$\beta$-Cyclodextrin polymer binding to DNA: Modulating the physicochemical parameters

Cyclodextrins and cyclodextrins-modified molecules have interesting and appealing properties due to their capacity to host components that are normally insoluble or poorly soluble in water. In this work, we investigate the interaction of a $\beta$-cyclodextrin polymer (poly-$\beta$-CD) with $\lambda$-DNA. The polymers are obtained by the reaction of $\beta$-CD with epichlorohydrin in alkaline conditions. We have used optical tweezers to characterize the changes of the mechanical properties of DNA molecules by increasing the concentration of poly-$\beta$-CD in the sample. The physical chemistry of the interaction is then deduced from these measurements by using a recently developed quenched-disorder statistical model. It is shown that the contour length of the DNA does not change in the whole range of poly-$\beta$-CD concentration $\left(<300\mu \mathrm{M}\right)$. On the other hand, significant alterations were observed in the persistence length that identifies two binding modes corresponding to the clustering of $\sim 2.6$ and $\sim 14$ polymer molecules along the DNA double helix, depending on the polymer concentration. Comparing these results with the ones obtained for monomeric $\beta$-CD, it was observed that the concentration of CD that alters the DNA persistence length is considerably smaller when in the polymeric form. Also, the binding constant of the polymer-DNA interaction is three orders of magnitude higher than the one found for native (monomeric) $\beta$-CD. These results show that the polymerization of the $\beta$-CD strongly increases its binding affinity to the DNA molecule. This property can be wisely used to modulate the binding of cyclodextrins to the DNA double helix.

Figure 1

Representative force-extension curves obtained at different poly-$\beta$-CD concentrations, along with the WLC fittings (solid lines). Black circles: bare DNA; blue squares: 11.4 $\mu \mathrm{M}$ of poly-$\beta$-CD; red diamonds: 153 $\mu \mathrm{M}$ of poly-$\beta$-CD.

Figure 2

Contour length $L$ of the DNA–poly-$\beta$-CD complexes as a function of the poly-$\beta$-CD total concentration in the sample ($C_T$). This mechanical parameter remains approximately constant as the poly-$\beta$-CD concentration increases, a result similar to the one found for the DNA interaction with monomeric $\beta$-CD [19, 26].

Figure 3

Persistence length $A$ for the DNA–poly-$\beta$-CD complexes as a function of the poly-$\beta$-CD total concentration in the sample ($C_T$). The value of $A$ decreases from 40 to 22 nm when $C_T$ increases to $\sim 10\mu \mathrm{M}$ and then presents a slight increase for higher concentrations, saturating at $\sim 26$ nm for $C_T>25\mu \mathrm{M}$. The solid line shows the fit obtained using our model [Eq. (2) plugged into Eq. (1)], which gives $K_1=(2.5\pm 0.3)\times {10}^5{\mathrm{M}}^{-1}$, $n_1=2.6\pm 0.7$, $K_2=(1.0\pm 0.2)\times {10}^5{\mathrm{M}}^{-1}$, and $n_2=14\pm 7$.

Figure 4

The two binding isotherms obtained from the fitting: ${\mathrm{BI}}_1$ (dashed green line) and ${\mathrm{BI}}_2$ (red dotted line). The first binding mode (clusters of 2 to 3 molecules) is the most important at the low concentration range ($C_T\lesssim 10\mu \mathrm{M}$), saturating at $C_T\sim 10\mu \mathrm{M}$. The second binding mode (clusters of around 14 molecules), otherwise, dominates the high concentration range $C_T>10\mu \mathrm{M}$. The transition from the first dominant mode to the second one is strongly correlated to the nonmonotonic behavior of the persistence length (black circles), also shown for comparison purposes.