Binding of netropsin to several DNA constructs: Evidence for at least two different 1:1 complexes formed from an –AATT-containing ds-DNA construct and a single minor groove binding ligand

Abstract

Isothermal titration calorimetry, ITC, has been used to determine the thermodynamics (Δ G, Δ H, and − TΔ S) for binding netropsin to a number of DNA constructs. The DNA constructs included: six different 20–22mer hairpin forming sequences and an 8-mer DNA forming a duplex dimer. All DNA constructs had a single –AT-rich netropsin binding with one of the following sequences, (A 2T 2) 2, (ATAT) 2, or (AAAA/TTTT). Binding energetics are less dependent on site sequence than on changes in the neighboring single stranded DNA (hairpin loop size and tail length). All of the 1:1 complexes exhibit an enthalpy change that is dependent on the fractional saturation of the binding site. Later binding ligands interact with a significantly more favorable enthalpy change (∂Δ H 1–2 from 2 to 6 kcal/mol) and a significantly less favorable entropy change (∂(− TΔ S 1–2)) from − 4 to − 9 kcal/mol). The ITC data could only be fit within expected experimental error by use of a thermodynamic model that includes two independent binding processes with a combined stoichiometry of 1 mol of ligand per 1 mol of oligonucleotide. Based on the biophysical evidence reported here, including theoretical calculations for the energetics of “trapping” or structuring of a single water molecule and molecular docking computations, it is proposed that there are two modes by which flexible ligands can bind in the minor groove of duplex DNA. The higher affinity binding mode is for netropsin to lay along the floor of the minor groove in a bent conformation and exclude all water from the groove. The slightly weaker binding mode is for the netropsin molecule to have a slightly more linear conformation and for the required curvature to be the result of a water molecule that bridges between the floor of the minor groove and two of the amidino nitrogens located at one end of the bound netropsin molecule.