Biological polymers, including proteins and the genome, undergo folding processes crucial for their proper functioning. Even slight changes in the folding structure of these biopolymers can have... Show moreBiological polymers, including proteins and the genome, undergo folding processes crucial for their proper functioning. Even slight changes in the folding structure of these biopolymers can have significant implications, leading to the development of various pathological conditions, such as neurodegenerative diseases and cancer. In this thesis, we leverage the theoretical framework of Circuit Topology and expand its application to real-world scenarios. By employing this approach, we quantify the folding patterns of biological polymers, offering valuable insights for detecting harmful misfolds. Furthermore, this research holds the potential to provide fundamental design principles for molecular engineering in the realm of pharmaceutical applications. Show less
Nucleoid associated proteins maintain the architecture of the bacterial chromosome and regulate gene expression, hinting that their role as transcription factors may involve local three-dimensional... Show moreNucleoid associated proteins maintain the architecture of the bacterial chromosome and regulate gene expression, hinting that their role as transcription factors may involve local three-dimensional chromosome re-modelling. This dissertation provides the first evidence to support this hypothesis. Using ensemble RT-qPCR and 3C-qPCR, in addition to in vivo and in vitro single molecule fluorescence microscopy techniques, the interplay between the expression of the H-NS-regulated, osmosensitive proVWX operon of Escherichia coli and structural re-modelling of the operon is shown. The formation of a loop anchored between the P2 promoter of proVWX and the terminus of the operon represses its expression. Destabilization of the loop activates transcription. The model presented in this thesis provides clues for how H-NS and H-NS-like proteins may regulate the expression of other operons and genes within their regulons. Show less
