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.

Conservation of k-mer Composition and Correlation Contribution between Introns and Intergenic Regions of Animalia Genomes

“…Another discovery made is that transcriptional factors are associated with local DNA topography [ 36 ]. This observation is of special interest for the interpretation of the observations made in this article, since dinucleotides (DNA words of length 2 bp) are often used to determine such structural and topological properties of DNA molecules [ 36 , 37 ] and the structures we observed to contribute most to intron intergenic correlations consist mainly of repeats of such dinucleotides. Since transcriptional factors influence distant genes through DNA loops [ 33 ], it seems reasonable that local physical DNA properties that favor such loops are beneficial when associated with transcriptional factor binding sites.…”

Eukaryotic Genomes Show Strong Evolutionary Conservation of k-mer Composition and Correlation Contributions between Introns and Intergenic Regions

“…Another interesting feature of transcription factors is their association with local DNA topology [38]. DNA topology, on the other hand, depends strongly on local dinucleotide compositions [39,40], which is influenced by the presence of dinucleotide repeats identified as conserved in this work.…”

Quaternion modeling of the helical path for analysis of the shape of the DNA molecule

“…Lastly, the curvature of the DNA molecule can be simply characterized by the ratio of the curvilinear distance (contour length) to the linear distance between the ends of the segment (SD value) (Eckdahl, Anderson, 1987;Tan, Harvey, 1987) and vice versa (Qc, (Dlakic, Harrington, 1998;Kanhere, Bansal, 2003;Matyašek et al, 2013)). Large values of C, d-max and SD indicate a more curved DNA fragment.…”