Advanced Evanescent-Wave Optical Biosensors for the Detection of Nucleic Acids: An Analytic Perspective.

Cesar S Huertas,Olalla Calvo-Lozano,Laura M Lechuga,Arnan Mitchell

doi:10.3389/fchem.2019.00724

Abstract

Evanescent-wave optical biosensors have become an attractive alternative for the screening of nucleic acids in the clinical context. They possess highly sensitive transducers able to perform detection of a wide range of nucleic acid-based biomarkers without the need of any label or marker. These optical biosensor platforms are very versatile, allowing the incorporation of an almost limitless range of biorecognition probes precisely and robustly adhered to the sensor surface by covalent surface chemistry approaches. In addition, their application can be further enhanced by their combination with different processes, thanks to their integration with complex and automated microfluidic systems, facilitating the development of multiplexed and user-friendly platforms. The objective of this work is to provide a comprehensive synopsis of cutting-edge analytical strategies based on these label-free optical biosensors able to deal with the drawbacks related to DNA and RNA detection, from single point mutations assays and epigenetic alterations, to bacterial infections. Several plasmonic and silicon photonic-based biosensors are described together with their most recent applications in this area. We also identify and analyse the main challenges faced when attempting to harness this technology and how several innovative approaches introduced in the last years manage those issues, including the use of new biorecognition probes, surface functionalization approaches, signal amplification and enhancement strategies, as well as, sophisticated microfluidic solutions.

Highlights

Nucleic acids (NA) have a key function in many important cellular mechanisms, such as cell differentiation, cell-division cycle, signal transduction, or metabolism (Fatica and Bozzoni, 2014; Mens and Ghanbari, 2018; Mori, 2018)
The objective of this work is to give a comprehensive overview of the analytical strategies that employ evanescentwave optical biosensors to deal with the complexities and challenges of effective NA detection, with applications ranging from identification of SPNs and epigenetic alterations in cancer, to the detection of indirect modifications of NA processes caused by bacterial infections
Different microfluidic designs can be fabricated on a single chip and disposed in customized arrangements to perform different procedures (Jung et al, 2015). This is of particular interest in NA analyses, since protocols usually involve multiple steps, such as sample lysis to expose NAs found in the cells or exosomes, their purification and extraction or their amplification to increase the target copy number before the eventual detection by the biosensors, as discussed in the previous section. mRNA isolation has been achieved by the purification with oligo that selectively hybridize to the poly (A) tail found mRNAs, achieving up to 70% efficiency (Satterfield et al, 2007)

Summary

Introduction

Nucleic acids (NA) have a key function in many important cellular mechanisms, such as cell differentiation, cell-division cycle, signal transduction, or metabolism (Fatica and Bozzoni, 2014; Mens and Ghanbari, 2018; Mori, 2018). Our DNA is the best-known NA molecule and it contains our genetic information. It is translated into proteins by the expression of messenger RNA (mRNAs). This translation may be more complex than faithful transcription of the DNA code to form proteins. Many species have cellular mechanisms that can edit the mRNAs by alternative splicing processes, resulting in a significant increase in protein diversity (Liu et al, 2012).

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