Thermodynamics of polyethylenimine-DNA binding and DNA condensation

Abstract

In this study, polyethylenimine (PEI) binding to DNA was examined by isothermal titration calorimetry. Two types of binding modes were found to describe the interactions between these polyelectrolytes in buffers and in water. One type of binding involves PEI binding to the DNA groove because the enthalpy change of this binding mode is positive, and PEI is deprotonated to bind to DNA. Another likely binding mode involves external binding of PEI to the DNA phosphate backbone, accompanied with DNA condensation. The enthalpy change is negative and PEI is protonated when it binds to DNA in this mode. The intrinsic enthalpy change of first binding mode is 1.1 kJ/mol and -0.88 kJ/mol for the second binding mode. This result implies that the PEI is rearranged from the groove to the phosphate backbone of DNA when DNA is condensed. The mechanism of DNA condensation caused by PEI is discussed in this study.

Figure 1

Calorimetric thermograms for titration of 20 mM PEI into 1.5 mM DNA in HEPES buffer (blue line) and into HEPES buffer alone without DNA (red line).

Figure 2

Integrated data obtained from titration of 20 mM PEI into 1.5 mM DNA (a) in 0.1 M HEPES buffer at pH 7, (b) in 0.1 M MES buffer at pH 7, and (c) in water adjusted to pH 7 by NaOH. The first point in c is out of figure (−1.4 ± 1.0 kJ/mol). The solid line represents the fitting data using the model proposed by Kim et al. (16). The data points are quadruplicate measurements.

Figure 3

The observed enthalpy of (a) first and (b) second binding stage of PEI to DNA versus buffer ionization enthalpies that are 20.5 kJ/mol for HEPES buffer and 14.6 kJ/mol for MES buffer (33).

Figure 4

Integrated data obtained from titration of 20 mM PEI into 1.5 mM DNA in 0.1 M NaCl. The pH values of the PEI solutions are (a) 6, (b) 7, and (c) 8. The solid line represents the fitting data using the SSIS model. The data acquisition was repeated at least two times and the data are summarized as mean ± SD of at least duplicate measurements.

Figure 5

pH change obtained from titration of (a) 20 mM PEI (pH 7) into 1.5 mM DNA in water (pH7), and (b) 20 mM PEI (pH 6, 7, and 8) into 1.5 mM DNA in 0.1 M NaCl. The data points are mean ± SD of (a) four measurements and (b) duplicate measurements.

Figure 6

The free DNA concentration remaining in solution after PEI binding and centrifugation. The data points are duplicate measurements. The data points larger than N/P = 2 were not shown because their values were 0.

Figure 7

The pH value obtained as a function the volume (V) of 0.1 M HCl added to 1 mM PEI solution (28.5 mL). The solid line represents the fitting data using the model proposed by Suh et al. (19) for measurements carried out in duplicate.