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Mechanism of DNA Compaction by Yeast Mitochondrial Protein Abf2p

Raymond W. Friddle ^* , Jennifer E. Klare ^*, Shelley S. Martin , Michelle Corzett , Rod Balhorn , Enoch P. Baldwin , Ronald J. Baskin  and Aleksandr Noy ^*

^* Biosecurity and Nanoscience Laboratory, Chemistry and Materials Science Directorate, and Biology and Biotechnology Program, Lawrence Livermore National Laboratory, Livermore, California; and Department of Molecular and Cellular Biology, University of California at Davis, Davis, California

Correspondence: Address reprint requests to Aleksandr Noy, E-mail: noy1{at}llnl.gov.

We used high-resolution atomic force microscopy to image the compaction of linear and circular DNA by the yeast mitochondrial protein Abf2p, which plays a major role in packaging mitochondrial DNA. Atomic force microscopy images show that protein binding induces drastic bends in the DNA backbone for both linear and circular DNA. At a high concentration of Abf2p DNA collapses into a tight nucleoprotein complex. We quantified the compaction of linear DNA by measuring the end-to-end distance of the DNA molecule at increasing concentrations of Abf2p. We also derived a polymer statistical mechanics model that provides a quantitative description of compaction observed in our experiments. This model shows that sharp bends in the DNA backbone are often sufficient to cause DNA compaction. Comparison of our model with the experimental data showed excellent quantitative correlation and allowed us to determine binding characteristics for Abf2p. These studies indicate that Abf2p compacts DNA through a simple mechanism that involves bending of the DNA backbone. We discuss the implications of such a mechanism for mitochondrial DNA maintenance and organization.

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