Int J Biochem Mol Biol 2011;2(2):129-137

Original Article
Nucleosomes structure and dynamics: effect of small molecules

Irina Menshikova, Evgeny Menshikov, Nina Filenko, Yuri L. Lyubchenko

Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA.

Received March 3, 2011; accepted March 6, 2011; Epub March 7, 2011; Published published April 30, 2011

Abstract: Dynamics of nucleosomes and spontaneous unwrapping of DNA are fundamental property of the chromatin enabling access to
nucleosomal DNA for regulatory proteins. Probing of such dynamics of nucleosomes performed by single molecule techniques revealed a
large scale dynamics of nucleosomes including their spontaneous unwrapping.  Dissociation of nucleosomes at low concentrations is a
complicating issue for studies with single molecule techniques. In this paper, we tested the ability of 3-[(3-Cholamidopropyl)dimethylammonio]
-1-propanesulfonate (CHAPS) to prevent dissociation of nucleosomes. The study was performed with mononucleosome system assembled
with human histones H2A, H2B, H3 and H4 on the DNA substrate containing sequence 601 that provides the sequence-specific assembly of
nucleosomes. We used atomic force microscopy (AFM) to directly identify nucleosomes and analyze their structure at the nanometer level.  
These studies showed that in the presence of CHAPS at millimolar concentrations, nucleosomes, even at sub-nanomolar concentrations,
remain intact over days compared to a complete dissociation of the same nucleosome sample over 10 min in the absence of CHAPS.
Importantly, CHAPS does not change the conformation of nucleosomes as confirmed by the AFM analysis. Moreover, 16 M CHAPS stabilizes
nucleosomes in over one hour incubation in the solution containing as low as 0.4 nM in nucleosomes.  The stability of nucleosomes is slightly
reduced at physiological conditions, although the nucleosomes dissociate rapidly at 300 mM NaCl. The sequence specificity of the
nucleosome in the presence of CHAPS decreased suggesting that the histone core translocates along the DNA substrate utilizing sliding
mechanism. (IJBMB1103001).

Keywords: Chromatin, nucleosome structure, AFM, single molecule analysis, DNA, CHAPS

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Address all correspondence to:
Yuri L. Lyubchenko, PhD
Department of Pharmaceutical Sciences
University of Nebraska Medical Center
986025 Nebraska Medical Center
Omaha, NE 68198-6025
Tel: 402-559-1971
Fax: 402-559-9543