Raman full widths at half-maximum (fwhm’s) and, correspondingly, in the global relaxation times of the functional groups in DNA, upon varying the physicochemical parameters, was of interest. , In these cases, solution dynamics of nucleic acids was under study. Besides, the surface dynamics of plant genomic DNA on silver nanoparticles was reported by us for several cases using surface-enhanced Raman scattering (SERS) (refs and and references therein).…”