Polypyrrole electrospotting for the construction of oligonucleotide arrays compatible with a surface plasmon resonance hybridization detection

The use of electropolymerized materials in the DNA sensors is reviewed with particular emphasis on their functions and specific interactions with DNA and oligonucleotides. Polyaniline, pollypyrrole, polythiophenes and polymeric forms of phenazines play significant role in the immobilization and signal transduction of DNA sensors for the detection of hybridization events, DNA–protein and other specific interactions on the sensor surface. The mechanism of electropolymerization and the influence of oligonucleotides are also considered for various types of polymers. The DNA sensor performance is classified in accordance with the biological targets and composition of the surface layer.

Cystic fibrosis is one of the most common genetically inherited diseases in Northern Europe, consisting of an inherited defect of chloride transport in the epithelium. Of the several mutations related to CF, the ΔF508 mutation occurs in ca. 70% of the cases. In this work the use of a gold nano-particle supported fluorescence molecular beacon was investigated as an optical sensing platform for the detection of the ΔF508 cystic fibrosis associated mutation. Different parameters such as molecular beacon design, Au nano-particle size, molecular beacon–nano-particle conjugation protocol, molecular beacon loading as well as experimental conditions were evaluated. A 31-base long molecular beacon, containing a 15-base recognition sequence specific for the mutant target, was linked via a thiol modified poly thymine linker (10 bases long) to a 13 nm gold nano-particle and was exposed to mutant and wild type targets, and a clear differentiation was achieved at target concentrations as low as 1 nM.

SPRi technology is a promising method for label-free detection and quantification of biomolecules interactions. In this present work, we present huge advance in multiplexing and reduction of the detection limit of SPRi technology, considering DNA interactions. We have used without electrodeposition an alternative chemistry for direct deposition of oligonucleotide probes on gold surface by using thiol-modified oligonucleotide probes. This immobilization of DNA probes is extremely efficient, reproducible and easy to implement. In addition we increased the spotting density up to 1000 spots, using commercial spotters dedicated to high-density microarrays. Increasing the roughness of the gold surface with gold nanoparticles prior to probe attachment, we amplified the optical signal of SPR by a factor 3 enabling the detection of DNA targets at concentrations as low as 2 nM. Finally, all these improvements make very attractive and competitive the SPRi technology.

In molecular biology, formamide (FA) is a commonly used denaturing agent for DNA. Although its influence on DNA duplex stability in solution is well established, little is known about immobilized DNA on microarrays. We measured thermal denaturation curves for oligonucleotides immobilized by two standard protocols: thiol self-assembling and pyrrole electrospotting. A decrease of the DNA denaturation temperature with increasing FA fraction of the solvent was observed on sequences with mutations for both surface chemistries. The average dissociation temperature decrease was found to be −0.58 ± 0.05 °C/% FA (v/v) independently of grafting chemistry and probe sequence.

The preparation of DNA-sensing architectures based on gold nanoparticles (Au-NPs) in conjunction with an “in situ” prepared ruthenium complex as a new route to improve the analytical properties of genosensors is described. In the development of these architectures several strategies to obtain Au-NPs modified gold electrodes (Au-NP/Au) have been essayed, in particular covalent binding and electrochemical deposition from a solution containing Au-NPs previously synthesized. UV–vis absorption measurements in conjunction with transmission electron microscope (TEM) images reveal that the synthesized Au-NPs are stable for at least 4 weeks and have a narrow size distribution. Atomic force microscopy (AFM) was employed to characterize the morphology and to estimate the Au-NPs surface coverage of the modified gold electrodes obtained following the different modification strategies. In order to assess the utility of these architectures as DNA-sensing devices, a thiolated capture probe sequence from Helicobacter pylori was immobilized onto the as-prepared surface. This sequence was chosen as a case of study within the framework of developing approaches of wide applicability. The hybridization event is detected using a water-soluble pentaamin ruthenium [3-(2-phenanthren-9-yl-vinyl)-pyridine] complex (Ru(NH₃)₅L) prepared “in situ”. This complex, due to its intercalative character, is able to bind to double stranded DNA more efficiently than to single stranded DNA. In addition, the metal provides with a redox center that can be used as an electrochemical indicator. On the basis of this strategy, complementary target sequences of H. pylori have been detected over the range of 40–800 pmol with a detection limit of 25 ± 2 pmol.

Electroactive 5-hydroxy-3-hexanedithiol-1,4-naphthoquinone (JUG_thio) has been self-assembled on gold. Electrochemical results show the surface coverage is 2.2 × 10⁻¹⁰ mol cm⁻², which is consistent with a dense monolayer. The JUG_thio shows one quasi-reversible and stable voltametric wave in aqueous buffered solution. A kinetic analysis of the redox reactions involving both electron and proton transfer has revealed an unusual behaviour of this molecule due to the presence of the hydroxyl function in the vicinity of the quinone group. The apparent kinetic rate constant and the anodic coefficient transfer of this reaction depend on the pH. In acid medium, a classical concerted 2e⁻/2H⁺ mechanism is obtained. In basic medium (pH > 7), strong intramolecular hydrogen interactions between the quinone and the hydroxyl function have a strong influence on the redox kinetics. These results show that JUG_thio electroactivity is very sensitive to hydrogen interactions in neutral and basic pH solution and is able to act as sensitive layer for electrochemical biosensing.