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As an advanced single molecule technique, atomic force microscopy (AFM) is a powerful and versatile tool for high resolution surface imaging and probing physical properties of soft, nonconductive bio-materials in vitro. Imaging of protein-protein and protein-DNA complexes provides structural and conformational information about the interactions of these biomolecular assemblies. In this study, we have used AFM to examine two different protein complexes: the eukaryotic RFC complex function in loading PCNA clamp onto different DNA substrate and eukaryotic MutS homologs function in the initiation of DNA mismatch repair (MMR). In the study of clamp loader RFC complex, we investigated the effect of nucleotide cofactors on the oligomerization states of RFC interacting with PCNA and DNA substrate. We observed that ATP binding induces a conformational change of RFC and that ATP hydrolysis causes RFC dissociation into small subcomplexes. However, PCNA inhibits the ATP-induced disassembly of RFC. Intriguingly, we found in the presence of ATP, some of the RFC subunits are ejected from DNA substrate, leaving RFC subcomplex bound to the DNA, and it appears that these subcomplexes form stable interaction with PCNA on the DNA. We proposed that this DNA-bound RFC subcomplex tethers PCNA ring at the single strand/double strand junction of primer-template DNA or nick DNA. We further suggest that dissociation of RFC subcomplex from PCNA and DNA substrate is promoted by downstream PCNA-interacting proteins, such as DNA polymerase. In addition to these insights into the complicated potential loading mechanism of PCNA, we observed other RFC-DNA complexes such as RFC-DNA filaments with nicked DNA without nucleotide cofactor and RFC-DNA spider-like complexes containing multiple RFCs and DNAs in the presence of ATP. Although we do not know the physiological role, if any, of such RFC-DNA complexes, these complexes suggest RFC can possess other functions besides as clamp loader, such as helicase. In the study of MMR initiation complexes, eukaryotic MutS homologs (MutSalpha and MutSbeta), we found, unlike their prokaryotic homologs, eukaryiotic MutS homologs bind different DNA substrates with similar conformation. MutSalpha and MutSbeta both exhibits weak binding specificity to their specific DNA substrates, which makes it more complicated to analyze their specific complexes. However, it appears that eukaryotic MutS homologs do not recognize mismatched bases simply depending on the formation of unbent complexes as seen in the prokaryotic MutS. It is possible they employ other high class mechanism in which the event of recognition of different mismatched DNA substrates happens downstream of mismatch binding.