Genotyping Single Nucleotide Polymorphisms Using Different Molecular Beacon Multiplexed within a Suspended Core Optical Fiber

Abstract

We report a novel approach to genotyping single nucleotide polymorphisms (SNPs) using molecular beacons in conjunction with a suspended core optical fiber (SCF). Target DNA sequences corresponding to the wild- or mutant-type have been accurately recognized by immobilizing two different molecular beacons on the core of a SCF. The two molecular beacons differ by one base in the loop-probe and utilize different fluorescent indicators. Single-color fluorescence enhancement was obtained when the immobilized SCFs were filled with a solution containing either wild-type or mutant-type sequence (homozygous sample), while filling the immobilized SCF with solution containing both wild- and mutant-type sequences resulted in dual-color fluorescence enhancement, indicating a heterozygous sample. The genotyping was realized amplification-free and with ultra low-volume for the required DNA solution (nano-liter). This is, to our knowledge, the first genotyping device based on the combination of optical fiber and molecular beacons.

Taming the Light in Microstructured Optical Fibers for Sensing

“…Further work has explored the use of these fibers for specific DNA detection and genotyping, where molecular beacons have been multiplexed to differentiate between wild‐ and mutant‐type sequences in MOFs …”

An Advanced Detection System for <i>In Situ</i> Hybridization Using a Fluorescence Resonance Energy Transfer-based Molecular Beacon Probe

“…Overcoming this energy barrier can be achieved with a perfectly matched target. Indeed, MB probes can be used to detect single-nucleotide polymorphisms based on the ability to discriminate single base differences in PCR [27,30]. In our study, the fluorescence intensity decreased dramatically in 1 or 2 basemismatch probes in both medium and tissue sections.…”

All-fiber all-optical quantitative polymerase chain reaction (qPCR)

“…For example, complementary ssDNA can be immobilized onto an optical fiber such as for the detection of quantum dot labelled ssDNA [ 40 ] or label-free detection using gold coated tapers fibers [ 41 ]. In our previous work, we demonstrated DNA detection with nanoliter samples by immobilizing molecular beacons to the internal surface of microstructured optical fiber [ [42] , [43] , [44] ]. However, these techniques are limited to relatively large concentrations of DNA and misses out on the amplification power of qPCR that allows it to detect and quantify ultra-low concentrations of DNA.…”