DNA topoisomerases

1. Lima, C.D., Wang, J.C. and Mondragón, A. Three-dimensional structure of the 67K N-terminal fragment of  E. coli DNA topoisomerase I.  Nature, 367, 138-146, 1994.
2. Sharma, A., Hanai, R. and Mondragón, A. Crystal Structure of the Amino Terminal Fragment of Vaccinia Virus DNA Topoisomerase I at 1.6 Å Resolution.  Structure, 2,767-777, 1994.
3. Lue, N., Sharma, A., Mondragón, A. and Wang, J.C. A 26 kDa yeast DNA topoisomerase I fragment: crystallographic structure and mechanistic implications.  Structure, 3, 1315-1322, 1995.
4. Mondragón, A. and DiGate, R. Structure of E. coli DNA topoisomerase III, Structure, 7,1373-1383,1999.
5. Feinberg, H., Lima, C.D. and Mondragón, A. Conformational changes in E. coli DNA topoisomerase I. Nature Struct. Biol., 6, 918-922, 1999.
6. Feinberg, H., Changela, A. and Mondragón, A. Protein-nucleotide interactions in E. coli DNA topoisomerase I. Nature Struct. Biol., 6, 961-968, 1999.
7. Li, Z., Mondragón, A., Hiasa, H., Marians, K.J., and DiGate, R.J. Identification of a unique domain essential for Escherichia coli DNA topoisomerase III-catalysed decatenation of replication intermediates. Mol. Microbiol., 35, 888-895, 2000.
8. Li, Z., Mondragón,A, and DiGate, R. The mechanism of type IA topoisomerase-mediated DNA topological transformations. Molecular Cell, 7, 301-307, 2001.
9. Changela, A., DiGate, R. and Mondragón, A. Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule. Nature, 411, 1077-1081, 2001.
10. Perry, K. and Mondragón, A. Biochemical Characterization of an Invariant Histidine Involved in Escherichia coli DNA Topoisomerase I Catalysis. J. Biol. Chem., 277, 13237-13245, 2002.
11. Perry K. and Mondragón A. Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA. Structure, 11, 1349-1358, 2003.
12. Patel, A. Shuman, S., and Mondragón, A. Crystal structure of bacterial type Ib DNA topoisomerase reveals a preassembled active site in the asbence of DNA. J. Biol. Chem. 281, 6030-6037, 2006.
13. Taneja, B., Patel, A., Slesarev, A., and Mondragón, A. Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases. EMBO J., 25, 398-408, 2006.
14. Changela, A., DiGate, R.J., and Mondragón, A, Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal A Novel Type IA Topoisomerase-DNA Conformational Intermediate, J. Mol. Biol., 2007, in press.

Catalytic RNA molecules

1.  Krasilnikov AS, Yang X, Pan T, Mondragón A. 2003. Crystal structure of the specificity domain of ribonuclease P., Nature, 421. 760-764, 2003.
2. Krasilnikov, A.S. and Mondragón, A. On the occurrence of the T-loop RNA folding motif in large RNA molecules. RNA, 9, 640-643, 2003.
3. Krasilnikov, A.S., Xiao,Y., Pan,T. and Mondragón,A. Basis for Stuctural Diversity in Homologous RNAs, Science, 306, 104-107, 2004.
4. Torres-Larios A., Swinger K. K., Krasilnikov A. S., Pan T., Mondragón A. Crystal structure of the RNA component of bacterial ribonuclease P. Nature. 437, 584-587, 2005.
5. Torres-Larios A., Swinger K. K., Pan T., Mondragón A. Structure of ribonuclease P - a universal ribozyme. Curr. Opin. Struct. Biol. 16, 327-335, 2006.
6. Baird N.J., Srividya N., Krasilnikov A.S., Mondragon A., Sosnick T.R., Pan T., Structural basis for altering the stability of homologous RNAs from a mesophilic and a thermophilic bacterium. RNA, 12, 598-606, 2006
   

Spectrin

1. Grum, V.L., Li, D., MacDonald,R.I. and Mondragón, A. Structures of two repeats of spectrin suggest models of flexibility. Cell, 98, 523-535, 1999.
2. Kusunoki, H., MacDonald, R.I., and Mondragón, A. Structural Insights into the Stability and Flexibility of Unusual Erythroid Spectrin Repeats. Structure, 12, 645-656, 2004.
3. Kusunoki, H., Minasov, G., MacDonald, R.I., and Mondragón, A. Independent Movement, Dimerization and Stability of Tandem Repeats of Chicken Brain a-Spectrin, J. Mol. Biol., 344, 495-511, 2004.