TETRALOOP RECEPTOR RNA STRUCTURAL INVESTIGATION

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. We are investigating the structure of the free tetraloop receptor. The tetraloop receptor is a commonly occurring motif that mediates tertiary folding of large, non-coding RNAs. We are investigating the tetraloop receptor structure as a function of temperature and ionic conditions. Previous work shows that the tetraloop receptor undergoes a conformational change upon tetraloop binding. We are also investigating the kinetics of this conformational change by NMR. NMR experiments that we will need to collect include: 1D (1H), 2D NOESY, 2D 1H-15N HSQC (normal and TROSY enhanced), 2D 1H-15N HNN COSY, 2D 1H-13C HSQC (normal and TROSY enhanced), 2D NOESY, 2D 1H,13C filter/edit NOESY, 3D 1H(13C)1H NOESY-HSQC, 3D 1H(13C)1H HCCH TOCSY and 3D 1H(13C)1H HCCH COSY. Residual dipolar couplings will be measured for samples in both isotropic and partially aligned states (via addition of Pf1 phage).