Raman Mapping of Biological Systems Interacting with a Disordered Nanostructured Surface: A Simple and Powerful Approach to the Label-Free Analysis of Single DNA Bases.

Valentina Mussi,Annalisa Convertino,Mario Ledda,Antonella Lisi

doi:10.3390/mi12030264

Abstract

This article demonstrates the possibility to use a novel powerful approach based on Raman mapping of analyte solutions drop casted on a disordered array of Ag covered silicon nanowires (Ag/SiNWs), to identify the characteristic spectral signal of the four DNA bases, adenine (A), thymine (T), cytosine (C), and guanine (G), at concentration as low as 10 ng/µL, and to study their specific way of interacting with the nanostructured substrate. The results show a distinctive and amplified interaction of guanine, the base that is most susceptible to oxidation, with the nanostructured surface. Our findings explain the recently revealed diverse behaviour of cancer and normal DNA deposited on the same Ag/SiNWs, which is ascribed to mechanical deformation and base lesions present on the oxidised DNA molecule backbone and causes detectable variation in the Raman signal, usable for diagnostic purposes. The notable bio-analytical capability of the presented platform, and its sensitivity to the molecule mechanical conformation at the single-base level, thus provides a new reliable, rapid, label-free DNA diagnostic methodology alternative to more sophisticated and expensive sequencing ones.

Highlights

Nanomedicine—the application of nanomaterials and nanotechnologies in the diagnostic and therapeutic field—is one of the greatest scientific innovations of recent years [1,2].Thanks to the reduced size, the high surface/volume ratio and the possibility to modify shape and surface chemistry, nanomaterials can interface and interact with biological systems and macromolecules at different scales of spatial resolution, from micro down to nanometre range, capturing physicochemical information and exchanging signals and organic matter with these biosystems
Au catalysed silicon nanowires (SiNWs) were produced by plasma-enhanced chemical vapour deposition (PECVD) on microscope glass slides and Si wafers
This study investigated the possibility of using a novel sensing approach, based on the SERS capability of a disordered array of Ag-covered silicon nanowires to analyse the characteristic Raman signal of the four DNA bases, at concentrations as low as

Summary

Introduction

Thanks to the reduced size, the high surface/volume ratio and the possibility to modify shape and surface chemistry, nanomaterials can interface and interact with biological systems and macromolecules (cells, DNA, proteins) at different scales of spatial resolution, from micro down to nanometre range, capturing physicochemical information and exchanging signals and organic matter with these biosystems. This will allow, in the very near future, the arrival of an early disease diagnosis and personalised therapies. The analysis of these DNA fragments in a peripheral blood sample, known as liquid biopsy, can influence clinical decisions, enabling the discovery of a tumour when it is not yet visible with traditional screening tools, which is a fundamental challenge in oncology [4,5]

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Conclusion