Abstract

RNA acts as information carriers, catalysts, and regulators in essential biological processes, and understanding RNA structure and function is intimately linked to combating diseases. The long-term objectives of this project is to advance our understanding of the RNA structure/function relationship via studying structure, conformational dynamics, and mechanism of function, in the phi29 packaging RNA (pRNA) that plays essential roles in the most powerful biological motor known today - the DNA packaging motor of the phi29 bacteriophage. ? ? The specific aims involve a parallel development of the site-directed spin labeling (SDSL) technique for studying RNA structure and dynamics, and application of SDSL and other methods to study pRNA structure and interaction. SDSL utilizes a nitroxide moiety attached to specific sites to obtain structural and dynamic information of the parent molecule, and has recently been shown to be able to provide unique information in RNA. Proposed RNA SDSL developments, which are driven by specific questions in pRNA studies, include: (I) establishing long-range distance measurements in nucleic acids using nitroxides attached to arbitrary sequences; and (ii) establishing the first empirical RNA SDSL line shape library for deducing RNA structural information from singly labeled nitroxides. ? ? These developments will find applications in packaging RNA studies.
Specific aims i ncludes: (I) studying structure and conformational changes in the pRNA using a combination of SDSL, NMR, and computational modeling; and (ii) mapping pRNA/protein and pRNA/pRNA interfaces in the motor via analyzing pRNA functional groups. ? ? The proposed studies will reveal information on packaging RNA structure and interaction that will aid in understanding the mechanism of phi29 packaging. It is believed that phi29 shares the same DNA packaging mechanism with many other double stranded DNA viruses, including a number of human pathogens. Understanding phi29 packaging motor function will aid in developing pharmacological approaches to combat these viruses. ? ? ?

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM069557-02
Application #
7260396
Study Section
Macromolecular Structure and Function C Study Section (MSFC)
Program Officer
Preusch, Peter C
Project Start
2006-08-01
Project End
2011-07-31
Budget Start
2007-08-01
Budget End
2008-07-31
Support Year
2
Fiscal Year
2007
Total Cost
$249,280
Indirect Cost

  Institution

Name
University of Southern California
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
072933393
City
Los Angeles
State
CA
Country
United States
Zip Code
90089

  Publications

Tangprasertchai, Narin S; Zhang, Xiaojun; Ding, Yuan et al. (2015) An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids. Methods Enzymol 564:427-53
Ding, Yuan; Zhang, Xiaojun; Tham, Kenneth W et al. (2014) Experimental mapping of DNA duplex shape enabled by global lineshape analyses of a nucleotide-independent nitroxide probe. Nucleic Acids Res 42:e140
Zhang, Xiaojun; Dantas Machado, Ana Carolina; Ding, Yuan et al. (2014) Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling. Nucleic Acids Res 42:2789-97
Nguyen, Phuong; Shi, Xuesong; Sigurdsson, Snorri Th et al. (2013) A single-stranded junction modulates nanosecond motional ordering of the substrate recognition duplex of a group I ribozyme. Chembiochem 14:1720-3
Chen, Yongheng; Zhang, Xiaojun; Dantas Machado, Ana Carolina et al. (2013) Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion. Nucleic Acids Res 41:8368-76
Zhang, Xiaojun; Tung, Chang-Shung; Sowa, Glenna Z et al. (2012) Global structure of a three-way junction in a phi29 packaging RNA dimer determined using site-directed spin labeling. J Am Chem Soc 134:2644-52
Popova, Anna M; Hatmal, Ma'mon M; Frushicheva, Maria P et al. (2012) Nitroxide sensing of a DNA microenvironment: mechanistic insights from EPR spectroscopy and molecular dynamics simulations. J Phys Chem B 116:6387-96
Nguyen, Phuong; Qin, Peter Z (2012) RNA dynamics: perspectives from spin labels. Wiley Interdiscip Rev RNA 3:62-72
Zhang, Xiaojun; Lee, Sang Won; Zhao, Liang et al. (2010) Conformational distributions at the N-peptide/boxB RNA interface studied using site-directed spin labeling. RNA 16:2474-83
Popova, Anna M; Qin, Peter Z (2010) A nucleotide-independent nitroxide probe reports on site-specific stereomeric environment in DNA. Biophys J 99:2180-9

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