Structure of an RNA/DNA dodecamer corresponding to the HIV-1 polypurine tract at 1.6 Å resolution

Acta Crystallographica Section D: Biological Crystallography

Volumn 68, Issue 2, 2012, Pages 169-175

  Drozdzal, Pawel ^a   Michalska, Karolina ^a   Kierzek, Ryszard ^b   Lomozik, Lechoslaw ^a,c   Jaskolski, Mariusz ^a,b  

^a ADAM MICKIEWICZ UNIVERSITY   (Poland)

^b INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

^c UNIVERSITY OF TECHNOLOGY AND LIFE SCIENCES   (Poland)

Author keywords

HIV 1 polypurine tract; reverse transcription; RNA DNA hybrid

Indexed keywords

PURINE DERIVATIVE; VIRUS DNA; VIRUS RNA;

ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; GENETICS; HUMAN IMMUNODEFICIENCY VIRUS 1; NUCLEOTIDE SEQUENCE; X RAY CRYSTALLOGRAPHY;

BASE PAIRING; BASE SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DNA, VIRAL; HIV-1; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PURINES; RNA, VIRAL;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84856483297     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444911053327     Document Type: Article

References (33)

1. Arnott, S. (1999). Oxford Handbook of Nucleic Acid Structure, edited by S. Neidle, pp. 1-38. Oxford University Press.
2. Brü nger, A. T. 1992). Nature (London), 355, 472-475.
3. Conn, G.L., Brown, T. & Leonard, G. A.1999). Nucleic Acids Res. 27, 555-561.
4. Cross, C. W., Rice, J. S. & Gao, X. (1997). Biochemistry, 36, 4096-4107.
5. DeLano, W.L.2002). PyMOL. http://www.pymol.org. Egli, M.2002). Chem. Biol. 9, 277-286.
6. Egli, M., Portmann, S. & Usman, N. (1996). Biochemistry, 35, 8489-8494.
7. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K.2010). Acta Cryst. D66, 486-501.
8. Fedoroff, O. Y., Salazar, M. & Reid, B.R.1993). J. Mol. Biol. 233, 509-523.
9. Feng, Z., Westbrook, J. & Berman, H. M.1998). Report NDB-407. Rutgers University, New Brunswick, New Jersey, USA.
10. Heinemann, U., Lauble, H., Frank, R. & Blö cker, H.1987). Nucleic Acids Res. 15, 9531-9550.
11. Ilyinskii, P. O. & Desrosiers, R. C. (1998). EMBO J. 17, 3766-3774.
12. Kennard, O. & Hunter,W. N. (1991). Angew. Chem. Int. Ed. Engl. 30, 1254-1277.
13. Kopka, M.L., Lavelle, L., Han, G. W., Ng, H.L. & Dickerson, R. E. (2003). J. Mol. Biol. 334, 653-665.
14. Lavery, R., Moakher, M., Maddocks, J. H., Petkeviciute, D. & Zakrzewska, K.2009). Nucleic Acids Res. 37, 5917-5929.
15. Lu, X.-J. & Olson, W. K.2003). Nucleic Acids Res. 31, 5108-5121.
16. McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. & Read, R. J.2007). J. Appl. Cryst. 40, 658-674.
17. Murshudov, G. N., Skubá k, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. & Vagin, A. A.2011). Acta Cryst. D67, 355-367.
18. Neidle, S. (2008). Principles of Nucleic Acid Structure, p. 33. London: Academic Press.
19. Olson, W. K. et al. (2001). J. Mol. Biol. 313, 229-237.
20. Otwinowski, Z. & Minor, W.1997). Methods Enzymol. 276, 307-326.
21. Painter, J. & Merritt, E. A.2006). J. Appl. Cryst. 39, 109-111.
22. Rattray, A. J. & Champoux, J. J.1989). J. Mol. Biol. 208, 445-456.
23. Sarafianos, S. G., Das, K., Tantillo, C., Clark, A. D., Ding, J., Whitcomb, J. M., Boyer, P.L., Hughes, S. H. & Arnold, E. (2001). EMBO J. 20, 1449-1461.
24. Sarafianos, S. G., Marchand, B., Das, K., Himmel, D. M., Parniak, M. A., Hughes, S. H. & Arnold, E. (2009). J. Mol. Biol. 385, 693-713.
25. Schneider, B., Cohen, D. & Berman, H. M.1992). Biopolymers, 32, 725-750.
26. Schneider, B., Morávek, Z. & Berman, H. M.2004). Nucleic Acids Res. 32, 1666-1677.
27. Shaw, N. N. & Arya, D. P. (2008). Biochimie, 90, 1026-1039.
28. Svozil, D., Kalina, J., Omelka, M. & Schneider, B. (2008). Nucleic Acids Res. 36, 3690-3706.
29. Tonelli, M., Ulyanov, N. B., Billeci, T. M., Karwowski, B., Guga, P., Stec, W. J. & James, T.L.2003). Biophys. J. 85, 2525-2538.
30. Winn, M. D. et al. (2011). Acta Cryst. D67, 235-242.
31. Xia, T., SantaLucia, J., Burkard, M. E., Kierzek, R., Schroeder, S. J., Jiao, X., Cox, C. & Turner, D. H.1998). Biochemistry, 37, 14719-14735.
32. Xiong, Y. & Sundaralingam, M.1998). Structure, 6, 1493-1501.
33. Yi-Brunozzi, H. Y., Brinson, R. G., Brabazon, D. M., Lener, D., Le Grice, S. F. & Marino, J. P. (2008). Chem. Biol. 15, 254-262.