The advent of click chemistry1
has led to the design of DNA analogs with modified nucleobases and backbones,2
thus allowing the development of a new generation of “smart” systems useful for chemical and biological applications.3
As a consequence of those synthetic efforts DNA analogs with improved stability, functionality and binding characteristics and with properties not present in natural nucleic acids have been produced.4
The new nucleic acid analogs have been also produced with the aim to develop innovative therapeutic agents5
or new tools for diagnostics.6
collectively referred to as functional nucleic acids, are RNA or DNA structures with binding and catalytic properties respectively. These systems have sequence-specific folds9
that achieve their tertiary folds and activities through a combination of different molecular interactions and motifs.10
Unfortunately, the use of functional nucleic acids in therapeutics has been hampered by their denaturation and/or biodegradation in body fluids. In this perspective, artificial nucleosides with unusual structural features may offer improved half-life in vivo, better structural stability, and could represent innovative systems to be used as novel interacting groups. Examples of promising non-natural nucleosides include conformationally restricted oligonucleotides such as peptide nucleic acid (PNA),11
locked nucleic acid (LNA),12
hexitol nucleic acid (HNA)13
and phosphoramidates morpholino (MORFs)14
Specific properties of artificial nucleosides have contributed to the development of more efficient tools for biosensing. In fact, artificial nucleoside probes have been used in combination with a number of different transduction platforms in order to achieve an even more sensitive and selective detection of nucleic acids and proteins.
Among the different platforms for multiplexed detection of protein markers and nucleic acids available, SPR15
has the greatest potential.16
In fact, recent improvements in instrumental and experimental design17
together with important features such as being real-time, label-free and having sensitive detection, make SPR a key technology for a wide range of potential therapeutic and diagnostic applications.18,19
The SPR phenomenon20
occurs when a plane-polarized radiation interacts with a metal film under total internal reflection conditions. At a specific incidence angle of the incoming radiation the intensity of the reflected light is attenuated. The resonance angle is dependent on the thickness and dielectric constant of both the metal film as well as its interfacing region. Keeping all the other conditions constant, the binding of molecules to the metal surface modifies the dielectric constant of the interface region, thus changing incident light/surface plasmons coupling conditions and the resonance angle. SPR experiments involve immobilizing one reactant on a metal surface (typically gold) and monitoring the reactant interaction with a second component which is typically available as a solute in a solution that flows over the sensor surface through a microfluidic cell.21
The SPR-based sensing benefits from the label-free detection22
and is useful for quantitative analysis and equilibrium and kinetic constants determination.23
In this paper, the state of the art technology of the currently available SPR applications based on functional and conformationally restricted artificial nucleic acids will be reviewed with specific attention to applications in diagnostics and detection of clinically relevant targets demonstrated over the past 15 years. A special emphasis will be given to DNA-like compounds such as aptamers and PNAs, which exhibit many advantages as recognition elements in biosensing when compared with traditional antibodies and DNA probes, respectively. In particular, this review will be aimed at introducing the SPR approach and at displaying how artificial DNAs can serve as bioreceptor components in SPR biosensing, while eliminating some processing steps that affect multiplex analysis capabilities. Moreover, this review will try to show how useful SPR is in addressing challenges associated with the study of artificial DNAs.
Due to the specific attention to applications in diagnostics and detection of clinically relevant targets this review will highlight those applications able to meet enhanced sensitivity requirements useful for their use in real matrices. Selected applications demonstrating lower sensitivity in target detection will be discussed when associated with significant advantages, such as the simplicity of the detection scheme or the use of innovative detection strategies. In this perspective, this review complements the existing ones from the past that mostly demonstrated the basic possibilities offered by SPR sensing and DNA analogs on model systems for proof-of-concept emphasis.