ABSTRACT
Found in all eukaryotic cells, linker histones H1 are known to bind to and rearrange nucleosomal linker DNA. In vitro, the fundamental nature of H1∕DNA interactions has attracted wide interest among research communities-from biologists to physicists. Hence, H1∕DNA binding processes and structural and dynamical information about these self-assemblies are of broad importance. Targeting a quantitative understanding of H1 induced DNA compaction mechanisms, our strategy is based on using small-angle x-ray microdiffraction in combination with microfluidics. The usage of microfluidic hydrodynamic focusing devices facilitates a microscale control of these self-assembly processes, which cannot be achieved using conventional bulk setups. In addition, the method enables time-resolved access to structure formation in situ, in particular, to transient intermediate states. The observed time dependent structure evolution shows that the H1∕DNA interaction can be described as a two-step process: an initial unspecific binding of H1 to DNA is followed by a rearrangement of molecules within the formed assemblies. The second step is most likely induced by interactions between the DNA and the H1's charged side chains. This leads to an increase in lattice spacing within the DNA∕protein assembly and induces a decrease in the correlation length of the mesophases, probably due to a local bending of the DNA.
ABSTRACT
DNA condensation in vivo usually requires proteins and/or multivalent salts. Here, we explore the in vitro compaction of DNA by cationic dendrimers having an intermediate size and charge. The dynamic assembly of DNA-dendrimer mesophases is discernible due to the laminar flow in a specially designed X-ray compatible microfluidic device. The setup ensures a nonequilibrium ascent of reactant concentration, and the resulting progression of DNA compaction was detected online using microfocused small-angle X-ray diffraction. The evolution of a DNA-dendrimer columnar square mesophase as a function of increasing dendrimer content is described. Additionally, in regions of maximum shear, an unexpected high-level perpendicular ordering of this phase is recorded. Furthermore, these assemblies are found to be in coexistence with a densely packed DNA-only mesophase in regions of excess DNA. The latter is reminiscent of dense packing found in bacteriophage and chromosomes, although surprisingly, it is not stabilized by direct dendrimer contact.
Subject(s)
DNA/chemistry , Microfluidics , X-Ray Diffraction/methods , Dendrimers/chemistry , Scattering, RadiationSubject(s)
Crystallization/methods , Dimethylpolysiloxanes/chemistry , Microchemistry/methods , Microfluidic Analytical Techniques/methods , Nanostructures/chemistry , Nanotechnology/methods , Nylons/chemistry , X-Ray Diffraction/methods , Macromolecular Substances/chemistry , Materials Testing , Microfluidic Analytical Techniques/instrumentation , Molecular Conformation , Nanostructures/ultrastructure , Nanotechnology/instrumentation , Particle Size , Pilot Projects , Surface PropertiesABSTRACT
We analyze microstructured multilayer films of poly(ethyleneimine) (PEI) and DNA by employing Raman and surface enhanced Raman spectroscopy (SERS). The microstructuring of the samples allows a simultaneous measurement of signal and reference in a single analytic process. Silver nanoparticles are implemented in the microstructured multilayers for SERS measurements. The recorded SERS spectra of PEI/DNA are dominated by the Raman bands of the DNA bases which show a larger mean enhancement than bands belonging to DNA backbone vibrations. Our results show that the combination of SERS and microstructured multilayer films provides an adapted way to characterize the polyelectrolytes as well as to measure the enhancement factor and the distance dependence for the SERS active silver nanoparticles. Furthermore, microstructured polyelectrolyte films containing SERS active nanoparticles are used for sensing molecules.
