title: Prediction of melting temperatures in fluorescence in situ hybridization (FISH) procedures using thermodynamic models.
abstract: The thermodynamics and kinetics of DNA hybridization, i.e. the process of self-assembly of one, two or more complementary nucleic acid strands, has been studied for many years. The appearance of the nearest-neighbor model led to several theoretical and experimental papers on DNA thermodynamics that provide reasonably accurate thermodynamic information on nucleic acid duplexes and allow estimation of the melting temperature. Because there are no thermodynamic models specifically developed to predict the hybridization temperature of a probe used in a fluorescence in situ hybridization (FISH) procedure, the melting temperature is used as a reference, together with corrections for certain compounds that are used during FISH. However, the quantitative relation between melting and experimental FISH temperatures is poorly described. In this review, various models used to predict the melting temperature for rRNA targets, for DNA oligonucleotides and for nucleic acid mimics (chemically modified oligonucleotides), will be addressed in detail, together with a critical assessment of how this information should be used in FISH.
authors.affiliation: a Department of Chemical Engineering, Faculty of Engineering, LEPABE , University of Porto , Porto , Portugal .|b Institute of Molecular Pathology and Immunology of the University of Porto , Porto , Portugal .|c Department of Physics, Chemistry and Pharmacy , Nucleic Acid Center, University of Southern Denmark , Odense M , Denmark , and.|d ICBAS, Institute of Biomedical Sciences Abel Salazar, University of Porto , Porto , Portugal.
authors.forename: Sílvia
authors.initials: S
authors.lastname: Fontenete
authors.affiliation: a Department of Chemical Engineering, Faculty of Engineering, LEPABE , University of Porto , Porto , Portugal .|b Institute of Molecular Pathology and Immunology of the University of Porto , Porto , Portugal .|c Department of Physics, Chemistry and Pharmacy , Nucleic Acid Center, University of Southern Denmark , Odense M , Denmark , and.
authors.forename: Nuno
authors.initials: N
authors.lastname: Guimarães
authors.affiliation: c Department of Physics, Chemistry and Pharmacy , Nucleic Acid Center, University of Southern Denmark , Odense M , Denmark , and.
authors.forename: Jesper
authors.initials: J
authors.lastname: Wengel
authors.affiliation: a Department of Chemical Engineering, Faculty of Engineering, LEPABE , University of Porto , Porto , Portugal .
authors.forename: Nuno Filipe
authors.initials: NF
authors.lastname: Azevedo
mesh_terms: D004247:DNA / Q000032:analysis / Q000737:chemistry; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D008962:Models, Theoretical; D009693:Nucleic Acid Hybridization; D020135:Peptide Nucleic Acids / Q000032:analysis / Q000737:chemistry; D013816:Thermodynamics; D044366:Transition Temperature
chemical_list: D020135:Peptide Nucleic Acids; D004247:DNA
keywords: DNA; locked nucleic acids; nucleic acid mimics; peptide nucleic acids