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

Abstract

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.

Keywords: (Sub)picosecond surface dynamics; Acidic pH; Genomic nucleic acids; Protonated DNA structures; Surface-enhanced Raman spectroscopy.