Mechanistic understanding of living things requires our understanding of how proteins and DNA interact together to generate functional chromosomes. This understanding is central to preserving human health, dealing with genetic disorders, and fighting pathogenic organisms. The proposed projects are focused on single-molecule analyses which permit direct visualization of biomolecule interactions, and can be used to analyze protein-DNA interactions in detail.
The aims of the proposal include careful study of an """"""""exchange"""""""" mechanism for removal of proteins from DNA that suggests a major revision of conventional descriptions of protein turnover on DNA, and which will affect a wide range of studies of gene regulatory and chromosome-structural proteins.
A second aim i s focused on direct study of mechanisms of large """"""""Structural Maintenance of chromosomes"""""""" protein complexes which mediate the folding of chromosomes in eukaryote cells. Finally, a third aim is focused on mechanisms underlying a family of """"""""cut and paste"""""""" DNA recombination systems responsible in part for generating bacteria genetic diversity. The highly mechanistic analyses of DNA-processing machinery that are proposed will give us a stronger understanding of how cells interpret, fold and change their genomes, leading to a better understanding of pathologies where those functions are impaired, and better understanding of how to target those functions in pathogenic organisms.
All genetic processes are ultimately controlled by protein-DNA interactions. Incorrect processing of DNA in humans lead to a wide range of genetic disorders, while induction of errors in DNA processing provides a strategy to control pathogenic organisms. The proposed project seeks to obtain mechanistic understanding of proteins that interact with DNA and thereby to advance our ability to control genetic processes.
| Skoruppa, Enrico; Nomidis, Stefanos K; Marko, John F et al. (2018) Bend-Induced Twist Waves and the Structure of Nucleosomal DNA. Phys Rev Lett 121:088101 |
| Erba?, Aykut; de la Cruz, Monica Olvera; Marko, John F (2018) Effects of electrostatic interactions on ligand dissociation kinetics. Phys Rev E 97:022405 |
| Gunn, Kathryn H; Marko, John F; Mondragón, Alfonso (2018) Single-Molecule Magnetic Tweezer Analysis of Topoisomerases. Methods Mol Biol 1703:139-152 |
| Stephens, Andrew D; Liu, Patrick Z; Banigan, Edward J et al. (2018) Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins. Mol Biol Cell 29:220-233 |
| Brahmachari, Sumitabha; Dittmore, Andrew; Takagi, Yasuharu et al. (2018) Defect-facilitated buckling in supercoiled double-helix DNA. Phys Rev E 97:022416 |
| Dittmore, Andrew; Brahmachari, Sumitabha; Takagi, Yasuharu et al. (2017) Supercoiling DNA Locates Mismatches. Phys Rev Lett 119:147801 |
| Brahmachari, Sumitabha; Marko, John F (2017) Torque and buckling in stretched intertwined double-helix DNAs. Phys Rev E 95:052401 |
| Brahmachari, Sumitabha; Gunn, Kathryn H; Giuntoli, Rebecca D et al. (2017) Nucleation of Multiple Buckled Structures in Intertwined DNA Double Helices. Phys Rev Lett 119:188103 |
| Gunn, Kathryn H; Marko, John F; Mondragón, Alfonso (2017) An orthogonal single-molecule experiment reveals multiple-attempt dynamics of type IA topoisomerases. Nat Struct Mol Biol 24:484-490 |
| Stephens, Andrew D; Banigan, Edward J; Adam, Stephen A et al. (2017) Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus. Mol Biol Cell 28:1984-1996 |
Showing the most recent 10 out of 33 publications
