Single Molecule DNA Stretching Studies of DNA Intercalation

Abstract

Many proteins and ligands bind double stranded (ds) DNA by inserting their hydrophobic residues in between the DNA bases, either partially or completely, thereby locally elongating, bending and unwinding the dsDNA. This intercalative binding mode is typical of many proteins that control transcription by locally deforming the dsDNA, such as HMG-type proteins or TATA box binding proteins. Also intercalative binding is typical of many small aromatic molecules that are used either as the research tool for dsDNA imaging (EtBr or Yo-Yo), or as anticancer drugs (ActinomysinD or Ruthenium threading intercalators). Conventional approaches to the study of intercalative binding are often limited as many of these molecules also have the non-intercalative binding modes, may cause DNA aggregation, intercalate weakly, or too slowly. Recently the single molecule stretching of polymeric dsDNA with Optical Tweezers in the presence of several intercalating molecules was employed to characterize their equilibrium dissociation constant, DNA elongation and the binding site size. In this theoretical work we discuss how the complete stretching curves of the DNA-intercalator complexes can be used to study the proteins with weak intercalative ability and slow binding kinetics, the effect of intercalators on the dsDNA duplex stability, flexibility and elasticity. In some cases, even the protein-induced dsDNA bending angle and elongation can be quantified based on the intercalator - dsDNA titrations coupled to DNA stretching. This approach also offers a new way to study the contributions of individual intercalating and non-intercalating groups of the protein to its DNA intercalative ability. For some proteins, such as nucleocapsid proteins of retroviruses, discovery of their intercalative nature by DNA stretching may suggest their novel physiological roles.