A statistical thermodynamic model applied to experimental AFM population and location data is able to quantify DNA-histone binding strength and internucleosomal interaction differences between acetylated and unacetylated nucleosomal arrays

Biophysical Journal
F J SolisD Lohr

Abstract

Imaging of nucleosomal arrays by atomic force microscopy allows a determination of the exact statistical distributions for the numbers of nucleosomes per array and the locations of nucleosomes on the arrays. This precision makes such data an excellent reference for testing models of nucleosome occupation on multisite DNA templates. The approach presented here uses a simple statistical thermodynamic model to calculate theoretical population and positional distributions and compares them to experimental distributions previously determined for 5S rDNA nucleosomal arrays (208-12,172-12). The model considers the possible locations of nucleosomes on the template, and takes as principal parameters an average free energy of interaction between histone octamers and DNA, and an average wrapping length of DNA around the octamers. Analysis of positional statistics shows that it is possible to consider interactions between nucleosomes and positioning effects as perturbations on a random positioning noninteracting model. Analysis of the population statistics is used to determine histone-DNA association constants and to test for differences in the free energies of nucleosome formation with different types of histone octamers, namely acetylate...Continue Reading

References

Aug 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·F DongK E van Holde
Oct 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·T E Shrader, D M Crothers
May 31, 1988·Biochemistry·D Lohr, T Torchia
Jan 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·R T Simpson, D W Stafford
Jul 28, 1995·The Journal of Biological Chemistry·M Garcia-RamirezJ Ausio
Jan 1, 1996·Critical Reviews in Eukaryotic Gene Expression·T M Fletcher, J C Hansen
Mar 20, 1997·Biochimica Et Biophysica Acta·S N KhrapunovA M Zagariya
Oct 27, 1997·The Journal of Biological Chemistry·D Lohr
Jan 16, 1999·Nucleic Acids Research·A P Wolffe, J J Hayes
Jun 18, 1999·Methods in Enzymology·K LugerT J Richmond
Jun 18, 1999·Methods in Enzymology·L M CarruthersJ C Hansen
Aug 26, 1999·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·K van Holde, J Zlatanova
Nov 4, 2000·Physical Review Letters·K K Kunze, R R Netz
Nov 30, 2000·Gene Expression·A T Annunziato, J C Hansen
May 1, 2001·Physical Review Letters·H SchiesselW M Gelbart
Sep 12, 2001·Biochemistry·J M Gottesfeld, K Luger
Feb 21, 2002·Proceedings of the National Academy of Sciences of the United States of America·Brent D Brower-TolandMichelle D Wang
May 4, 2002·Annual Review of Biophysics and Biomolecular Structure·Jeffrey C Hansen
Jun 25, 2002·Journal of Molecular Biology·Curt A DaveyTimothy J Richmond

❮ Previous
Next ❯

Citations

Dec 20, 2005·Chromosoma·Rachel A Horowitz-Scherer, Christopher L Woodcock
Apr 21, 2009·Nature Structural & Molecular Biology·Maarten KruithofJohn van Noort
Sep 8, 2010·Journal of Neuroscience Methods·Pritika J Narayan, Michael Dragunow
Jul 29, 2008·Biophysical Journal·René StehrGero Wedemann
Mar 17, 2006·Current Opinion in Structural Biology·Christopher L Woodcock
Mar 10, 2011·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Vladimir B Teif, Karsten Rippe
Nov 28, 2019·Epigenomes·Rahul R SinghRick J Jansen
Jan 8, 2015·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Guénola DrillonAlain Arneodo
Aug 7, 2007·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Wei LiPeng-Ye Wang

❮ Previous
Next ❯

Related Concepts

Related Feeds

AFM in situ DNA

AFM in situ DNA describes in situ analysis (or study) of DNA using atomic force microscopy. Discover the latest research on AFM in situ DNA here.