Packaging DNA into condensed structures is integral to the transmission of genomes. The mammalian mitochondrial genome (mtDNA) is a high copy, maternally inherited genome in which mutations cause a variety of multisystem disorders. In all eukaryotic cells, multiple mtDNAs are packaged with protein into spheroid bodies called nucleoids, which are the fundamental units of mtDNA segregation. The mechanism of nucleoid formation, however, remains unknown. Here, we show that the mitochondrial transcription factor TFAM, an abundant and highly conserved High Mobility Group box protein, binds DNA cooperatively with nanomolar affinity as a homodimer and that it is capable of coordinating and fully compacting several DNA molecules together to form spheroid structures. We use noncontact atomic force microscopy, which achieves near cryo-electron microscope resolution, to reveal the structural details of protein-DNA compaction intermediates. The formation of these complexes involves the bending of the DNA backbone, and DNA loop formation, followed by the filling in of proximal available DNA sites until the DNA is compacted. These results indicate that TFAM alone is sufficient to organize mitochondrial chromatin and provide a mechanism for nucleoid formation. INTRODUCTIONMutations affecting mitochondrial oxidative phosphorylation cause a variety of multisystem disorders (DiMauro and Schon, 2003;Taylor and Turnbull, 2005) with an estimated incidence of 1:5000 live births (Thorburn, 2004). The majority of these mutations are found in the mitochondrial genome (mtDNA), which encodes the core hydrophobic proteins involved in oxidative phosphorylation and some of the molecules required for their expression, such as tRNAs and rRNAs. The mutant mtDNA genomes generally coexist alongside wild-type copies in affected patients, a situation referred to as heteroplasmy. The segregation pattern of heteroplasmic DNAs in different tissues is an important determinant of the severity of the clinical phenotype. To develop an animal model of heteroplasmy, our laboratory generated mice containing polymorphisms in otherwise normal mtDNA, and we identified three nuclear quantitative trait loci that affect mtDNA segregation in liver, spleen, and kidney (Jenuth et al., 1997;Battersby et al., 2003). The selection of one variant of the mtDNA over another could be explained by differences in their organization or packaging.Mammalian mtDNA is packaged in protein-DNA complexes termed nucleoids, which can be visualized as small submitochondrial bodies in the matrix (Nass, 1969). The nucleoid contains two to seven genomes, depending on cell type, and it is present as 450 -800 distinct foci in cultured cells (Nass, 1969;Iborra et al., 2004;Legros et al., 2004). Several mammalian mitochondrial nucleoid proteins have been identified after enrichment by sedimentation and immunoprecipitation (Wang and Bogenhagen, 2006;He et al., 2007). However, other than the components of the mitochondrial replisome and transcription apparatus, the only proteins that have been fo...

Conductance switching associated with the photoisomerization of azobenzene-based (Azo) molecules was observed in nanoscopic metal-molecule-metal junctions. The junctions were formed by using a conducting atomic force microscope (C-AFM) approach, where a metallic AFM tip was used to electrically contact a gold-supported Azo self-assembled monolayer. The measured 30-fold increase in conductance is consistent with the expected decrease in tunneling barrier length resulting from the conformational change of the Azo molecule.

Conductive atomic force microscopy (C-AFM) has been used to correlate the detailed structural and electrical characteristics of graphene derived from graphene oxide. Uniform large currents were measured over areas exceeding tens of micrometers in few-layer films, supporting the use of graphene as a transparent electrode material. Moreover, defects such as electrical discontinuities were easily detected. Multilayer films were found to have a higher conductivity per layer than single layers. It is also shown that a local AFM-tip-induced electrochemical reduction process can be used to pattern conductive pathways on otherwise-insulating graphene oxide. Transistors with micrometer-scale tip-reduced graphene channels that featured ambipolar transport and an 8 order of magnitude increase in current density upon reduction were successfully fabricated.