title: Evaluation of DNA bending models in their capacity to predict electrophoretic migration anomalies of satellite DNA sequences.
abstract: DNA containing a sequence that generates a local curvature exhibits a pronounced retardation in electrophoretic mobility. Various theoretical models have been proposed to explain relationship between DNA structural features and migration anomaly. Here, we studied the capacity of 15 static wedge-bending models to predict electrophoretic behavior of 69 satellite monomers derived from four divergent families. All monomers exhibited retarded mobility in PAGE corresponding to retardation factors ranging 1.02-1.54. The curvature varied both within and across the groups and correlated with the number, position, and lengths of A-tracts. Two dinucleotide models provided strong correlation between gel mobility and curvature prediction; two trinucleotide models were satisfactory while remaining dinucleotide models provided intermediate results with reliable prediction for subsets of sequences only. In some cases, similarly shaped molecules exhibited relatively large differences in mobility and vice versa. Generally less accurate predictions were obtained in groups containing less homogeneous sequences possessing distinct structural features. In conclusion, relatively universal theoretical models were identified suitable for the analysis of natural sequences known to harbor relatively moderate curvature. These models could be potentially applied to genome wide studies. However, in silico predictions should be viewed in context of experimental measurement of intrinsic DNA curvature.
authors.affiliation: Laboratory of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i, Brno, Czech Republic. matyasek@ibp.cz
authors.forename: Roman
authors.initials: R
authors.lastname: Matyášek
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Fulneček
authors.forename: Aleš
authors.initials: A
authors.lastname: Kovařík
mesh_terms: D001483:Base Sequence; D003198:Computer Simulation; D018744:DNA, Plant / Q000737:chemistry; D004276:DNA, Satellite / Q000737:chemistry*; D024202:Electrophoretic Mobility Shift Assay / Q000379:methods* / Q000592:standards; D008956:Models, Chemical; D008969:Molecular Sequence Data; D063347:Native Polyacrylamide Gel Electrophoresis / Q000379:methods* / Q000592:standards; D015203:Reproducibility of Results; D016415:Sequence Alignment; D014026:Nicotiana / Q000737:chemistry
chemical_list: D018744:DNA, Plant; D004276:DNA, Satellite
keywords: Computer modelling; DNA curvature; DNA satellites; Electrophoretic migration