Evaluation of DNA bending models in their capacity to predict electrophoretic migration anomalies of satellite DNA sequences

0422254 - BFÚ 2014 RIV US eng J - Journal Article
Matyášek, Roman - Fulneček, Jaroslav - Kovařík, Aleš
Evaluation of DNA bending models in their capacity to predict electrophoretic migration anomalies of satellite DNA sequences.
Electrophoresis. Roč. 34, č. 17 (2013), s. 2511-2521. ISSN 0173-0835. E-ISSN 1522-2683
R&D Projects: GA ČR(CZ) GA206/09/1751; GA ČR(CZ) GAP501/10/0208; GA ČR(CZ) GA13-10057S
Institutional research plan: CEZ:AV0Z50040702
Institutional support: RVO:68081707
Keywords : HIGHLY REPETITIVE DNA * DOUBLE-HELICAL DNA * CURVED DNA
Subject RIV: AC - Archeology, Anthropology, Ethnology
Impact factor: 3.161, year: 2013

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.
Permanent Link: http://hdl.handle.net/11104/0228561