Synthesis of mixed-sequence oligonucleotides on mesoporous silicon: chemical strategies and material stability.

Monica Terracciano,Giorgia Oliviero,Stefano D'Errico,Fabrizia Nici,Nicola Borbone,Ivo Rendina,Gennaro Piccialli,Ilaria Rea,Luca De Stefano

doi:10.1186/1556-276x-9-317

Abstract

Rapid screening tests in medical diagnostic and environmental analysis are often based on oligonucleotide biochips. In this paper, we studied the stability of functionalized mesoporous silicon supports in the solid-phase synthesis of oligonucleotides, exploiting several chemical procedures. A 19-mer mixed sequence has been successfully synthesized on aminosilane-modified porous silicon photonic structures. The process and the materials have been characterized by optical reflectivity, atomic force microscopy and high-performance liquid chromatography.

Highlights

DNA chip technology has greatly evolved over the last decade, moving from pure genomics towards a number of biotechnology applications such as human disease diagnostics [1], environmental monitoring and food control [2,3]
We successfully demonstrated that even using the less aggressive carbonate/methanol solution as the ON deprotection system, hybridization with the complementary ON target took place, confirming that ONs can be synthesized and deprotected on the Porous silicon (PSi) surface
We describe the results of alternative PSi-friendly ON deprotection conditions during the in situ synthesis of mixed-sequence ONs on PSi supports by using standard phosphoramidite nucleoside monomers, without using ultra-mild reagents

Summary

Introduction

DNA chip technology has greatly evolved over the last decade, moving from pure genomics towards a number of biotechnology applications such as human disease diagnostics [1], environmental monitoring and food control [2,3]. DNA chips can be classified as a special class of biosensors since they are realized by immobilization of single-stranded oligonucleotides (ONs), the bioprobe, on a transducer surface. Any molecular interaction between the bioprobe and its ligands, such as hybridization to the complementary DNA sequence or protein binding, is transduced into an analytical signal by an electrochemical-, optical- or surface plasmon resonancebased or electrical device, depending on the specific technology used. Porous silicon (PSi) is by far one of the most popular transducer materials due to its peculiar physical and chemical properties [4]. PSi is fabricated by electrochemical etching of crystalline silicon in aqueous hydrofluoric acid. Current density and acid concentration, several porous morphologies can be obtained, from micropores (average pore size 50 nm) [5]. The resulting sponge-like matrix possesses a very large specific

Methods

Results

Conclusion