Nucleocapsid annealing-mediated electrophoresis (NAME) assay allows the rapid identification of HIV-1 nucleocapsid inhibitors

Journal of Visualized Experiments

Volumn , Issue 95, 2015, Pages

  Sosic, Alice ^a   Cappellini, Marta ^a   Scalabrin, Matteo ^b   Gatto, Barbara ^a  

^a UNIVERSITY OF PADOVA   (Italy)

^b STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

Annealing; DNA; Gel electrophoresis; HIV 1; Immunology; Issue 95; NAME; NCp7; Nucleocapsid protein; Oligonucleotides; TAR RNA

Indexed keywords

CHAPERONE; GAG PROTEIN; NCP7 PROTEIN, HUMAN IMMUNODEFICIENCY VIRUS 1; NUCLEOCAPSID PROTEIN; VIRUS DNA;

ANTAGONISTS AND INHIBITORS; CHEMISTRY; CONFORMATION; ELECTROPHORESIS; GENETICS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; METABOLISM; PROCEDURES; VIRUS NUCLEOCAPSID;

DNA, VIRAL; ELECTROPHORESIS; GAG GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; HIV-1; HUMANS; MOLECULAR CHAPERONES; NUCLEIC ACID CONFORMATION; NUCLEOCAPSID; NUCLEOCAPSID PROTEINS;

EID: 84921666538     PISSN: 1940087X     EISSN: None     Source Type: Journal    
DOI: 10.3791/52474     Document Type: Article

References (21)

1. Druillennec, S., et al. A mimic of HIV-1 nucleocapsid protein impairs reverse transcription and displays antiviral activity. Proc Natl Acad Sci USA. 96, 4886-4891 (1999).
2. Darlix, J. L., Garrido, J. L., Morellet, N., Mely, Y., de Rocquigny, H. Properties, functions, and drug targeting of the multifunctional nucleocapsid protein of the human immunodeficiency virus. Adv Pharmacol.55, 299-346 (2007).
3. Thomas, J. A., Gorelick, R. J. Nucleocapsid protein function in early infection processes. Virus Res. 134, 39-63 (2008).
4. Mirambeau, G., Lyonnais, S., Gorelick, R. J. Features, processing states, and heterologous protein interactions in the modulation of the retroviral nucleocapsid protein function. RNA Biol. 7, 724-734 (2010).
5. Zeng, Y., et al. Probing nucleation, reverse annealing, and chaperone function along the reaction path of HIV-1 single-strand transfer. Proc Natl Acad Sci USA. 104, 12651-12656 (2007).
6. Basu, V. P., et al. Strand transfer events during HIV-1 reverse transcription. Virus Res. 134, 19-38 (2008).
7. Guo, J., Henderson, L. E., Bess, J., Kane, B., Levin, J. G. Human immunodeficiency virus type 1 nucleocapsid protein promotes efficient strand transfer and specific viral DNA synthesis by inhibiting TAR-dependent self-priming from minus-strand strong-stop DNA. J Virol. 71, 5178-5188 (1997).
8. Godet, J., Mely, Y. Biophysical studies of the nucleic acid chaperone properties of the HIV-1 nucleocapsid protein. RNA Biol. 7, 687-699 (2010).
9. Darlix, J. L., et al. Flexible nature and specific functions of the HIV-1 nucleocapsid protein. J Mol Biol. 410, 565-581 (2011).
10. Lapadat-Tapolsky, M., Pernelle, C., Borie, C., Darlix, J. L. Analysis of the nucleic acid annealing activities of nucleocapsid protein from HIV-1. Nucleic Acids Res. 23, 2434-2441 (1995).
11. Vo, M. -N., Barany, G., Rouzina, I., Musier-Forsyth, K. Mechanistic studies of mini-TAR RNA/DNA annealing in the absence and presence of HIV-1 nucleocapsid protein. J Mol Biol. 363, 244-261 (2006).
12. Beltz, H., et al. Structural determinants of HIV-1 nucleocapsid protein for cTAR DNA binding and destabilization, and correlation with inhibition of self-primed DNA synthesis. J Mol Biol. 348, 1113-1126 (2005).
13. Mori, M., et al. Nucleocapsid Protein: a Desirable Target for Future Therapies against HIV-1. Curr Top Microbiol Immunol. Forthcoming Forthcoming.
14. Sosic, A., et al. Design, synthesis and biological evaluation of TAR and cTAR binders as HIV-1 nucleocapsid inhibitors. MedChemComm. 4, 1388-1393 (2013).
15. Tabarrini, O., et al. Studies of Anti-HIV Transcription Inhibitor Quinolones: Identification of Potent N1-Vinyl Derivatives. Chemmedchem. 5, 1880-1892 (2010).
16. Hagan, N., Fabris, D. Direct mass spectrometric determination of the stoichiometry and binding affinity of the complexes between nucleocapsid protein and RNA stem-loop hairpins of the HIV-1 Psi-recognition element. Biochemistry. 42, 10736-10745 (2003).
17. Ivanyi-Nagy, R., Davidovic, L., Khandjian, E. W., Darlix, J. L. Disordered RNA chaperone proteins: from functions to disease. Cell Mol Life Sciences: CMLS. 62, 1409-1417 (2005).
18. Zagotto, G., et al. Tuning G-quadruplex vs double-stranded DNA recognition in regioisomeric lysyl-peptidyl-anthraquinone conjugates. Bioconjug Chem. 22, 2126-2135 (2011).
19. Carlson, C. B., Vuyisich, M., Gooch, B. D., Beal, P. A. Preferred RNA binding sites for a threading intercalator revealed by in vitro evolution. Chem Biol. 10, 663-672 (2003).
20. Gooch, B. D., Beal, P. A. Recognition of duplex RNA by helix-threading peptides. J Am Chem Soc. 126, 10603-10610 (2004).
21. Kanevsky, I., et al. Structural determinants of TAR RNA-DNA annealing in the absence and presence of HIV-1 nucleocapsid protein. Nucleic Acids Res. 39, 8148-8162 (2011).