Correlation of MFOLD-predicted DNA secondary structures with separation patterns obtained by capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) analysis

Human Mutation
Damjan GlavacMetka Ravnik-Glavac

Abstract

We have studied 57 different mutations within three beta-globin gene promoter fragments with sizes 52 bp, 77 bp, and 193 bp by fluorescent capillary electrophoresis CE-SSCP analysis. For each mutation and wild type, energetically most-favorable predicted secondary structures were calculated for sense and antisense strands using the MFOLD DNA-folding algorithm in order to investigate if any correlation exists between predicted DNA structures and actual CE migration time shifts. The overall CE-SSCP detection rate was 100% for all mutations in three studied DNA fragments. For shorter 52 bp and 77 bp DNA fragments we obtained a positive correlation between the migration time shifts and difference in free energy values of predicted secondary structures at all temperatures. For longer 193 bp beta-globin gene fragments with 46 mutations MFOLD predicted different secondary structures for 89% of mutated strands at 25 degrees C and 40 degrees C. However, the magnitude of the mobility shifts did not necessarily correlate with their secondary structures and free energy values except for the sense strand at 40 degrees C where this correlation was statistically significant (r = 0.312, p = 0.033). Results of this study provided more direct in...Continue Reading

References

May 2, 1986·Science·R M MyersT Maniatis
Jan 26, 1996·Journal of Chromatography. a·H ArakawaA Tsuji
Mar 21, 1998·Proceedings of the National Academy of Sciences of the United States of America·J SantaLucia
Dec 21, 2000·Combinatorial Chemistry & High Throughput Screening·S Merkelbach-BruseR Buettner
Jun 1, 2001·Human Mutation·W Xiao, P J Oefner
Jul 14, 2001·Nucleic Acids Research·P Kozlowski, W J Krzyzosiak

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Citations

Sep 11, 2008·Analytical Biochemistry·Gi Won ShinGyoo Yeol Jung
Oct 13, 2006·Electrophoresis·Christa N Hestekin, Annelise E Barron
Dec 30, 2004·Electrophoresis·Piotr Kozlowski, Wlodzimierz J Krzyzosiak
Nov 2, 2007·Chemical Reviews·Karel Kleparník, Petr Bocek

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