Tuning DNA Compaction

Abstract

DNA compaction is the collapse of long DNA chains into well-organized condensates of complex, hierarchical nanostructure induced by the presence of cationic agents. Although much progress has been made in understanding underlying interaction mechanisms of in vivo DNA compaction, the interplay of the myriad compaction agents and their types of interactions with DNA still raise a wealth of unanswered, fundamental questions. In particular, the hierarchical organization of chromatin is widely unclear. There, the DNA is first wrapped around histone cores and the formed beads-on-a-string structure is successively shifted towards higher order forms of chromatin structure. The latter process involves linker histones as major antagonists.Here, new results are presented that are derived from bio-mimetic investigations of the simplest possible DNA compaction model system containing only dendrimers, which can be viewed as uniformly charged cationic nanospheres, and unspecific, polydisperse DNA. Small angle X-ray (micro-)diffraction is employed as a principle method of analysis that accesses relevant molecular length scales. Targeting a quantitative understanding of compaction mechanisms, X-ray (micro-)diffraction measurements performed under laminar flow conditions in hydrodynamic focusing microfluidic devices provides microscale control of the self-assembly process. In addition, the method enables time-resolved access to structure formation in situ, in particular to transient intermediate states.Utilizing the high level of control over dendrimer size and charge, DNA compaction is systematically tuned and analyzed in detail. Results show that dendrimers bridge the entire spectrum of biological condensation agents from small cations, such as spermine/spermidine encountered in viruses, to the much larger histone proteins found in eukaryotic cells. Despite its simplicity, the dendrimer/DNA system reproduces characteristic features of DNA compaction in vivo. In particular, PAMAM 6 dendrimers (having a size and charge comparable to histone core proteins) induce a complete wrapping of the DNA around the cation. As such, PAMAM 6/DNA entities are structurally artificial equivalents of nucleosome core particles. For cationic dendrimers having an intermediate size and charge, which is conveniently between that of small multivalent organic cations and larger histone-like proteins, an alternate route of DNA compaction aside from the established salt or macroion condensation is observed in microflow below the isoelectric point, where DNA is in excess of dendrimers.In addition, the phenomenon of charge-induced dendrimer swelling has been experimentally quantified in detail over a wide range of generations. Results clearly show highly predictable, charge-induced changes of the dendrimer conformation and therefore eliminate the discrepancy between theory and experiments that previously existed in literature.Besides artificial model-proteins, the interaction of linker histones H1 and DNA has been studied in microflow. The time-resolved access to struture formation dynamics clearly shows that the interaction of H1 with DNA is a two step process: an initial unspecific binding of H1 to DNA is followed by a rearrangement of molecules in the formed complexes. Results suggest that the conformational transition of H1 tails from their rather extended conformation, in aqueous solution, to their fully folded state, upon interaction with DNA, is most likely the motor of the conformational phase transition of H1/DNA assemblies.Results obtained in this thesis are expected to have a direct bearing on the understanding of the hierarchical organization of chromatin in vivo. Underlying concepts and techniques may be generalized and used to experimentally address also other relevant protein/DNA systems. Moreover, the studied systems are of inherent importance to the field of biotechnology and are expected to contribute towards the design of new vectors for DNA gene delivery.