Prediction of melting temperatures in fluorescence in situ hybridization (FISH) procedures using thermodynamic models

Sílvia Fontenete, Nuno Guimarães, Jesper Wengel, Nuno Filipe Azevedo

Research output: Contribution to journalReviewResearchpeer-review

Abstract

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.

Original languageEnglish
JournalCritical Reviews in Biotechnology
Volume36
Issue number3
Pages (from-to)566-577
ISSN0738-8551
DOIs
Publication statusPublished - 2016

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title = "Prediction of melting temperatures in fluorescence in situ hybridization (FISH) procedures using thermodynamic models",
abstract = "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.",
author = "S{\'i}lvia Fontenete and Nuno Guimar{\~a}es and Jesper Wengel and Azevedo, {Nuno Filipe}",
year = "2016",
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language = "English",
volume = "36",
pages = "566--577",
journal = "Critical Reviews in Biotechnology",
issn = "0738-8551",
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}

Prediction of melting temperatures in fluorescence in situ hybridization (FISH) procedures using thermodynamic models. / Fontenete, Sílvia; Guimarães, Nuno; Wengel, Jesper; Azevedo, Nuno Filipe.

In: Critical Reviews in Biotechnology, Vol. 36, No. 3, 2016, p. 566-577.

Research output: Contribution to journalReviewResearchpeer-review

TY - JOUR

T1 - Prediction of melting temperatures in fluorescence in situ hybridization (FISH) procedures using thermodynamic models

AU - Fontenete, Sílvia

AU - Guimarães, Nuno

AU - Wengel, Jesper

AU - Azevedo, Nuno Filipe

PY - 2016

Y1 - 2016

N2 - 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.

AB - 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.

U2 - 10.3109/07388551.2014.993589

DO - 10.3109/07388551.2014.993589

M3 - Review

C2 - 25586037

VL - 36

SP - 566

EP - 577

JO - Critical Reviews in Biotechnology

JF - Critical Reviews in Biotechnology

SN - 0738-8551

IS - 3

ER -