Systematic evaluation of single mismatch stability predictors for fluorescence in situ hybridization

Environmental Microbiology
L Safak YilmazDaniel R Noguera

Abstract

The mismatch discrimination potential of probes in fluorescence in situ hybridization can be defined as the difference between the melting formamide points of perfect complementary and mismatched duplexes (Delta[FA](m)). Using a combined experimental and theoretical approach, Delta[FA](m) was determined for a set of 35 mismatched probes targeting seven locations in the 16S rRNA of Escherichia coli. The mismatches were created by changing single nucleotides on the probes, while maintaining the target unmodified. Estimated Delta[FA](m) values were used to systematically evaluate four predictors of mismatch stability: weighted mismatch (WM) scores from the software arb, published statistical summary of microarray hybridizations, free energy of mismatch stability (DeltaDeltaG degrees (1)) and theoretical Delta[FA](m) estimations obtained with a thermodynamic model. Based on the predictors' ability to explain variability in Delta[FA](m) and to discriminate weak mismatches from strong ones, DeltaDeltaG degrees (1) and WM scores from arb (with an updated set of relative strength parameters) were demonstrated to be adequate estimators of mismatch stability, with DeltaDeltaG degrees (1) offering the benefit of capturing the variability ...Continue Reading

References

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Dec 3, 2004·Applied and Environmental Microbiology·L Safak Yilmaz, Daniel R Noguera
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Jan 5, 2006·Applied and Environmental Microbiology·L Safak YilmazDaniel R Noguera
Aug 1, 2006·Biotechnology and Bioengineering·L Safak Yilmaz, Daniel R Noguera
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Citations

Nov 2, 2014·Applied Microbiology and Biotechnology·Daniel R NogueraL Safak Yilmaz
Jan 15, 2015·Critical Reviews in Biotechnology·Sílvia FonteneteNuno Filipe Azevedo
Jul 12, 2014·Nucleic Acids Research·Hisae Tateishi-Karimata, Naoki Sugimoto
Nov 15, 2011·Current Opinion in Biotechnology·Michael Wagner, Susanne Haider
Jun 22, 2016·Systematic and Applied Microbiology·Daniela TrojanAndreas Schramm
Jan 29, 2017·Critical Reviews in Microbiology·Hagen FrickmannSven Poppert
Apr 25, 2018·Biophysics Reviews·Hisae Tateishi-Karimata, Naoki Sugimoto
May 11, 2021·Frontiers in Microbiology·Jannie Munk KristensenPer Halkjaer Nielsen

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