Label-free microarray imaging for direct detection of DNA hybridization and single-nucleotide mismatches

Abstract

A novel method is proposed for direct detection of DNA hybridization on microarrays. Optical interferometry is used for label-free sensing of biomolecular accumulation on glass surfaces, enabling dynamic detection of interactions. Capabilities of the presented method are demonstrated by highthroughput sensing of solid-phase hybridization of oligonucleotides. Hybridization of surface immobilized probes with 20 base pair-long target oligonucleotides was detected by comparing the label-free microarray images taken before and after hybridization. Through dynamic data acquisition during denaturation by washing the sample with low ionic concentration buffer, melting of duplexes with a single nucleotide mismatch was distinguished from perfectly matching duplexes with high confidence interval (>97%). The presented technique is simple, robust, and accurate, and eliminates the need of using labels or secondary reagents to monitor the oligonucleotide hybridization.

Label-free pathogen sensing: Microarray studies for clinical and research applictions

“…This system has been demonstrated to have high sensitivity, precision, and reproducibility for different biomolecular interactions [1][2][3]. The IRIS platform benefits from real time and endpoint measurement capabilities and is simple to use, requires inexpensive equipment, and utilizes well-characterized silicon-based solid phase assay components.…”

Electrical sensing of DNA-hybridization using two-port network based on suspended carbon nanotube membrane

“…Methods for label-free DNA hybridization detection are in demand because they are simple, fast, and able to realize real-time, in-situ detection. They are currently achieved mainly by optical (Bougot-Robin et al 2014;Toccafondo et al 2010;Özkumur et al 2010;Suter et al 2008;Zhu et al 2014), mechanical (Ramos et al 2009;Su et al 2003;Ilic et al 2005;Huber et al 2013;Zuniga et al 2009;, and electrical (Zebda et al 2010;Paleček et al 1998;Zaffino et al 2014;Sensors et al 2012;Khan et al 2010;Martins et al 2011;Archer et al 2004) technologies.…”

LED-based Interferometric Reflectance Imaging Sensor for quantitative dynamic monitoring of biomolecular interactions

“…To detect molecular interactions, this technique uses common-path interferometry through a Si/SiO 2 layered substrate acting as the sensor surface by monitoring local optical path length changes attributed to mass accumulation at the surface. IRIS has proven to be a versatile platform to monitor antigen-antibody binding, DNA hybridization, and single nucleotide polymorphisms (SNPs) through DNA denaturation kinetics (Özkumur et al, 2010;Ozkumur et al, 2008Ozkumur et al, , 2009. The IRIS platform relied on a tunable laser source to monitor the spectral signature of the reflection from the layered sensor surface in an imaging modality.…”