Investigation of structural transition of dsDNA on various substrates studied by atomic force microscopy

Structural transition of single dsDNA molecule which is immobilized on 3-aminopropyltriethoxysilane (APTES) treated substrate (APTES/substrate) or alkylthiol treated substrate (alkylthiol/substrate) has been investigated by atomic force microscopy (AFM). The obtained force versus distance (F-D) curves are used to dissect the transition from B-form to S-form, the melting from double stranded (ds) to single stranded (ss) DNA, and its Young's modulus as well as persistence length. The melt from dsDNA to ssDNA is evidenced by fitting with freely jointed chain (FJC) model. FJC fit and Young's modulus or persistence length values when the molecules are fixed on alkylthiol/substrate are more agreeable with other studies than those on APTES. We have clarified the different results of those experiments by analyzing the binding force between DNA molecules and APTES or alkylthiol linkers on the substrate. The DNA binding to APTES linker is much stronger than that on alkylthiol/substrate.