Abstract
We study the behavior of single-stranded DNA (ssDNA) in the presence of well-knowndrugs with either an intercalating binding mode, such as daunorubicin, actinomycin D, andchloroquine, or a minor groove binding mode, such as netropsin and berenil, by atomicforce microscopy (AFM). At very low salt conditions, ssDNA molecules adopt anunstructured conformation without secondary structures. We observe that under theseconditions additions of drugs that bind to double-stranded DNA (dsDNA) promote theformation of secondary structures in ssDNA. Furthermore, with an increase ofconcentration of the drugs, the extension as well as the thermal stabilization of thesehairpins was observed.
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