Distinguishing genomic DNA of Brassica juncea and Arabidopsis thaliana using surface‐enhanced Raman scattering

Abstract

AbstractThe emergence of the surface‐enhanced Raman scattering (SERS) technique as a prospective approach for the label‐free detection and fingerprinting of deoxyribonucleic acid (DNA) of microorganisms motivated us to detect traces of genomic DNA (gDNA) of Brassicaceae plant species, namely, Brassica juncea and Arabidopsis thaliana. DNA from the young leaf tissue of germinated B. juncea was extracted by modified cetyl trimethyl ammonium bromide extraction method and added to silver (Ag) and gold (Au) nanoparticles (NPs). The reduction in the absorbance of the surface plasmon resonance band of the metal NPs along with the appearance of a red‐shifted band indicated that DNA gets adsorbed on the metal NPs. The change in helicity of gDNA upon interaction with metal NPs was confirmed from circular dichroism studies. Dynamic light scattering measurements indicated that extent of aggregation is more in gDNA functionalized Au NPs than in Ag NPs. The transmission electron microscopy results corroborated the dynamic light scattering data. The marginal change in zeta potential value of Ag and Au NPs after binding to gDNA indicated good stability of the functionalized metal NPs. The SERS spectra revealed that adenine and deoxyribose were the active sites of gDNA that interacted with the metal NPs. From SERS, the limit of detection of gDNA was found to be ~10 and 1 ng μl−1 with Ag and Au NPs. The wavelength‐dependent Raman study showed that the charge transfer effect contributed to the SERS enhancement in addition to the electromagnetic effect. The SERS spectra of gDNA of A. thaliana functionalized Ag NPs were found to be different as compared with the gDNA of B. juncea probably due to the difference in their genome length and biochemical variability. Moreover, the Raman spectral signatures might differ due to changes in the adsorption pattern of the nucleotide bases on metal NPs surfaces.