In Situ Surface Plasmon Resonance Imaging Detection of DNA Hybridization to Oligonucleotide Arrays on Gold Surfaces

Abstract

A new method for constructing oligonucleotide arrays on gold surfaces has been developed, and these arrays have been used in DNA hybridization experiments with in situ surface plasmon resonance (SPR) imaging detection. The detection technique was able to differentiate between single- and double-stranded DNA regions on the gold surface. The hybridization of both oligonucleotides and PCR-amplified DNA fragments was detectable, with the latter exhibiting slower hybridization kinetics. Temperature control of the in situ SPR cell was used to discriminate between perfectly matched duplexes and single-base-mismatched duplexes. The SPR detection technique requires no label on the DNA, but fluorescently labeled targets were also tested and detected by fluorescence imaging as an independent verification of the hybridization behavior of these DNA arrays. The in situ SPR imaging method for detection of DNA hybridization is expected to complement other existing methods for study of DNA interactions and might find future uses in mutation screening assays and DNA resequencing.

Discovery and verification of functional single nucleotide polymorphisms in regulatory genomic regions: Current and developing technologies

“…This technique has been utilized to measure many kinds of biomolecular interactions including antibody-epitope recognition (i.e. protein-protein interaction) [53], DNA: DNA or DNA:RNA oligomerization [54][55][56][57] and DNA-protein interactions [58][59][60][61]. DNA microarray technology has been combined with SPR imaging analysis to create a medium to high-throughput methodology for quantifying DNA-protein interactions [62] in which a recently modified DNA array generation process has enhanced detection of interactions with double-stranded sequences of similar makeup (i.e., SNPs in binding regions) [63].…”

Rapid label-free DNA analysis in picoliter microfluidic droplets using FRET probes

“…Analysis of DNA sequences with single nucleotide polymorphism (SNP) is one of the major methods for diagnosing genetic diseases. Microarray (Lipshutz et al 1999;van't Veer et al 2002), quartz crystal microbalance (QCM) (Caruso et al 1997;Okahata et al 1998) and surface plasmon resonance (SPR) (Thiel et al 1997;He et al 2000) are examples that have been developed to analyze DNA hybridization, sequencing and SNP. However, these methods are often carried out in bulk solutions with immobilized sensing probes on the substrate surface, which is dependent on the passive diffusion of DNA samples toward the sensing probes.…”

Detection of Avian Influenza-DNA Hybridization Using Wavelength-scanning Surface Plasmon Resonance Biosensor

“…Therefore, a simple, rapid, and sensitive detection method to overcome the limitations of conventional virological techniques is required. Surface plasmon resonance (SPR), a surface-limited optical technique that senses refractive index changes that occur in the vicinity of a thin metal surface, has been used to measure DNA hybridization [3]. SPR biosensors have attracted significant interest because they can be used for real-time monitoring and sensitive and quantitative detection [4].…”

“…Among various SPR measurement schemes, SPR imaging systems have been explored extensively due to their potential for use in high-throughput sensing applications [3,5,6]. An intensity-based SPR imaging system comprising a monochromatic light source and a fixed incidence angle has a simple structure.…”

“…However, the application of NIR to SPR microarray imaging is limited, because as the surface plasmon propagation length increases with wavelength, the lateral image resolution becomes significantly poorer. Moreover, accurate quantification of DNA hybridization is challenging, though SPR analysis of oligonucleotide arrays on gold surfaces can differentiate between single-and double-stranded DNA regions [3].…”