Structural Characterization of DNA from Allium Leaves and E. coli by Surface-Enhanced Raman Spectroscopy (SERS)

Abstract

The label-free detection of biological molecules was demonstrated for different types of DNA. Surface-enhanced Raman spectroscopy (SERS) investigation on nucleic acids extracted from leaves of different Allium cepa cultivars (cvs.) De Buzău, Aurie de Buzău, Rubiniu, Roşie de Arieş as well as taxa A. ursinum, A. senescens subsp. montanum, A. schoenoprasum, A. obliquum, and A. fistulosum was performed using 532-nm laser excitation. Main SERS vibrations of these nucleic acids have been characterized, highlighting those at 658, 704, 1089, and 1125 cm−1 attributed to dG and dA phosphodiester groups as well as deoxyribose, specific constituents of DNA. The mild basic pH conditions of the samples can induce a partial breaking of the hydrogen bonds from the dsDNA, which affects the A = T/T = A as well as C≡G/G≡C base pairs and causes the aggregation of AgNPs mixed with DNA of the Allium cultivars and species. Also, SERS profiles of genomic DNA from E. coli 1559 were analyzed at decreasing pHs from 7 to 4. Protonation of the nitrogen N3 of the aromatic six-membered ring of both deoxyadenosine and deoxyguanosine, respectively, induces the decrease of the peak’s intensity at 1588 cm-1. Furthermore, SERS characteristics of plasmidic DNA from E. coli 7832 and of chromosomal DNA from E. coli MG 1655 are provided, with specific SERS modes indicated and new SERS bands found upon nucleic acids in vitro aging. Principal component analysis (PCA) in the full SERS spectrum range of bacterial DNA was performed.