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Characterizing RNA Structure and synthesis by Raman Microscopy

Chen, Yuanyuan
http://rave.ohiolink.edu/etdc/view?acc_num=case1277761094

Abstract Details

2010, Doctor of Philosophy, Case Western Reserve University, Biochemistry.
Raman microscopy has been broadly applied to the structural studies of macromolecules, such as proteins and RNAs. Using isotopically labeled samples, we are able to identify the signals from specific regions of the molecule or the complex, so that the structural or chemical information from local regions of a big molecule or complex can be investigated. In this thesis, isotopically edited samples have been used in two different applications: 1) probing the adenine rings and linked backbone conformation of domain V (D5) of Group II intron in solution, using isotopically edited Raman spectroscopy; 2) monitoring transcription initiation in a single crystal containing N4 mini-vRNA polymerase in real-time, using time-dependent Raman microscopy. In the first case, the D5 RNA was specifically labeled with 13C and 15N on the A base rings and the linked ribose. All the A ring modes and A-linked backbone conformations are identified; helical and non-helical backbone conformations, as well as local base ring conformations are compared in the presence and absence of Mg2+; the Mg2+•••PO2- (backbone) interaction is shown to be affected differently by monovalent ions, which can be anti-correlated with the in vitro activities of the reconstructed ribozyme in the corresponding monovalent ion conditions. In the second project, the first phosphoryltransfer reaction during transcription initiation, occurring in a single crystal, was monitored in real-time by time Raman spectroscopy. Multiple events including substrate binding, conformational changes, metal site formation and disappearance, decrease of substrate and increase of product, are probed individually during the partial or complete reactions occurring on the transcription initiation pathway.
Paul Carey, Ph. D (Advisor)
Vivien Yee, Ph. D (Committee Chair)
Irene Lee, Ph. D (Committee Member)
Michael Harris, Ph. D (Committee Member)
Eckhard Jankowsky, Ph. D (Committee Member)
180 p.
Biochemistry; Biology; Chemistry; Virology
Domain V; group II intron; Raman spectroscopy; RNA; isotope labeling; structure; transcription; RNA polymerase; N4 viron; initiation; NTP; maganesium

Recommended Citations

Citations

  • Chen, Y. (2010). Characterizing RNA Structure and synthesis by Raman Microscopy [Doctoral dissertation, Case Western Reserve University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=case1277761094

    APA Style (7th edition)

  • Chen, Yuanyuan. Characterizing RNA Structure and synthesis by Raman Microscopy. 2010. Case Western Reserve University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=case1277761094.

    MLA Style (8th edition)

  • Chen, Yuanyuan. "Characterizing RNA Structure and synthesis by Raman Microscopy." Doctoral dissertation, Case Western Reserve University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=case1277761094

    Chicago Manual of Style (17th edition)

case1277761094
1,228
© 2010, some rights reserved.Creative Commons License Characterizing RNA Structure and synthesis by Raman Microscopy by Yuanyuan Chen is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. Based on a work at etd.ohiolink.edu.
This open access ETD is published by Case Western Reserve University School of Graduate Studies and OhioLINK.