title: Specificity of SNP detection with molecular beacons is improved by stem and loop separation with spacers.
abstract: Molecular beacons (MBs) are valuable tools in molecular biology, clinical diagnostics and analytical chemistry. Here we describe a novel approach for the design of MBs with nucleotide or non-nucleotide linkers between the stem and loop regions. Such modified MBs have significantly improved specificity and performance for single nucleotide polymorphism (SNP) detection. These advantages are especially distinct, when compared to the classic MBs, in the case of possible interactions between the stem and loop regions. We demonstrated the applicability of such modified MBs for the discrimination of common Factor V, NOS3 and ADRB2 SNPs in model plasmids and in clinical samples. The developed approach could be applicable not only to fluorescently labeled MBs, but also to other biosensors based on nucleic acids with stem-loop structures.
authors.affiliation: Skolkovo Institute of Science and Technology, 3 Nobel Street, Innovation Center "Skolkovo", 143026 Skolkovo, Russia. t.zatsepin@skoltech.ru and Central Research Institute of Epidemiology, Novogireevskaya 3a, 111123 Moscow, Russia.
authors.forename: Valentina M
authors.initials: VM
authors.lastname: Farzan
authors.affiliation: Research Institute of Occupational Health, Prospekt Budenogo 31, 105275 Moscow, Russia.
authors.forename: Mikhail L
authors.initials: ML
authors.lastname: Markelov
authors.affiliation: Metkinen Chemistry Oy., Microkatu 1, MicroTower Part-M, FI-70210 Kuopio, Finland.
authors.forename: Alexander Yu
authors.initials: AY
authors.lastname: Skoblov
authors.affiliation: Central Research Institute of Epidemiology, Novogireevskaya 3a, 111123 Moscow, Russia.
authors.forename: German A
authors.initials: GA
authors.lastname: Shipulin
authors.affiliation: Skolkovo Institute of Science and Technology, 3 Nobel Street, Innovation Center "Skolkovo", 143026 Skolkovo, Russia. t.zatsepin@skoltech.ru and Central Research Institute of Epidemiology, Novogireevskaya 3a, 111123 Moscow, Russia and Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119992 Moscow, Russia.
authors.forename: Timofei S
authors.identifier: http://orcid.org/0000-0003-0030-9174
authors.initials: TS
authors.lastname: Zatsepin
mesh_terms: D015374:Biosensing Techniques; D009696:Nucleic Acids / Q000737:chemistry*; D015345:Oligonucleotide Probes / Q000737:chemistry*; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity
chemical_list: D009696:Nucleic Acids; D015345:Oligonucleotide Probes