Dissertation Information for Vanvimon SaksmerpromeNAME:
DEGREE:
DISCIPLINE:
SCHOOL: ADVISORS: COMMITTEE MEMBERS: MPACT Status: Incomplete - Not_Inspected Title: Kinetic analysis of natural and engineered hammerhead ribozymes Abstract: The hammerhead ribozyme (hRz) is a small catalytic RNA motif that cleaves a specific phosphodiester bond, generating a terminal 5 ' hydroxyl and a 2 ' 3 ' -cyclic phosphate. Natural hRz's are found in satellite RNAs of some plant viroid pathogens and in the repetitive DNA of newts, cave crickets, and flukes. Since the active core, termed "minimal hRz," can be readily engineered into a trans -acting catalyst with programmable specificity, the ribozyme has become a popular tool in biology and medicine. In the TRAP design (t[barbelow]argeted r[barbelow]eversibly-a[barbelow]ttenuated p[barbelow]robes), two sequences are appended onto the hRz's catalytic core, generating an oligonucleotide-responsive ribozyme. Because cleavage activity of TRAP ribozyme results from formation of an active structure, monitoring cleavage kinetics sheds light on the parameters that affect RNA folding. Resulting kinetic and thermodynamic parameters favors a model in which regulation arises from equilibration between the active and inactive conformations of the TRAP, and that cleavage kinetics are primarily governed by the relative stabilities of the activating and attenuating helices. Probing conformational equilibrium of TRAPS as a function of pH and urea concentrations suggests the possibility that deprotonation of the 2 ' hydroxyl group serves a dual role of favoring productive folding and enhancing the nucleophilicity of this oxygen. |
MPACT Scores for Vanvimon SaksmerpromeA = 0 Advisors and Advisees Graph |