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Center for the Study of Systems Biology
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ItemRNA Enzymes: From Folding to Function in Living Cells(Georgia Institute of Technology, 2008-03-25) Fedor, Martha J.Our research aims to generate fundamental insights into catalysis by RNA enzymes and into the pathways through which RNAs form specific functional structures. RNA catalysis remains an intriguing puzzle that has grown in significance since the recent discoveries that the ribosome itself is an RNA enzyme and that human and bacterial mRNAs contain self-cleaving ribozymes. The hairpin ribozyme catalyzes a reversible self-cleavage reaction in which nucleophilic attack of a ribose 2’ hydroxyl on an adjacent phosphorus proceeds through a trigonal bipyramidal trasition state that leads to the formation of 2’,3’-cyclic phosphate and 2’ hydroxyl termini. The metal cation independence of activity and the availability of high-resolution active site structures have made the hairpin ribozyme the prototype for nucleobase-mediated catalytic chemistry. A network of stacking and hydrogen bonding interactions align the reactive phosphate in the appropriate orientation for an SN2-type nucleophilic attack and orient nucleotide base functional groups near the reactive phosphate to facilitate catalytic chemistry. Two active site nucleobases, G8 and A38, adopt orientations reminiscent of the histidine residues that mediate general acid base catalysis in ribonuclease A, a protein enzyme that catalyzes the same phosphodiester cleavage chemistry. However, our biochemical experiments argue against analogous roles for G8 and A38 in hairpin ribozyme catalysis and suggest that these residues contribute to catalysis through positioning and orientation and electrostatic stabilization of the electronegative transition site. Ribozymes are useful model systems for investigation of RNA folding, since self-cleavage reflects the assembly of a precise functional structure. To learn how structure-function principles revealed through in vitro experiments translate to the behavior of RNA in living cells, we devised a way to evaluate RNA assembly in vivo using RNA self-cleavage rates to quantify assembly of functional RNA structures. Results of these studies show that intracellular RNA folding kinetics and equilibria are indistinguishable from RNA folding behavior in vitro, provided that in vitro folding reactions approximate the ionic conditions characteristic of an intracellular environment. These studies contribute basic knowledge of RNA structure and function and provide a framework for developing technical and therapeutic application involving RNAs as targets and reagents.
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ItemPositive Selection on Non-coding Sequences During Human Evolution: From Genome to Nucleotide(Georgia Institute of Technology, 2008-03-04) Wray, Gregory
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ItemBetter living through biosensors(Georgia Institute of Technology, 2008-02-19) Plaxco, KevinThe ideal sensor will be sensitive, specific, versatile, small enough to hold in your hand, and selective enough to work even when faced with complex, contaminant-ridden samples. Given the affinity, specificity and generalizability of biomolecular recognition, biosensors have been widely touted for their potential to meet these challenging goals. To date, however, the translation of protein- and DNA-binding events into convenient, highly selective sensing platforms has proven problematic. We have solved this problem by employing the ligand-induced folding of proteins, peptides and DNA as a robust signal transduction mechanism. Our folding-based sensors are rapid (minutes to seconds), sensitive (micromolar to femtomolar), fully electronic, and generalizable to an enormous range of protein, nucleic acid and small molecule targets. The sensors are also reagentless, greater than 99% reusable, and selective enough to be employed in (and re-used from) blood, soil and other grossly contaminated materials. Because of their sensitivity, background suppression, operational convenience and impressive scalability folding-based biosensors appear ideally suited for electronic, on-chip applications in pathogen detection, proteomics and genomics.
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ItemSystems Biology and its Role in Predictive Health and Personalized Medicine(Georgia Institute of Technology, 2008-02-05) Voit, Eberhard O.
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ItemMechanisms of Chromosomal Fragility and Rearrangements Triggered by Human Unstable Repeats(Georgia Institute of Technology, 2008-01-22) Lobachev, KirillResearch of my lab focuses on understanding how chromosomal rearrangements arise and lead to hereditary diseases and cancer. Chromosomes containing repeats that can adopt stable secondary structures are highly prone for double-strand breaks and various types of rearrangements. Molecular mechanisms for this type of genetic instability in eukaryotes are poorly understood. Using yeast, S. cerevisiae, we are investigating the chromosomal fragility mediated by two sequence motifs: cruciform-forming inverted repeats and H-DNA-forming GAA/TTC triplet repeats. Both types of repeats strongly induce breakage which results from the replication arrest by the secondary structures. However, genetic requirements for fragility, mode of breakage and consequences for the genome integrity are different for these two types of repeats. We propose that the nature of the secondary structure predisposes chromosomes for the specific pattern of gross chromosomal rearrangements. These rearrangements are strikingly similar to carcinogenic aberration suggesting that repeat-mediated instability might be a general phenomenon that operates not only in yeast but also in humans. I will present recent data from my lab on proteins that are involved into the fragility.
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ItemHybrid Experiments: Linking Real-Time Simulations to In Vitro Electrophysiology Experiments(Georgia Institute of Technology, 2007-10-30) Butera, Robert J.