Introduction to the RNA World
A partial summary of readings for Biol 801, The RNA World
Junichi Komoto
Graduate student, Department of Molecular Biosciences, The University of Kansas-Lawrence. Mentor: Fusao Takusagawa.
© March-May 2000
Edited by Peter Gegenheimer
Department of Molecular Biosciences, The University of Kansas-Lawrence.
Contents
Section 1
Section 2
Section 3
Section 4
  
References
Table of Contents
tRNA Tertiary Structure
Structure Determination Methods
The Hammerhead Ribozyme
In vitro Evolution of RNA
 
Reading list
REFS:>>
Structure
Methods |
RNA-protein
Hammerhead
In vitro Evolution
 
 
References [ Top  ] 
About the figures: All figures of crystal structures were prepared by the molecular graphics program RasMol v. 2.7.1.

The tertiary structure of transfer RNAPhe   [ back to top ]

1. Kim, S. H., Suddath, F. L., Quigley, G. J., McPherson, Sussman, J. L., Wang, A. H. J., Seeman, N. C., and Rich, A. Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science (1974) 185, 435-440

2. Quigley, G. J. and Rich, A. Structural domains of transfer RNA molecules. Science (1976) 194, 796-806.

3. Soll, D. Transfer RNA: an RNA for all seasons,  Ch. 7 in The RNA world, Gesteland, R. F. and Atkins, J. F., ed., Cold Spring Harbor Laboratory Press (1993)

Interaction between tRNA and aminoacyltransfer RNA synthetase [ back to top ]

1. Francklyn, C., Musier-Forsyth, K., and Schimmel, P. Small RNA helices as substrates for aminoacylation and their relationship to charging of transfer RNAs. Eur. J. Biochem. (1992) 206, 315-321.

2. Kim, S. and Schimmel, P. Functional independence of microhelix aminoacylation from anticodon binding in a class I tRNA synthetase. J. Biol. Chem. (1992) 267, 15563-15567.

3. Perona, J. J., Swanson, R. N., Rould, M. A., Steitz, T. A., and Soll, D. Structural basis for  misaminoacylation by mutant E. coli glutaminyl-tRNA synthetase enzymes. Science (1989) 246, 1152-1154.

v4. Rould, M. A., Perona, J. J., Soll, D., and Steitz, T. A. Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNAGln and ATP at 2.8 angstrom resolution. Science (1989) 246, 1135-1142.

5. Ruff, M., Krishnaswamy, S., Boeglin, A., Poterszman, A., Mitschler, A., Podjarny, A., Rees, B., Thierry, J. C., and Moras, D. Class II aminoacyl transfer RNA synthetases: Crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNAAsp. Science (1991) 252, 1682-1689.

Methods for studying RNA structure and function [ back to top ]

1. Brown, J. W., Nolan, J. M., Haas, E. S., Rubio, M. A. T., Major, F., and Pace, N. R. Comparative analysis of ribonuclease P RNA using gene sequences from natural microbial populations reveals tertiary structural elements. Proc. Natl. Acad. Sci. USA (1996) 93, 3001-3006.

2. Felden, B., Himeno, H., Muto, A., McCutcheon, J. P., Atkins, J. F., and Gesteland, R. F. Probing the structure of the Escherichia coli 10Sa RNA (tmRNA). RNA (1997) 3, 89-103.

3. Harris, M. E., Nolan, J. M., Malhotra, A., Brown, J. W., Harvey, S. C., and Pace, N. R. Use of photoaffinity crosslinking and molecular modeling to analyze the global architecture of ribonuclease P RNA. EMBO J. (1994) 13, 3953 -3963.

4. Harris, M. E. and Pace, N. R. Identification of phosphate involved in catalysis by the ribozyme RNase P RNA. RNA (1995) 1, 210-218.

5. Muto, A., Ushida, C., and Himeno, H. A bacterial RNA that functions as both a tRNA and an mRNA. Trends Biochem Sci (1998) 23, 25-29.

6. Pace, N. R., Thomas, B. C., and Woese, C. R. Probing RNA structure, function, and history by comparative analysis. The RNA World, Second Ed. Cold Spring Harbor Laboratory Press (1999)

7. Strobel, S. A. A chemogenetic approach to RNA function / structure analysis. Curr Opin Struct Biol (1999) 9, 346-352.

8. Williams, K. P. and Bartel, D. P. Phylogenetic analysis of tmRNA secondary structure. RNA (1996) vol. 2, 1306-1310.

9. Zuker, M. Computer Prediction of RNA Structure  Methods  Enzymol. (1989) 180, 262-288

The Hammerhead ribozyme [ back to top ]

1. Branch, A. D., Robertson, H. D., and Dickson, E. Longer-than-unit-length viroid minus strands are present in RNA from infected plants. Proc. Natl. Acad. Sci. USA (1981) 78, 6381-6385.

2. Branch, A. D., Robertson, H. D., Greer, C., Gegenheimer, P, Peebles, C., and Abelson, J. Cell-free circularization of viroid progeny RNA by an RNA ligase from wheat germ. Science (1982) 217, 1147-1149.

3. Buzayan, J. M., Gerlach, W. L., and Gruening, G. Satellite tobacco ringspot virus RNA:  A subset of the RNA sequence is sufficient for autolytic processing. Proc. Natl. Acad. Sci. USA (1986) 83, 8859-8862.

4. Dahm, S. C., Derrick, W. B., and Uhlenbeck, O. C. Evidence of the role of solvated metal hydroxide in the hammerhead cleavage mechanism. Biochemistry (1993) 32, 13040-13045.

5. Diener, T. O., Viroids and satellites: molecular parasites at the frontier of life, Ch. 1 in Maramorosch, K., ed., CRC press, Inc., Boca Raton, (1991).

6. Pan, T., Long, D. M., and Uhlenbeck, O. C., Ch. 12 in The RNA World, Gesteland, R. F. and Atkins, J. F., ed., Cold Spring Harbor Laboratory Press (1993)

7. Pely, H. W., Flasherty, K. M., and McKay, D. B. Three-dimentional structure of a hammerhead ribozyme:  Nature (1994) 372,  68-74.

Evolution in vitro [ back to top ]

1. Bartel D. P. and Szostak J. W. Isolation of new ribozymes from a large pool of random sequences. Science (1993) 261, 1411-1418.

2. Beaudry, A. A. and Joyce, G. F. Directed evolution of an RNA enzyme. Science (1992) 257, 635-641.

3. Benner S. A. Catalysis: Design versus selection. Science (1993) 261:1402-1403.

4. Ellington, A. D. and Szostak, J. W. In vitro selection of RNA molecules that bind specific ligands. Nature (1990) 346:818-822.

5. Illangasekare, M., Sanchez, G., Nickles, T., and Yarus, M. Aminoacyl-RNA synthesis catalyzed by an RNA. Science (1995) 267:643-647.

6. Noller, H. F., Hoffarth, V., and Zimniak, L. Unusual resistance of peptidyl transferase to protein extraction procedures. Science (1992) 256:1416-1419.

7. Piccirilli, J. A., McConnell, T. S., Zaug, A. J., Noller, H. F., and Cech, T. R. Aminoacyl esterase activity of the Tetrahymena ribozyme. Science (1992) 256:1420-1424.

8. Wright M. C. and Joyce, G. F. Continuous in vitro evolution of catalytic function. Science (1997) 276:614-617.

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Last updated: 1:27am on 1/20/09 by pgegen@ku.edu