Synergy of condensing agents and macromolecular crowding on DNA condensation
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- Institutt for fysikk 
Imagine the packing of 100,000 meters of very thin copper wire inside a basketball!!! To add more complexity to the problem, imagine that the wire is highly negatively charged, causing repulsion. Further, consider quickly unpacking and finding a specific region on the wire, in order to read the information written on that wire. This is the same problem every cell faces; bacterial chromosomes, for example, are much longer than the cells in which they reside. For example, Caulobacter crescentus packages a 1.3 mm ( 4.0 Mega base pair) genome in a 2 μm cell. This spatial constraint is considered a fundamental problem in the field of biophysics and molecular biology. To understand bacterial genetics, it is fundamental to know the basic physical aspects of genetic material. That is effectively packed but, at the same time, needs to be specifically accessible for interaction with regulatory factors to perform replication, transcription, translation, repair and recombination. Inside bacterial cells, the genome is well compacted into a nucleoid. The organization of the nucleoid has been shown to be driven by special proteins called Nucleoid-Associated Proteins (NAPs), DNA supercoiling and macromolecular crowding (MMC). Even though there is wealth of knowledge on how various NAPs are involve in genome compaction and maintenance, still there is lack of knowledge about how these and other condensing agents behave in the presence of MMC. In this thesis, we aim at understanding DNA compaction induced by H-NS and various condensing agents, polycations and cationic surfactants, in crowded environment. By using various biophysical techniques, such as fluorescence correlation spectroscopy (FCS), fluorescence spectroscopy (FS) and circular dichroism (CD) we show that the presence of MMC has a significant role in driving the DNA compaction process in the presence of condensing agents.