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Dr. Ivan J. Dmochowski - Assistant Professor |
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Our
research is directed towards developing small molecule probes, molecular
biology strategies, and spectroscopic tools for studying and controlling
specific gene and protein functions in living systems. Our focus on protein-nucleic acid
interactions is driven by interesting problems in biology, namely
understanding how gene regulation leads to early embryonic development
and how biological systems protect DNA during conditions of oxidative
stress. We aim to extend
traditional biological imaging techniques to not only observe, but
also perturb living systems to yield answers to these intriguing
questions. Energy- and electron-transfer processes
allow biomolecule assemblies to be characterized both in vitro
and in vivo. In
Vivo Chemical Biology We
have recently developed confocal laser scanning microscopy methods
to quantify fluorescence in living embryos, such as sea urchins. Although green fluorescent protein
(GFP) is used widely in biology to indicate regions of gene expression,
it is only now possible to measure accurately this fluorescent biomolecule
in real time in living three-dimensional organisms. Thus, we can perturb specific genes and observe the effects
using GFP and other genetically encoded and small molecule reporters.
To this end, my group is synthesizing small molecules, such
as RNA anti-sense probes, which are activated by infrared, 2-photon
excitation. By uncaging these molecules, we hope to alter protein expression
within a particular cell and at a particular time during development.
In addition, we are developing fluorescence assays to monitor
enzyme-specific activity in vivo.
The characterization of molecular interactions, such as factors
cooperatively bound to DNA, will be accomplished using fluorescence
energy-transfer, lifetime, and correlation measurements. Getting
a Charge out of Ferritin Ferritin
is a large family of iron storage proteins, and was shown recently
to be required for life and to bind DNA.
A related family of proteins in bacteria protects DNA during
conditions of oxidative stress by an unknown mechanism. We are investigating whether electron-transfer
pathways in ferritin-like proteins play important roles in their
function. Mechanistic
studies of ferritin will hopefully shed light on certain pathologies;
for example, hyper-ferritinemia is linked to one form of cataracts. The methodologies we develop for synthesizing
and manipulating ferritin (a 24-mer of 4-helix bundles containing
an 8nm diameter hollow cavity) should have many interesting applications,
including agents for drug delivery, and new probes for in vivo
spectroscopic studies.
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