Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences

Our laboratories recently completed SELEX experiments to isolate DNA sequences that most-strongly favor or disfavor nucleosome formation and positioning, from the entire mouse genome or from even more diverse pools of chemically synthetic random sequence DNA. Here we directly compare these selected...

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Bibliographic Details
Published in:Journal of molecular biology 1999-04, Vol.288 (2), p.213-229
Main Authors: Thåström, A, Lowary, P.T, Widlund, H.R, Cao, H, Kubista, M, Widom, J
Format: Article
Language:English
Subjects:
affinity
Animals
Base Pairing
Base Sequence
chromatin
Chromatin - metabolism
DNA - genetics
Fourier Analysis
histone
Histones - metabolism
Mice
Nucleic Acid Conformation
nucleosome
Nucleosomes - physiology
positioning
Protein Binding
Regulatory Sequences, Nucleic Acid
Thermodynamics
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Summary:Our laboratories recently completed SELEX experiments to isolate DNA sequences that most-strongly favor or disfavor nucleosome formation and positioning, from the entire mouse genome or from even more diverse pools of chemically synthetic random sequence DNA. Here we directly compare these selected natural and non-natural sequences. We find that the strongest natural positioning sequences have affinities for histone binding and nucleosome formation that are sixfold or more lower than those possessed by many of the selected non-natural sequences. We conclude that even the highest-affinity sequence regions of eukaryotic genomes are not evolved for the highest affinity or nucleosome positioning power. Fourier transform calculations on the selected natural sequences reveal a special significance for nucleosome positioning of a motif consisting of ∼10 bp periodic placement of TA dinucleotide steps. Contributions to histone binding and nucleosome formation from periodic TA steps are more significant than those from other periodic steps such as AA (=TT), CC (=GG) and more important than those from the other YR steps (CA (=TG) and CG), which are reported to have greater conformational flexibility in protein-DNA complexes even than TA. We report the development of improved procedures for measuring the free energies of even stronger positioning sequences that may be isolated in the future, and show that when the favorable free energy of histone-DNA interactions becomes sufficiently large, measurements based on the widely used exchange method become unreliable.
ISSN:0022-2836
1089-8638
DOI:10.1006/jmbi.1999.2686