Darrell R. Davis
Professor of Medicinal Chemistry and of Biochemistry
B.S. University of Puget Sound
Ph.D. University of Utah
Research
My laboratory is involved in the study of nucleic acid and protein structure using high-field NMR spectroscopy. In the RNA area we are focused on the affect of naturally occurring nucleoside modifications on the structure and dynamics of RNA. Of the natural RNA molecules, tRNA and ribosomal RNA contain the highest numbers of conserved nucleoside modifications.
An interesting biochemical role for tRNA is as a primer for retroviral reverse transcriptases. When the HIV-1 virus assembles from human cells, a particular tRNA, tRNA Lys,3, is selectively packaged in the virion. The tRNA primer forms several secondary structural interactions with complementary regions of the HIV genome. In the figure, a 3D model is presented that accommodates the tRNA/viral RNA interactions to form a folded structure for the primer/template complex. The 3' end of the tRNA forms an 18 base-pair "PBS" helix in orange, the T y C region of the tRNA forms a short "PAS" heiix in blue, and the anticodon of the tRNA forms a loop-loop "A-loop" helix in green. This structure may explain why a specific human lysine tRNA has been selected by HIV as the reverse transcription primer.
The laboratory has been particularly intrigued by how tRNA functions are affected by modification. The top figure highlights a structural interaction involving a nucleoside in lysine tRNA that is modified with the amino acid threonine. When the tRNA binds its complementary codon on the ribosome, the modified ms2t6A37 nucleoside stacks over the first adeonsine of the codon, thereby stabilizing the codon-anticodon interaction. The modified nucleosides of the t6A family represent an evolutionarily conserved solution for fine tuning the ribosomal machinery. Current studies in our laboratory are focussed on comparing structures of the modified E. coli and human lysine tRNAs, and determining the structure of the HIV-1 RNA primer/template complex.
References
1. Klaiman D, Amitsur M, Blanga-Kanfi S, Chai M, Davis DR, Kaufmann G (2007) Parallel dimerization of PrrC-anticodon nuclease region implicated in tRNALys recognition. Nucleic Acids Res. 35:4704-14
2. Durant PC, Bajji AC, Sundaram M, Kumar RK, Davis DR (2005) Structural effects of hypermodified nucleosides in the E. coli and human tRNALys anticodon loop: The effect of nucleosides s2U, mcm5U, mcm5s2U, mnm5s2U, t6A, and ms2t6A. Biochemistry 44:8078-8089
3. Davis DR, Bajji AC (2005) Introduction of hyper-modified nucleotides in RNA. Methods Mol. Biol. 288:187-204
4. Wagner TM, Nair V, Guymon R, Pomerantz SC, Crain PF, Davis DR, McCloskey JA (2004) A novel method for sequence placement of modified nucleotides in mixtures of transfer RNA. Nucleic Acids Symp Series 48:263-264
5. Alam SL, Sun J, Payne M, Welch BD, Blake BK, Davis DR, Meyer HH, Emr SD, Sundquist WI (2004) Ubiquitin interactions of NZF zinc fingers. EMBO J. 23:1411-1421
6. Bajji AC, Sundaram M, Myszka DG, Davis DR (2002 ) An RNA complex of the HIV-1 A-loop and tRNA Lys,3 is stabilized by nucleoside modifications. J. Am. Chem. Soc. 124:14302-14303
7. Wang B, Alam SL, Payne M, Meyer HH, Payne M, Stemmler TL, Warren G, Davis DR, Sundquist WI (2003) Structure and Ubiquitin Interactions of the Conserved NZF Domain of Npl4. J. Biol. Chem. 278: 20225-20234
8. Pornillos OW, Alam SL, Rich RL, Myszka DG, Davis DR, Sundquist WI (2002) Structure and functional interactions of the Tsg101 UEV domain. EMBO J. 21:2397-2406
9. Jiang Y, Blanga S, Amitsur M, Meidler R, Krivosheyev E, Sundaram M, Bajji AC, Davis DR, Kaufmann G (2002) Structural features of tRNALys favored by anticodon nuclease as inferred from reactivities of anticodon stem and loop substrate analogs. J. Biol. Chem. 277:3836-3841
10. Grahn E, Moss T, Helgstrand C, Fridborg K, Sundaram M, Tars K, Lago H, Stonehouse NJ, Davis DR, Stockley PG, Liljas L (2001) Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat protein complex. RNA 7:1616-1627
