Formation of noncanonical DNA structures mediated by human ORC4, a protein component of the origin recognition complex

Biochemistry

Volumn 47, Issue 33, 2008, Pages 8760-8767

  Stefanovic, Dragana ^a   Kusic, Jelena ^a   Divac, Aleksandra ^a   Tomic, Branko ^a  

^a INSTITUTE OF MOLECULAR GENETICS AND GENETIC ENGINEERING   (Serbia)

Author keywords

[No Author keywords available]

Indexed keywords

CHLORINE COMPOUNDS; COMPLEXATION; DNA; GENES; HYDROGEN; HYDROGEN BONDS; NONMETALS; NUCLEIC ACIDS; OLIGONUCLEOTIDES; ORGANIC ACIDS;

BASE PAIRINGS; CHEMICAL AGENTS; DNA REPLICATIONS; DNA STRUCTURES; DNA-BINDING; ENVIRONMENTAL CONDITIONING; GENOMIC SEQUENCING; NOVEL STRUCTURES; ORIGIN RECOGNITION COMPLEX; STRUCTURAL MOTIFS; STRUCTURAL REARRANGEMENTS; THERMAL STABILITY; TRIPLEXES;

DNA SEQUENCES;

7 DEAZA DEOXY ADENOSINE MONOPHOSPHATE; ADENINE DERIVATIVE; ADENOSINE PHOSPHATE; ADENOSINE TRIPHOSPHATE; MAGNESIUM; ORC4 PROTEIN; PROTEIN; SINGLE STRANDED DNA;

ARTICLE; CHEMICAL REACTION; DNA BINDING; DNA REPLICATION; DNA STRUCTURE; HYDROGEN BOND; PRIORITY JOURNAL; PROTEIN CONFORMATION;

CELL CYCLE PROTEINS; DNA; DNA REPLICATION; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; HUMANS; HYDROGEN BONDING; MUTATION; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; ORIGIN RECOGNITION COMPLEX; TRANSCRIPTION INITIATION SITE;

EID: 49749152737     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi800684f     Document Type: Article

References (28)

1. Erzberger, J. P., Mott, M. L., and Berger, J. M. (2006) Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling. Nat. Struct. Mol. Biol. 13, 676-683.
2. Clarey, M. G., Erzberger, J. P., Grob, P., Leschziner, A. E., Berger, J. M., Nogales, E., and Botchan, M. (2006) Nucleotide-dependent conformational changes in the DnaA-like core of the origin recognition complex. Nat. Struct. Mol. Biol. 13, 684-690.
3. Cunningham-Dueber, E. L., Corn, J. E., Bell, S. D., and Berger, J. M. (2007) Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex. Science 317, 1210-1213.
4. Gaudier, M., Schuwirth, B. S., Westcott, S. L., and Wigley, D. B. (2007) Structural basis of DNA replication origin recognition by an ORC protein. Science 317, 1213-1216.
5. Ogura, T., and Wilkinson, A. J. (2001) AAA+ superfamily ATPases: Common structure-diverse function. Genes Cells 6, 575-597.
6. Giordano-Coltart, J., Ying, C. Y., Gautier, J., and Hurwitz, J. (2005) Studies of the properties of human origin recognition complex and its Walker A motif mutants. Proc. Natl. Acad. Sci. U.S.A. 102, 69-74.
7. Ranjan, A., and Gossen, M. (2006) A structural role for ATP in the formation and stability of the human origin recognition complex. Proc. Natl. Acad. Sci. U.S.A. 103, 4864-4869.
8. Siddiqui, K., and Stillman, B. (2007) ATP dependent assembly of the human origin recognition complex. J. Biol. Chem. 282, 32370-32383.
9. Stefanovic, D., Stanojcic, S., Vindigni, A., Ochem, A., and Falaschi, A. (2003) In vitro protein-DNA interactions at the human lamin B2 replication origin. J. Biol. Chem. 278, 42737-42743.
10. Gaillard, C., Shlyakhtenko, L. S., Lyubchenko, Y. L., and Strauss, F. (2002) Structural analysis of hemicatenated DNA loops. BMC Struct. Biol. 2, 7-19.
11. Lyubchenko, Y. L., Shlyakhtenko, L. S., Binus, M., Gaillard, C., and Strauss, F. (2002) Visualization of hemiknot DNA structure with an atomic force microscope. Nucleic Acids Res. 30, 4902-4909.
12. Johnston, B. H., and Rich, A. (1985) Chemical probes of DNA conformation: Detection of Z-DNA at nucleotide resolution. Cell 42, 713-724.
13. n triplex. Nucleic Acids Res. 19, 7145-7154.
14. Altman, L., and Fanning, E. (2001) The Chinese hamster dihydrofolate reductase replication origin β is active at multiple ectopic chromosomal locations and requires specific DNA sequence elements for activity. Mol. Cell. Biol. 21, 1098-1110.
15. Paixao, S., Colaluca, I. N., Cubells, M., Peverali, F. A., Destro, A., Giadrossi, S., Giacca, M., Falaschi, A., Riva, S., and Biamonti, G. (2004) Modular structure of the human lamin B2 replicator. Mol. Cell. Biol. 24, 2958-2967.
16. Altman, L., and Fanning, E. (2004) Defined sequence modules and an architectural element cooperate to promote initiation at an ectopic mammalian chromosomal replication origin. Mol. Cell. Biol. 24, 4138-4150.
17. Aladjem, M. I., and Fanning, E. (2004) The replicon revisited: An old model learns new tricks in metazoan chromosomes. EMBO Rep. 5, 686-691.
18. Kusic, J., Kojic, S., Divac, A., and Stefanovic, D. (2005) Noncanonical DNA elements in the lamin B2 origin of DNA replication. J. Biol. Chem. 280, 9848-9854.
19. Kiyama, R., and Camerini-Otero, R. D. (1991) A triplex DNA-binding protein from human cells: Purification and characterization. Proc. Natl. Acad. Sci. U.S.A. 88, 10450-10454.
20. Burge, S., Parkinson, G. N., Hazel, P., Todd, A. K., and Neidle, S. (2006) Quadruplex DNA: Sequence, topology and structure. Nucleic Acids Res. 34, 5402-5415.
21. Remus, D., Beall, E. L., and Botchan, M. R. (2004) DNA topology, not DNA sequence, is a critical determinant for Drosophila ORC-DNA binding. EMBO J. 23, 897-907.
22. Abdurashidova, G., Radulescu, S., Sandoval, O., Zahariev, S., Danailov, M. B., Demidovich, A., Santamaria, L., Biamonti, G., Riva, S., and Falaschi, A. (2007) Functional interactions of DNA topoisomerases with a human replication origin. EMBO J. 26, 998-1009.
23. Speck, C., and Stillman, B. (2007) Cdc6 ATPase activity regulates ORC x Cdc6 stability and the selection of specific DNA sequences as origins of DNA replication. J. Biol. Chem. 282, 11705-11714.
24. You, Z., Ishimi, Y., Mizuno, T., Sugasawa, K., Hanaoka, F., and Masai, H. (2003) Thymine-rich single-stranded DNA activates Mcm4/6/7 helicase on Y-fork and bubble-like substrates. EMBO J. 22, 6148-6160.
25. Kitamura, E., Blow, J. J., and Tanaka, T. U. (2006) Live-cell imaging reveals replication of individual replicons in eukaryotic replication factories. Cell 125, 1297-1308.
26. Alberts, B. M., Barry, J., Bedinger, P., Formosa, T., Jongeneel, C. V., and Kreuzer, K. N. (1983) Studies on DNA replication in the bacteriophage T4 in vitro system. Cold Spring Harbor Symp. Quant. Biol. 47, 655-668.
27. Falaschi, A. (2000) Eukaryotic DNA replication: A model for a fixed double replisome. Trends Genet. 16, 88-92.
28. Shimada, K., and Gasser, S. M. (2007) The origin recognition complex functions in sister-chromatid cohesion in Saccharomyces cerevisiae. Cell 128, 85-99.