The power and prospects of fluorescence microscopies and spectroscopies.
Annu Rev Biophys Biomol Struct 32 (2003) 161-182
Abstract:
Recent years have witnessed a renaissance of fluorescence microscopy techniques and applications, from live-animal multiphoton confocal microscopy to single-molecule fluorescence spectroscopy and imaging in living cells. These achievements have been made possible not so much because of improvements in microscope design, but rather because of development of new detectors, accessible continuous wave and pulsed laser sources, sophisticated multiparameter analysis on one hand, and the development of new probes and labeling chemistries on the other. This review tracks the lineage of ideas and the evolution of thinking that have led to the actual developments, and presents a comprehensive overview of the field, with emphasis put on our laboratory's interest in single-molecule microscopy and spectroscopy.Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex.
Cell 108:5 (2002) 599-614
Abstract:
We have used systematic fluorescence resonance energy transfer and distance-constrained docking to define the three-dimensional structures of bacterial RNA polymerase holoenzyme and the bacterial RNA polymerase-promoter open complex in solution. The structures provide a framework for understanding sigma(70)-(RNA polymerase core), sigma(70)-DNA, and sigma(70)-RNA interactions. The positions of sigma(70) regions 1.2, 2, 3, and 4 are similar in holoenzyme and open complex. In contrast, the position of sigma(70) region 1.1 differs dramatically in holoenzyme and open complex. In holoenzyme, region 1.1 is located within the active-center cleft, apparently serving as a "molecular mimic" of DNA, but, in open complex, region 1.1 is located outside the active center cleft. The approach described here should be applicable to the analysis of other nanometer-scale complexes.Three-dimensional strictures of RNA polymerase holoenzyme and the RNA polymerase-promoter open complex: Systematic fluorescence resonance energy transfer and distance-constrained docking
BIOPHYSICAL JOURNAL 82:1 (2002) 185A-185A
Site-specific incorporation of fluorescent probes into protein: hexahistidine-tag-mediated fluorescent labeling with (Ni(2+):nitrilotriacetic Acid (n)-fluorochrome conjugates.
J Am Chem Soc 123:48 (2001) 12123-12125
Mean DNA bend angle and distribution of DNA bend angles in the CAP-DNA complex in solution.
J Mol Biol 312:3 (2001) 453-468