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Nancy L. Greenbaum

Professor
 
Department :
Chemistry
Membership :
Associate Member
Core Research :
General
Office :
Room 1305B North
Email :
Office Phone :
(212) 772-5354
Lab Room:
Room 1305 North
Education :
  • Ph.D., University of Pennsylvania, 1984
  • Postdoc, Rockefeller University, 1985-1989
  • Postdoc, Columbia University, 1992-1996
Research Interest :

RNA structural biology; Investigation of RNA, metallo-RNA, and protein-RNA complexes by solution NMR and other spectroscopic techniques; design of theragnostic agents for detection and treatment of cancer.
As the major research focus of our laboratory, we attempt to answer questions about how RNA molecules fold and interact with other RNA, metal ions, and proteins in order to carry out the complex activity of precursor messenger (pre-m)RNA splicing. This process, by which noncoding sequences of pre-mRNA molecules, or introns, are excised, and flanking coding regions, or exons, are ligated together, is an essential step in preparation of mRNA transcripts prior to translation of their message into protein sequences; splicing at alternative pre-determined sites also provides a critical role in the generation of diverse gene products. Studies of structure/function relationships that lead to a more profound understanding of this process are therefore of great biomedical interest.

Pre-mRNA splicing in eukaryotic (compartmentalized) cells is performed within the nucleus by a dynamic supremolecular assembly called the spliceosome, which comprises five recyclable small nuclear (sn)RNA molecules and a large number (>150) of associated proteins. By comparison, the same splicing chemistry is carried out in a number of prokaryotic organisms and organelles of eukaryotic organisms by a simpler system, called a Group II intron, in which part of the RNA intron itself folds into a six-domain structure to excise itself without the need for proteins. A growing body of evidence lends support to the hypothesis that the spliceosomal reaction is also catalyzed by its RNA components.

Using a combination of biochemistry, biophysical, and spectroscopy techniques, we are pursuing several lines of investigation that contribute to our overall understanding of the structural biology of pre-mRNA splicing: 1) NMR studies of RNA structural elements and RNA-RNA interactions in the spliceosome and the Group II intron; NMR studies of RNA-protein interactions; 2) NMR-based refinement of structural features of ion-binding sites within RNA complexes by information from distance-dependent perturbations of chemical shift and relaxation properties induced by bound paramagnetic Ln3+ ion; and 3) luminescence and fluorescence resonance energy transfer between luminescent lanthanide metal ions and organic dyes as indicators of distances and metal ion-dependent conformational changes.

Selected Publications :
  • Popović, M., and Greenbaum, N.L. (2014) Role of helical constraints of the EBS1-IBS1 duplex of a group II intron on demarcation of the 5′ splice site.  RNA 20, 24-35. http://www.rnajournal.org/cgi/doi/10.1261/ rna.039701.113    
  • Ahmed, S. A., Mneimneh, S., Greenbaum N. (2013) A Combinatorial Approach to Multiple RNA Interaction: Formulations, Approximations, and Heuristics. In Editor (D.-Z. Du and G. Zhang, Eds.) COCOON 2013, Lecture Notes in Computer Science 7936 (421-433). Hangzhu, China: Springer-Verlag.
  • Mneimneh S, Ahmed SA, Greenbaum NL.  (2013) Multiple RNA Interaction: Formulations, Approximations, and Heuristics. Bioinformatics 2013: 242-249.
  • Zhao, C.* Bachu, R.*, Popović, M., Devany, M., Brenowitz, M., Schlatterer, J.C., and Greenbaum, N.L.  (2013) Conformational heterogeneity of the protein-free human spliceosomal U2-U6 snRNA complex.  RNA 19, 561-573. doi:10.1261/rna.038265.113.    *these authors contributed equally to the manuscript.
  • Popović, M., Nelson, J.D., Schroeder, K.T., and Greenbaum, N.L.  (2012) Impact of base pair identity 5 to the spliceosomal branch site adenosine on branch site conformation.  RNA 18, 2093-2103. doi:10.1261/rna.035782.112
  • Greenbaum, N.L., and Ghose, R. (2010) Nuclear magnetic resonance (NMR) spectroscopy: structure determination of proteins and nucleic acids. In: Encyclopedia Of Life Sciences 2010, John Wiley & Sons, Ltd: Chichester http://www.els.net/ [DOI: 10.1002/9780470015902.a0003100.pub2]
  • Yuan, F., and Greenbaum, N.L. (2010) Use of RNA bound Tb3+ as FRET donor. Methods Enz. (RNA: from Sequence to Structure and Dynamics, Adrian R. Ferré-D'Amaré, ed.) 52, 173-179.
  • Schlatterer, J.C., and Greenbaum, N.L. (2008) Specificity of Mg2+ binding at the Group II intron branch site. Biophysical Chemistry 136, 96-100.
  • Breiner, B., Schlatterer, J.C., Kovalenko, S.V., Greenbaum, N.L., and Alabugin, I.V.  (2007) DNA damage-site recognition by lysine-conjugates.  Proc. Natl. Acad. Sci. 104, 13016-13021.
  • Xu, D., Landon, T., Greenbaum, N.L., and Fenley, M.O. (2007). The electrostatic properties of G.U wobble base pairs. Nucleic Acids Res. 35: 3836-3847.
  • Yuan, F., Griffin, L., Phelps, L., Buschmann, V., Weston, K., and Greenbaum. (2007). Use of a novel Forster resonance energy transfer method to identify locations of site-bound metal ions in the U2-U6 snRNA complex. Nucleic Acids Res. 35: 2833-2845
  • Schlatterer, J.C., Crayton, S.H., and Greenbaum, N.L. (2006). Conformation of the Group II Intron Branch Site in Solution. J. Am. Chem. Soc. 128: 3866-3867.
  • Jennings, T.L., Schlatterer, J.C., Greenbaum, N.L., and Strouse, G.F. (2006). NSET molecular beacon analysis of hammerhead RNA substrate binding and catalysis. Nano Lett. 6: 1318-1324.
  • Schroeder, K., Skalicky, J.J., and Greenbaum, N.L. (2005). NMR spectroscopy of RNA duplexes containing pseudouridine in supercooled water. RNA 11: 1012-1016.
  • Xu, D., Greenbaum, N.L., and Fenley, M.O. (2005). Solvent accessible surface area and electrostatic surface potential of the spliceosomal branch site helix. Nucleic Acids Res. 33: 1154-1161.
  • Newby, M.I., and Greenbaum, N.L. (2002). Investigation of Overhauser effects between pseudouridine and water protons in RNA helices. Proc. Natl. Acad. Sci. 99: 12697-12702.
  • Newby, M.I., and Greenbaum, N.L. (2002). Sculpting of the spliceosomal branch site recognition motif by a conserved pseudouridine. Nature Structural Biology 9: 958-965.
  • Mundoma, C., and Greenbaum, N.L. (2002). Sequestering of Eu(III) by a GAAA RNA tetraloop. J. Am. Chem. Soc. 124: 3525-3532.
  • Newby, M.I., and Greenbaum, N.L. (2001). A conserved pseudouridine modification in eukaryotic U2 snRNA induces a change in branch site architecture. RNA 7: 833-845.
  • Greenbaum, N.L., Mundoma, C., and Peterman, D.R. (2001). Probing of metal-binding domains of RNA hairpin loops by laser-induced lanthanide(III) luminescence. Biochemistry 40: 1124-1134.