Development of a nano sensor for direct-electric free-label detection of DNA’s hybridization and single nucleotide polymorphism

Abstract

The search for analytical tools suitable for wide-scale application of DNA analysis is an hot research topic, although thanks to well-established microarray based technology, analysis of DNA sequences and SNP detection can be worked out through a fairly laboratory routine.

DNA analysis has nowadays become of increasing interest for several different purposes, mainly thanks to the successful employment of microarray technology, characterized by high sensitiveness and high-throughput analysis, which rapidly advanced genetics leading to devel- opment of many fields of application of DNA analysis, which keeps high the trend in alternative technologies, which could overcome inherent limitations of microarrays technology.

In this regard, many efforts have been spent to study electrochemical/electrical based detection strategies by means of which it could be possible to accomplish sensitive analysis by using portable equipments, cheaper and more practical than optical ones, and with scalable-devices compatibles with standard microelectronic processing.

Emerging nano-probes with increased chemical-physical properties are considered with growing interest in DNA biosensors as ideal candidates to enhance electrochemical/electrical based detection systems. Among these, nano-gaps adjusted to fit DNA, or in general analyte molecules sizes, are very promising because they can enable direct electrical detec- tion schemes, thus providing a straightforward electronic analogue of the successful DNA microarray standard.

Electrical properties of DNA have been the principal focus of many experimental and theoretical research, since early experimental founding confirmed an old hypothesis, for its relevance in the biological function of DNA, being related both with damage and base repair, but also for the appealing potential for biosensor and, in general, in bioelectronic applications.

Thanks to its peculiar interactions, it allows versatile manipulations of the structure, compared to other organic and synthetic polymers which have been considered for such purposes. Even though many questions still are open on electrical properties of DNA, it is generally accepted that DNA's conductivity is intimately linked with details of the sequences involved, its length and the overall environment in which molecule is found. The sensitivity to structure's alteration, as that induced by the presence of a mutation, confirmed by experimental and theoretical works allows to exploit DNA electrical properties for biosensor applications.

Relying on this agreed description of DNA electrical properties features, the general aim of this thesis was to explore the possibility of developing a platform for the direct transduction of DNA hybridization event based on a nano-gap device and electrical signaling enabled by long range electron transport through DNA molecules.

La detección de hibridación de cadenas de ADN es un reto relevante científicamente y tecnológicamente, que puede aprovechar de las posibilidades proporcionadas por los alcances en los procesos de nano fabricación y caracterización, inspiradores de la idea de una medicina en el punto de atención.

El propósito de este trabajo es de establecer un sistema de detección de hibridación de ADN, y polimorfismo de un solo nucleótido (SNP), basado en la medida eléctrica de la reasistencia de un nano-gap funcional izado con el ADN diana.

El desarrollo y test del sistema se ha llevado a cabo fijando diferentes objetivos.

Un estudio preliminar de la literatura relacionada con las propiedades eléctricas del ADN se ha conducido con la finalidad de establecer el marco de factibilidad del proyecto. De acuerdo con los resultados de este estudio ha sido posible idear el sistema y optimizar su eficacia respeto a las experiencias reportadas.

Fijar una estrategia de fabricación de los dispositivos capaz de proveer nano-gaps aptos a la medida de conductividad muy baja, según una rutina de fácil implementación y con alta reproducibilidad de los resultados. Estos se han caracterizados mediante el utilizo de diferentes técnicas basadas primariamente en métodos de detección Óptica y Eléctrica/Electro-química.

Obtener la bio-funcionalización selectiva de los electrodos en el nano-gap testando y caracterizando métodos diferentes.

Probar el principio de funcionamiento del sistema a través de la medida de la conductividad en los nano-gap durante las diferentes etapas de funcionalización con los bio-receptores y el DNA target.

Optimizar el sensor testando su selectividad respeto a la presencia de mutaciones, la sensibilidad a medir diferentes concentraciones del target, y finalmente la posibilidad de regeneración del dispositivo después desnaturalización del ADN hibridado