S TRAIN INDUCED VARIATIONS IN MICRODOMAIN SIZE

In addition to peak positions, average in-plane microdomain sizes for H1/DNA complexes can be determined by investigating the full width at half maximum ∆q of the reflections at q1 and q2 (Figure 9-4). As discussed in chapter 9.3.2, it is usefull to analyze correlation lengths LC given in terms of the lattice spacings d: LC/d = q1/∆q1. Figure 9-14 shows q1/∆q1 in dependence of the N/P ratio. Since q2/∆q2 exhibits a qualitatively identical behavior, data are not shown. Plotting q1/∆q1 against N/P is

9. DNA Compaction: Linker histones H1

Figure 9-14: Dependence of ∆q1 on complex composition N/P. Solid lines are guides to the eyes only.

expected to allow for collapsing of data collected at different flow velocities onto a master plot reflecting the H1/DNA complex composition dependence of q1/∆q1. In Figure 9-14, however, such a behavior is only partly observable: Although all three data sets are following similar courses and are exhibiting analog systematic changes, their absolute values are significantly different and obviously depending on the magnitude of the flow velocity.

At N/P ≈ 0.2, q1/∆q1 reaches maximal values for all flow velocities. This is exactly the complex composition at which minimal values of q1 and q2 are found (Figure 9-6).

Following, for all three flow velocities maximal values of q1/∆q1 = 6.4, 7.8 and 9.1, respectively, are found at N/P ≈ 1.8 when the feature at q2 is disappeared. This finding is consistent with the evolution of the ratio of intensity I2/I1 shown in Figure 9-8.

Parallel to the observed shift in peak position q1 to smaller q values with further increasing H1 concentration, q1/∆q1 is increasing to its values q1/∆q1 = 4.4 at the final complex composition (N/P ≈ 3.3).

Besides their dependence on complex composition, Figure 9-14 shows a clear and systematic dependence of q1/∆q1 on the flow velocity. Throughout all N/P ratios, q1/∆q1

is increasing with increasing strain rate. This is indicative for a strong correlation of microdomain size and strain induced orientation, which is superimposed to the N/P dependence of q1/∆q1. In order to discuss this phenomenon, in Figure 9-15 q1/∆q1 is given in dependence of the position x along the reaction channel since local strain rates are intrinsically depending on x and not on N/P (chapter 9.4.1). The abscissa is divided

9. DNA Compaction: Linker histones H1

Figure 9-15: Dependence of ∆q₁ on the position x along the reaction channel. The black arrow indicates the position of maximum strain rate ε_&max. The dashed lines mark positions corresponding to N/P ≈ 0.2. Blue points are used toLC1 in Figure 7-16.

in a way that access to variations in q1/∆q1 at positions x < 2000µm is improved. As expected, data sets are not showing parallel changes any more. At N/P ≈ 0.2, q1/∆q1

exhibits maxima due to its complex composition dependence as can be readily seen in Figure 9-14. Consistently, q1/∆q1 adopts maximal values at corresponding x-positions marked with dashed lines in Figure 9-15. However, q1/∆q1 obtained from all three data sets develops an additional maximum at the position of maximum strain rate, xmax ≈ 300µm, which is indicated by the arrow in Figure 9-15. For the data set recorded at uDNA = 150µm^.s^-1, both maxima due to the N/P dependence of H1/DNA complexes and due to hydrodynamic strain are coinciding at xmax ≈ 300µm (green dashed line and arrow in Figure 9-15). The superposition of both effects is responsible for the fact that the data set recorded at uDNA = 150µm^.s^-1 exhibits similar q1/∆q1 values as the data set recorded at the higher flow velocity uDNA = 600µm^.s^-1. The last maximum observed a different position for each curve reflects the position where the feature at q2 is disappeared.

These findings provide interesting insights into the response of a 2D mesophase of long chain DNA molecules to external strain. The strain rate induced extensive alignment of H1/DNA assemblies’ leads to an increase in q1/∆q1 with applied external strain. In order to quantify for the strain effect on q1/∆q1, only data points that accomplish the following conditions must be considered: Firstly, in order to account for compositional

9. DNA Compaction: Linker histones H1

0 5 10 15 20 25 30 35 40 45 50 2

4 6 8 10

in flow bulk, N/P = 2.5

q 1/∆q 1

ε.max / s^-1

Figure 9-16: Dependence of the microdomain size on the maximal strain rate superimposed. Data from bulk measurements are given for comparison.

changes in q1/∆q1, considered data points must be recorded from H1/DNA complexes exhibiting similar N/P ratios for all three data sets. Secondly, no hydrodynamic strain must be active any more and the complexes have to be already sufficiently relaxed, i.e.

∆χ1 ≈ 90°. Only data points marked blue in Figure 9-15 fulfill both conditions simultaneously exhibiting N/P = 1.9-2.0 and ∆χ1 = 78°-80°. In Figure 9-16, q1/∆q1 are given in dependence of the maximum strain rate. Data points at ε_&max> 10s^-1 are obtained from data sets recorded at initial flow velocities of 1000, 2000, and 4000µm^.s^-1, which are not as comprehensive as the three data sets discussed to this point. In addition, q/∆q recorded from a bulk sample with a composition of N/P = 2.5 is shown. Figure 9-16 shows that already a low maximum strain rate of 0.6s^-1 at u = 60µm^.s^-1 results in a dramatic effect the on microdomain size: q1/∆q1 more than doubles. With increasing strain rate, q1/∆q1 is continuously increasing up to

1 max ≈10s⁻

ε_& . Further increasing the strain rates has only minor effects. The fact that it

is possible to significantly improve the correlation length of biomaterials by superimposing external strain is a clear advantage of using flow to assemble such materials. In the context of X-ray diffraction analysis, this phenomenon can be utilized to improved the characterization of biomolecular materials, which are difficult to crystallize and normally form liquid-crystalline structures ^{57, 63, 64}.

9. DNA Compaction: Linker histones H1

Figure 9-17: (a) SAXS profiles of H1/DNA bulk complexes at different N/P. (b) SAXS profiles of successive measurements at a fixed position (N/P = 2.5).