title: 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.
authors.affiliation: Institute for Photonics and Advanced Sensing (IPAS) and The ARC Centre for Nanoscale Biophotonics, The University of Adelaide, Adelaide 5005, Australia. vietlinh.nguyen@adelaide.edu.au.
authors.forename: Linh Viet
authors.initials: LV
authors.lastname: Nguyen
authors.affiliation: Information Engineering Department, University of Parma, Parma 43100, Italy. s.giannetti87@gmail.com.
authors.forename: Sara
authors.initials: S
authors.lastname: Giannetti
authors.affiliation: Institute for Photonics and Advanced Sensing (IPAS) and The ARC Centre for Nanoscale Biophotonics, The University of Adelaide, Adelaide 5005, Australia. stephen.warrensmith@adelaide.edu.au.
authors.forename: Stephen
authors.initials: S
authors.lastname: Warren-Smith
authors.affiliation: Australian Centre for Ancient DNA (ACAD), The University of Adelaide, Adelaide 5005, Australia. alan.cooper@adelaide.edu.au.
authors.forename: Alan
authors.initials: A
authors.lastname: Cooper
authors.affiliation: Information Engineering Department, University of Parma, Parma 43100, Italy. stefano.selleri@unipr.it.
authors.forename: Stefano
authors.initials: S
authors.lastname: Selleri
authors.affiliation: Information Engineering Department, University of Parma, Parma 43100, Italy. annamaria.cucinotta@unipr.it.
authors.forename: Annamaria
authors.initials: A
authors.lastname: Cucinotta
authors.affiliation: Institute for Photonics and Advanced Sensing (IPAS) and The ARC Centre for Nanoscale Biophotonics, The University of Adelaide, Adelaide 5005, Australia. tanya.monro@adelaide.edu.au.
authors.forename: Tanya
authors.initials: T
authors.lastname: Monro
mesh_terms: D004247:DNA / Q000235:genetics*; D005453:Fluorescence; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D055100:Optical Fibers; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*
chemical_list: D004247:DNA
references.citation: Proc Natl Acad Sci U S A. 1993 Nov 1;90(21):10325-9
references.pmid: 8234293
references.citation: Anal Chem. 1999 Nov 15;71(22):5054-9
references.pmid: 10575961
references.citation: Nature. 2001 Feb 15;409(6822):928-33
references.pmid: 11237013
references.citation: Opt Express. 2012 Dec 31;20(28):29378-85
references.pmid: 23388765
references.citation: Opt Express. 2008 Oct 27;16(22):18514-23
references.pmid: 18958130
references.citation: J Am Chem Soc. 2009 Dec 30;131(51):18192-3
references.pmid: 19961226
references.citation: Nat Biotechnol. 1996 Mar;14(3):303-8
references.pmid: 9630890
references.citation: Phys Rev Lett. 2005 Mar 18;94(10):108101
references.pmid: 15783528
references.citation: Nat Genet. 1999 Jan;21(1 Suppl):42-7
references.pmid: 9915500
references.citation: Genome Res. 1999 May;9(5):499-505
references.pmid: 10330130
references.citation: Anal Chem. 2006 Jun 15;78(12):3859-74
references.pmid: 16771528
references.citation: Am J Hum Genet. 1993 Jan;52(1):46-59
references.pmid: 8434605
references.citation: Langmuir. 2011 May 3;27(9):5680-5
references.pmid: 21469740
references.citation: Genomics. 1989 Nov;5(4):874-9
references.pmid: 2687159
references.citation: Nat Nanotechnol. 2013 Oct;8(10):729-34
references.pmid: 23995455
references.citation: Opt Express. 2014 Jan 27;22(2):1480-9
references.pmid: 24515155
references.citation: Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):7276-80
references.pmid: 1871133
references.citation: Clin Chim Acta. 2006 Jan;363(1-2):48-60
references.pmid: 16111667
references.citation: J Mass Spectrom. 2000 Jan;35(1):1-12
references.pmid: 10633229
references.citation: Hum Mutat. 1998;11(5):345-53
references.pmid: 9600452