Tinoco Group --- How RNA folds and unfolds

Tinoco Research Group

Department of Chemistry University of California, Berkeley

Selected structures solved by Tinoco group

Two C-G base pairs in the kissing hairpin complex between two tetraloops GACG

PDB: 1F5U

1. Conformation and Dynamics of an RNA Internal Loop, G. Varani, B. Wimberly & I. Tinoco, Jr., Biochemistry 28, 7760-7772 (1989).

2. Z-RNA: The Solution NMR structure of r(CGCGCG), P. W. Davis, R. W. Adamiak & I. Tinoco, Jr., Biopolymers 29, 109-122 (1990).

3. Solution Conformation of an RNA Hairpin Loop, J. D. Puglisi, J. R. Wyatt & I. Tinoco, Jr., Biochemistry 29, 4215-4226 (1990).

4. Conformation of an RNA Pseudoknot, J. D. Puglisi, J. R. Wyatt & I. Tinoco, Jr., J. Mol. Biol. 214, 437-453 (1990).

5. Solution Structure of an Unusually Stable RNA Hairpin, 5'GGAC(UUCG)GUCC, C. Cheong, G. Varani & I. Tinoco, Jr., Nature 346, 680-682 (1990).

6. Structure of an Unusually Stable RNA Hairpin, G. Varani, C. Cheong & I. Tinoco, Jr., Biochemistry 30, 3280-3289 (1991).

7. Crystal Structure of an RNA Double Helix Incorporating a Track of Non-Watson-Crick Base Pairs, S. Holbrook, C. Cheong, I. Tinoco, Jr. & S.-H. Kim, Nature, 353, 579-581 (1991). PDB: 255D

8. A Base-Triple Structural Domain in RNA, M. Chastain and I. Tinoco, Jr., Biochemistry 31, 12733-12741 (1992).

9. The Conformation of Loop E of Eukaryotic 5S Ribosomal RNA, B. Wimberly, G. Varani and I. Tinoco, Jr., Biochemistry 32, 1078-1087 (1993).

10. Structure of a Small RNA Hairpin, P. W. Davis, W. Thurmes and I. Tinoco, Jr., Nucleic Acids Res. 21, 537-545 (1993).

11. The Solution Structure of a d[C(TTCG)G] DNA Hairpin and Comparison to the Unusually Stable RNA Hairpin, J. K. James and I. Tinoco, Jr., Nucleic Acids Res. 21, 3287-3293 (1993).

12. An NMR Study of the HIV-1 TAR Element Hairpin, J. A. Jaeger and I. Tinoco, Jr., Biochemistry, 32, 12522-12530 (1993)

13. Nucleoside Triples from the Group I Intron, M. Chastain and I. Tinoco, Jr., Biochemistry 32, 14220-14228 (1993).

14. Structural and Functional Studies of Retroviral RNA Pseudoknots Involved in Ribosomal Frameshifting: Nucleotides at the Junction of the Two Stems Are Important for Efficient Ribosomal Frameshifting, X. Chen, M. Chamorro, S. Lee, L. X. Shen, J. V. Hines, I. Tinoco, Jr. and H. E. Varmus, EMBO J. 14, 842-852 (1995).

15. The Structure of an RNA Pseudoknot that Causes Efficient Frameshifting in Mouse Mammary Tumor Virus, L. X. Shen and I. Tinoco, Jr. J. Mol. Biol. 247, 963-978 (1995). PDB: 1RNK

16. Conformation of an RNA Molecule that Models the P4/P6 Junction from Group I Introns, J. Nowakowski and I. Tinoco, Jr., Biochemistry 35, 2577-2585 (1996).

17. Conformation of a Non-Frameshifting RNA Pseudoknot from Mouse Mammary Tumor Virus, H. Kang, J. V. Hines and I. Tinoco, Jr., J. Mol. Biol. 259, 135-147 (1996). PDB: 1KAJ

18. Solution Structure of Loop A from the Hairpin Ribozyme from Tobacco Ringspot Virus Satellite, Z. Cai and I. Tinoco, Jr., Biochemistry 35, 6026-6036 (1996).

19. A Characteristic Bent Conformation of RNA Pseudoknots Causes Minus-one Frameshifting During Translation of Retroviral RNA, X. Chen, H. Kang, L. X. Shen, M. Chamorro, H. E. Varmus and I. Tinoco, Jr., J. Mol. Biol. 260, 479-483 (1996).

20. NMR Structure of a Bacteriophage T4 RNA Hairpin Involved in Translational Repression, S. R. Mirmira and I. Tinoco, Jr., Biochemistry 35, 7664-7674 (1996).

21. The Structure of an RNA "Kissing" Hairpin Complex of the HIV TAR Hairpin Loop and its Complement, K.-Y. Chang and I. Tinoco, Jr., J. Mol. Biol. 269, 52-66 (1997). PDB: 1KIS

22. A Mutant RNA Pseudoknot That Promotes Ribosomal Frameshifting In Mouse Mammary Tumor Virus, H. Kang and I. Tinoco, Jr., Nucleic Acids Res. 25, 1943-1949 (1997). PDB: 1KPD

23. Solution Conformation of a Five-Nucleotide RNA Bulge Loop from a Group I Intron, K. J. Luebke, S. M. Landry and I. Tinoco, Jr., Biochemistry 36, 10246-10255 (1997). PDB: 1AJL 1AJT

24. Solution Structure of a Metal-Binding Site in the Major Groove of RNA Complexed with Cobalt (III) Hexammine, J. S. Kieft and I. Tinoco, Jr., Structure 5, 713-721 (1997). PDB: 1AJF

25. The Structure of the L3 Loop from the Hepatitis Delta Virus Ribozyme: a syn Cytidine, S. R. Lynch and I. Tinoco, Jr., Nucleic Acids Res. 26, 980-987 (1998).

26. Structure and Thermodynamics of Metal Binding in the P5 helix of a Group I Intron Ribozyme, G. Colmenarejo and I. Tinoco, Jr., J. Mol. Biol.290, 119-135 (1999). PDB: 1C0O

27. Solution Structure and Thermodynamics of a Divalent Metal Ion Binding Site in an RNA Pseudoknot, R. L. Gonzalez, Jr. and I. Tinoco, Jr., J. Mol. Biol. 289, 1267-1282 (1999).

28. Solution Structure of Cobalt(III)Hexammine Complexed to the GAAA Tetraloop, and Metal-Ion Binding to G·A Mismatches, S. Rüdisser and I. Tinoco, Jr., J. Mol. Biol. 295, 1211-1223 (2000). PDB: 1EOR 1F9L

29. RNA motifs that determine specificity between a viral replicase and its promoter. C.-H. Kim, C. C. Kao, and I. Tinoco, Jr., Nature Structural Biology, 7, 415-423, (2000). PDB: 1ESH

30. Solution Structure and Metal-Ion Binding of the P4 Element from Bacterial RNase P RNA. M. Schmitz and I. Tinoco, Jr. RNA, 6,1212-1225 (2000). PDB: 1F6X 1F6Z 1F78 1F79 1F7F 1F7G 1F7H 1F7I

31. A retroviral RNA kissing complex containing only two G•C base pairs. C.-H. Kimand I. Tinoco, Jr., Proc. Natl. Acad. Sci. USA 97, 9396-9401 (2000). PDB: 1F5U

32. Structural and thermodynamic studies on mutant RNA motifs that impair the specificity between a viral replicase and its promoter. C.-H. Kim and I. Tinoco, Jr., J. Mol. Biol. 307, 827-839 (2001). PDB: 1I46 1I4B 1I4C

33. Formation of a GNRA tetraloop in P5abc can disrupt an inter-domain interaction in the Tetrahymena group I ribozyme. M. Zheng, M. Wu and I. Tinoco, Jr., Proc. Natl. Acad. Sci. USA, 98, 3695-3700 (2001).