Ultrafast structural fluctuations and rearrangements of water's hydrogen bonded network

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, February 2007."December 2006." Vita.Includes bibliographical references.Aqueous chemistry is strongly influenced by water's ability to form an extended network of hydrogen bonds. It is the fluctuations and rearrangements of this network that stabilize reaction products and drive the transport of excess protons through solution. Experimental observations of the dynamics of the hydrogen bonded network are difficult because (1) the timescales are exceedingly fast with relevant fluctuations occurring on a tens of femtosecond period and (2) the experimental probe must be sensitive to the local hydrogen bonded structure. In this thesis I address these experimental challenges through the development of ultrafast nonlinear infrared spectroscopy of the OH stretch of HOD in D20. The frequency of the OH stretch, OH, is sensitive to the configuration of the hydrogen bonded pair. Therefore, time-dependent changes in OoH can be correlated with changes in the hydrogen bonded geometry. I describe how broadband homodyne echo and polarization-dependent pump-probe experiments can be utilized to separate the contributions of spectral diffusion, vibrational relaxation and molecular reorientation. These experiments observe the underdamped motion of the hydrogen bonded pair and the librational motion of the OH dipole on the 180 and 50 fs timescales, respectively.(cont.) These dynamics occur on a relatively local (i.e. molecular) length scale. At times greater than ~300 fs the experiments observe signatures of a kinetic regime. No longer can the spectral relaxation be ascribed to a clear molecular motion. Instead, the decay originates from the collective reorganization of many molecules. Two dimensional infrared spectroscopy (2D IR) is applied to further investigate the mechanism of hydrogen bond rearrangement. 2D IR is an optical analogue of multidimensional NMR. As a correlation spectroscopy, time dependent changes in 2D IR line shapes track how vibrational oscillators relax from one frequency to another. I describe two methods of acquiring high fidelity 2D line shapes at wavelengths of 3 gtm. Both methods utilize a HeNe laser as a frequency standard and balanced detection of the signal field. Spectral diffusion is found to dominate the evolution of the 2D line shapes of the OH stretch up to the vibrational lifetime of 700 fs. At times beyond this point the line shapes change substantially, indicating population relaxation out of the v= 1 state and the formation of a spectroscopically distinct vibrationally excited ground state. Frequency dependent relaxation of the 2D IR line shapes reveals that molecules in hydrogen bonded and non-bonded configurations experience qualitatively different fluctuations.(cont.) Non-bonded configurations are found to return to band center on -100 fs timescale indicating that these configurations are inherently unstable. Hydrogen bonded oscillators undergo underdamped oscillations at the hydrogen bond stretching frequency before subsequent barrier crossing. Hydrogen bonding not only affects COOH. The transition dipole, gi, is modulated by the hydrogen bonding interaction, resulting in higher oscillator strength for strong hydrogen bonds. I describe how modeling the temperature dependent behavior of IR and Raman line shapes in combination with nonlinear IR spectroscopies can extract the frequency dependent magnitude of gi. The variation in the transition dipole with frequency is found to be roughly linear on resonance but is found to be strongly nonlinear for weak hydrogen bonds on the high frequency side of the OH line shape.by Joseph J. Loparo.Ph.D

The Gene-Silencing Protein MORC-1 Topologically Entraps DNA and Forms Multimeric Assemblies to Cause DNA Compaction

Microrchidia (MORC) ATPases are critical for gene silencing and chromatin compaction in multiple eukaryotic systems, but the mechanisms by which MORC proteins act are poorly understood. Here, we apply a series of biochemical, single-molecule, and cell-based imaging approaches to better understand the function of the Caenorhabditis elegans MORC-1 protein. We find that MORC-1 binds to DNA in a length-dependent but sequence non-specific manner and compacts DNA by forming DNA loops. MORC-1 molecules diffuse along DNA but become static as they grow into foci that are topologically entrapped on DNA. Consistent with the observed MORC-1 multimeric assemblies, MORC-1 forms nuclear puncta in cells and can also form phase-separated droplets in vitro. We also demonstrate that MORC-1 compacts nucleosome templates. These results suggest that MORCs affect genome structure and gene silencing by forming multimeric assemblages to topologically entrap and progressively loop and compact chromatin