HIV RNA dimerisation interference by antisense oligonucleotides targeted to the 5' UTR structural elements

Virus Research

Volumn 169, Issue 1, 2012, Pages 63-71

  Reyes Darias, José A ^a   Sánchez Luque, Francisco J ^a   Berzal Herranz, Alfredo ^a  

^a INSTITUTO DE PARASITOLOGÍA Y BIOMEDICINA LÓPEZ NEYRA   (Spain)

Author keywords

Anti HIV targets; Antiviral antisense ODNs; Genomic RNA structural domains; HIV 1; RNA dimerisation

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; VIRUS RNA;

5' UNTRANSLATED REGION; ARTICLE; DIMERIZATION; GENE EXPRESSION; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; POLYADENYLATION; PRIORITY JOURNAL; VIRUS REPLICATION;

5' UNTRANSLATED REGIONS; ANTIVIRAL AGENTS; BASE SEQUENCE; CELL LINE; DIMERIZATION; HIV-1; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES, ANTISENSE; RNA, VIRAL; VIRUS REPLICATION;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84867191740     PISSN: 01681702     EISSN: 18727492     Source Type: Journal    
DOI: 10.1016/j.virusres.2012.07.004     Document Type: Article

References (46)

1. Abbink T.E., Berkhout B. A novel long distance base-pairing interaction in human immunodeficiency virus type 1 RNA occludes the Gag start codon. Journal of Biological Chemistry 2003, 278(13):11601-11611.
2. Adachi A., Gendelman H.E., Koenig S., Folks T., Willey R., Rabson A., Martin M.A. Production of acquired immunodeficiency syndrome-associated retrovirus in human and nonhuman cells transfected with an infectious molecular clone. Journal of Virology 1986, 59(2):284-291.
3. Amarasinghe G.K., De Guzman R.N., Turner R.B., Chancellor K.J., Wu Z.R., Summers M.F. NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of the psi-RNA packaging signal. Implications for genome recognition. Journal of Molecular Biology 2000, 301(2):491-511.
4. Amarasinghe G.K., Zhou J., Miskimon M., Chancellor K.J., McDonald J.A., Matthews A.G., Miller R.R., Rouse M.D., Summers M.F. Stem-loop SL4 of the HIV-1 psi RNA packaging signal exhibits weak affinity for the nucleocapsid protein. Structural studies and implications for genome recognition. Journal of Molecular Biology 2001, 314(5):961-970.
5. Andersen E.S., Contera S.A., Knudsen B., Damgaard C.K., Besenbacher F., Kjems J. Role of the trans-activation response element in dimerization of HIV-1 RNA. Journal of Biological Chemistry 2004, 279(21):22243-22249.
6. Barroso-delJesus A., Tabler M., Berzal-Herranz A. Comparative kinetic analysis of structural variants of the hairpin ribozyme reveals further potential to optimize its catalytic performance. Antisense and Nucleic Acid Drug Development 1999, 9(5):433-440.
7. Bender W., Davidson N. Mapping of poly(A) sequences in the electron microscope reveals unusual structure of type C oncornavirus RNA molecules. Cell 1976, 7(4):595-607.
8. Berkhout B. Structure and function of the human immunodeficiency virus leader RNA. Progress in Nucleic Acid Research and Molecular Biology 1996, 54:1-34.
9. Berkhout B., Ooms M., Beerens N., Huthoff H., Southern E., Verhoef K. In vitro evidence that the untranslated leader of the HIV-1 genome is an RNA checkpoint that regulates multiple functions through conformational changes. Journal of Biological Chemistry 2002, 277(22):19967-19975.
10. Clever J.L., Parslow T.G. Mutant human immunodeficiency virus type 1 genomes with defects in RNA dimerization or encapsidation. Journal of Virology 1997, 71(5):3407-3414.
11. Clever J.L., Wong M.L., Parslow T.G. Requirements for kissing-loop-mediated dimerization of human immunodeficiency virus RNA. Journal of Virology 1996, 70(9):5902-5908.
12. Damgaard C.K., Andersen E.S., Knudsen B., Gorodkin J., Kjems J. RNA interactions in the 5' region of the HIV-1 genome. Journal of Molecular Biology 2004, 336(2):369-379.
13. Darlix J.L., Gabus C., Nugeyre M.T., Clavel F., Barre-Sinoussi F. Cis elements and trans-acting factors involved in the RNA dimerization of the human immunodeficiency virus HIV-1. Journal of Molecular Biology 1990, 216(3):689-699.
14. Fu W., Rein A. Maturation of dimeric viral RNA of Moloney murine leukemia virus. Journal of Virology 1993, 67(9):5443-5449.
15. Gotte M., Li X., Wainberg M.A. HIV-1 reverse transcription: a brief overview focused on structure-function relationships among molecules involved in initiation of the reaction. Archives of Biochemistry and Biophysics 1999, 365(2):199-210.
16. Greatorex J., Gallego J., Varani G., Lever A. Structure and stability of wild-type and mutant RNA internal loops from the SL-1 domain of the HIV-1 packaging signal. Journal of Molecular Biology 2002, 322(3):543-557.
17. Haddrick M., Lear A.L., Cann A.J., Heaphy S. Evidence that a kissing loop structure facilitates genomic RNA dimerisation in HIV-1. Journal of Molecular Biology 1996, 259(1):58-68.
18. Ho S.P., Bao Y., Lesher T., Malhotra R., Ma L.Y., Fluharty S.J., Sakai R.R. Mapping of RNA accessible sites for antisense experiments with oligonucleotide libraries. Nature Biotechnology 1998, 16(1):59-63.
19. Ho S.P., Britton D.H., Stone B.A., Behrens D.L., Leffet L.M., Hobbs F.W., Miller J.A., Trainor G.L. Potent antisense oligonucleotides to the human multidrug resistance-1 mRNA are rationally selected by mapping RNA-accessible sites with oligonucleotide libraries. Nucleic Acids Research 1996, 24(10):1901-1907.
20. Hoglund S., Ohagen A., Goncalves J., Panganiban A.T., Gabuzda D. Ultrastructure of HIV-1 genomic RNA. Virology 1997, 233(2):271-279.
21. Huthoff H., Berkhout B. Two alternating structures of the HIV-1 leader RNA. RNA 2001, 7(1):143-157.
22. Kasprzak W., Bindewald E., Shapiro B.A. Structural polymorphism of the HIV-1 leader region explored by computational methods. Nucleic Acids Research 2005, 33(22):7151-7163.
23. Laptev A.V., Lu Z., Colige A., Prockop D.J. Specific inhibition of expression of a human collagen gene (COL1A1) with modified antisense oligonucleotides. The most effective target sites are clustered in double-stranded regions of the predicted secondary structure for the mRNA. Biochemistry 1994, 33(36):11033-11039.
24. Laughrea M., Jette L. A 19-nucleotide sequence upstream of the 5' major splice donor is part of the dimerization domain of human immunodeficiency virus 1 genomic RNA. Biochemistry 1994, 33(45):13464-13474.
25. Laughrea M., Jette L. HIV-1 genome dimerization: formation kinetics and thermal stability of dimeric HIV-1Lai RNAs are not improved by the 1-232 and 296-790 regions flanking the kissing-loop domain. Biochemistry 1996, 35(29):9366-9374.
26. Laughrea M., Jette L. Kissing-loop model of HIV-1 genome dimerization: HIV-1 RNAs can assume alternative dimeric forms, and all sequences upstream or downstream of hairpin 248-271 are dispensable for dimer formation. Biochemistry 1996, 35(5):1589-1598.
27. Laughrea M., Jette L., Mak J., Kleiman L., Liang C., Wainberg M.A. Mutations in the kissing-loop hairpin of human immunodeficiency virus type 1 reduce viral infectivity as well as genomic RNA packaging and dimerization. Journal of Virology 1997, 71(5):3397-3406.
28. Livak K.J., Schmittgen T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001, 25(4):402-408.
29. Marquet R., Paillart J.C., Skripkin E., Ehresmann C., Ehresmann B. Dimerization of human immunodeficiency virus type 1 RNA involves sequences located upstream of the splice donor site. Nucleic Acids Research 1994, 22(2):145-151.
30. Matveeva O., Felden B., Audlin S., Gesteland R.F., Atkins J.F. A rapid in vitro method for obtaining RNA accessibility patterns for complementary DNA probes: correlation with an intracellular pattern and known RNA structures. Nucleic Acids Research 1997, 25(24):5010-5016.
31. Muriaux D., Fosse P., Paoletti J. A kissing complex together with a stable dimer is involved in the HIV-1Lai RNA dimerization process in vitro. Biochemistry 1996, 35(15):5075-5082.
32. Muriaux D., Girard P.M., Bonnet-Mathoniere B., Paoletti J. Dimerization of HIV-1Lai RNA at low ionic strength. An autocomplementary sequence in the 5' leader region is evidenced by an antisense oligonucleotide. Journal of Biological Chemistry 1995, 270(14):8209-8216.
33. Ooms M., Verhoef K., Southern E., Huthoff H., Berkhout B. Probing alternative foldings of the HIV-1 leader RNA by antisense oligonucleotide scanning arrays. Nucleic Acids Research 2004, 32(2):819-827.
34. Paillart J.C., Marquet R., Skripkin E., Ehresmann B., Ehresmann C. Mutational analysis of the bipartite dimer linkage structure of human immunodeficiency virus type 1 genomic RNA. Journal of Biological Chemistry 1994, 269(44):27486-27493.
35. Paillart J.C., Shehu-Xhilaga M., Marquet R., Mak J. Dimerization of retroviral RNA genomes: an inseparable pair. Nature Reviews Microbiology 2004, 2(6):461-472.
36. Paillart J.C., Skripkin E., Ehresmann B., Ehresmann C., Marquet R. A loop-loop kissing complex is the essential part of the dimer linkage of genomic HIV-1 RNA. Proceedings of the National Academy of Sciences of the United States of America 1996, 93(11):5572-5577.
37. Sakuragi J., Sakuragi S., Shioda T. Minimal region sufficient for genome dimerization in the human immunodeficiency virus type 1 virion and its potential roles in the early stages of viral replication. Journal of Virology 2007, 81(15):7985-7992.
38. Sakuragi J.I., Ode H., Sakuragi S., Shioda T., Sato H. A proposal for a new HIV-1 DLS structural model. Nucleic Acids Research 2012, 40(11):5012-5022.
39. Sakuragi J.I., Panganiban A.T. Human immunodeficiency virus type 1 RNA outside the primary encapsidation and dimer linkage region affects RNA dimer stability in vivo. Journal of Virology 1997, 71(4):3250-3254.
40. Sánchez-Luque F.J., Reyes-Darias J.A., Puerta-Fernández E., Berzal-Herranz A. Inhibition of HIV-1 replication and dimerization interference by dual inhibitory RNAs. Molecules 2010, 15(7):4757-4772.
41. Shen N., Jette L., Liang C., Wainberg M.A., Laughrea M. Impact of human immunodeficiency virus type 1 RNA dimerization on viral infectivity and of stem-loop B on RNA dimerization and reverse transcription and dissociation of dimerization from packaging. Journal of Virology 2000, 74(12):5729-5735.
42. Shen N., Jette L., Wainberg M.A., Laughrea M. Role of stem B, loop B, and nucleotides next to the primer binding site and the kissing-loop domain in human immunodeficiency virus type 1 replication and genomic-RNA dimerization. Journal of Virology 2001, 75(21):10543-10549.
43. Skripkin E., Paillart J.C., Marquet R., Ehresmann B., Ehresmann C. Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro. Proceedings of the National Academy of Sciences of the United States of America 1994, 91(11):4945-4949.
44. Southern E.M., Milner N., Mir K.U. Discovering antisense reagents by hybridization of RNA to oligonucleotide arrays. Ciba Foundation Symposia 1997, 209:38-44. discussion 44-6.
45. Takahashi K., Baba S., Hayashi Y., Koyanagi Y., Yamamoto N., Takaku H., Kawai G. NMR analysis of intra- and inter-molecular stems in the dimerization initiation site of the HIV-1 genome. Journal of Biochemistry 2000, 127(4):681-686.
46. Vrolijk M.M., Ooms M., Harwig A., Das A.T., Berkhout B. Destabilization of the TAR hairpin affects the structure and function of the HIV-1 leader RNA. Nucleic Acids Research 2008, 36(13):4352-4363.