A Biosensor Approach for DNA Sequences Detection in Non‐amplified Genomic DNA

Abstract

A biosensor approach using optical transduction based on surface plasmon resonance is adopted for the direct detection of target sequences in genomic DNA of several origins. In particular, the sensor was applied to three different sequences, representative of different living organisms from plant to human and differing in terms of copies in the relative genome.The sample pretreatment consisted in a fragmentation with restriction enzymes, followed by an optimized denaturation step. The biosensor resulted specific both with oligonucleotides and with genomic non-amplified DNA. The sensor could represent an alternative method to traditional biomolecular techniques for the identification of DNA sequences in digested DNA, bypassing the amplification step.

Ultrasensitive detection of non-amplified genomic DNA by nanoparticle-enhanced surface plasmon resonance imaging

“…However, a limited number of label-free or non-labeling applications on non-amplified genomic DNA samples have been so far described (Zhu et al, 2008;Zhang and Appella, 2007;Ho et al, 2005;Minunni et al, 2007;Goodrich et al, 2004;Stoeva et al, 2006;Storhoff et al, 2004). Most of the methods detect genomic DNA with pM-fM sensitivity.…”

“…The detection of 7 fM genomic DNA has been obtained by using an enzymatically amplified SPRI-based analytical approach (Goodrich et al, 2004) while the direct detection of 10 ppm solutions of plant, bovine and human genomic DNAs has been obtained by using spectral SPR (Minunni et al, 2007).…”

SPR-Based Affinity Biosensors as Innovative Analytical Devices

“…One probe is immobilized on the surface and the target sequence flows in solution. This approach has been applied in piezoelectric and SPR biosensing for ultrasensitive detection of fully complementary DNA sequences, avoiding PCR amplification of the template DNA [50][51][52]. If the focus of the analysis is instead SNPs detection, sandwich-like assay are better suited.…”

Quantitation of non-amplified genomic DNA by bead-based hybridization and template mediated extension coupled to alkaline phosphatase signal amplification

“…However, amplification bias and requirements for additional steps such as purification, introduce an additional source of errors on the final conclusions. In this view, efforts are being directed at the detection of non amplified DNA sequences (Arora et al 2008;Avarre et al 2007;Hill et al 2007;Minunni et al 2007).…”