HIV-1 nucleocapsid protein activates transient melting of least stable parts of the secondary structure of TAR and its complementary sequence

Journal of Molecular Biology

Volumn 317, Issue 3, 2002, Pages 385-399

  Bernacchi, Serena ^a   Stoylov, Stoyl ^a   Piémont, Etienne ^a   Ficheux, Damien ^b   Roques, Bernard P ^c   Darlix, Jean Luc ^d   Mély, Yves ^a  

^a UNIVERSITÉ DE STRASBOURG   (France)

^b INSTITUT DE BIOLOGIE ET CHIMIE DES PROTÉINES   (France)

^c Laboratoire de Pharmacochimie   (France)

^d UNIVERSITÉ DE LYON   (France)

Author keywords

Chaperone; Fluorescence; Fraying; NCp7; TAR

Indexed keywords

COMPLEMENTARY DNA; DYE; NUCLEOCAPSID PROTEIN; NUCLEOTIDE; OLIGONUCLEOTIDE; PEPTIDE; PROTEIN NCP7; UNCLASSIFIED DRUG;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; CORRELATION ANALYSIS; DNA BASE COMPOSITION; DNA STRAND BREAKAGE; FLUORESCENCE SPECTROSCOPY; HUMAN IMMUNODEFICIENCY VIRUS 1; MELTING POINT; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; TERMINAL SEQUENCE; THERMOSTABILITY; ULTRAVIOLET SPECTROSCOPY; VIRUS NUCLEOCAPSID; ZINC FINGER MOTIF;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0036298272     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2002.5429     Document Type: Article

References (81)

1. First glimpses at structure-function relationships of the nucleocapsid protein of retroviruses
2. Structure of the retroviral genome
3. Potential metal-binding domains in nucleic acid binding proteins
4. Tightly bound zinc in human immunodeficiency virus type 1, human T-cell leukemia virus type I, and other retroviruses
5. Nucleocapsid zinc-fingers detected in retroviruses: EXAFS studies of intact viruses and the solution-state structure of the nucleocapsid protein from HIV-1
6. Zinc finger motif for single-stranded nucleic acids? Investigations by nuclear magnetic resonance
7. Determination of the structure of the nucleocapsid protein NCp7 from the human immunodeficiency virus type 1 by 1H NMR
8. Spatial proximity of the HIV-1 nucleocapsid protein zinc-fingers investigated by time-resolved fluorescence and fluorescence resonance energy transfer
9. Cis elements and trans-acting factors involved in the RNA dimerization of the human immunodeficiency virus HIV-1
10. Formation of stable and functional HIV-1 nucleoprotein complexes in vitro
11. Mutations of RNA and protein sequences involved in human immunodeficiency virus type 1 packaging result in production of noninfectious virus
12. Specific binding of human immunodeficiency virus type 1 gag polyprotein and nucleocapsid protein to viral RNAs detected by RNA mobility shift assays
13. Analysis of binding elements in the human immunodeficiency virus type 1 genomic RNA and nucleocapsid protein
14. An RNA chaperone activity of nonspecific RNA binding proteins in hammerhead ribozyme catalysis
15. RNA chaperones and the RNA folding problem
16. DNA strand exchange and selective DNA annealing promoted by the human immunodeficiency virus type 1 nucleocapsid protein
17. Nucleic-acid-chaperone activity of retroviral nucleocapsid proteins: Significance for viral replication
18. HIV-1 reverse transcriptase specifically interacts with the anticodon domain of its cognate primer tRNA
19. Trans-activation of the 5′ to 3′ viral DNA strand transfer by nucleocapsid protein during reverse transcription of HIV1 RNA
20. Analysis of the nucleic acid annealing activities of nucleocapsid protein from HIV-1
21. Characterization of human immunodeficiency virus type 1 dimeric RNA from wild-type and protease-defective virions
22. Maturation of dimeric viral RNA of Moloney murine leukemia virus
23. Transactivation of the minus-strand DNA transfer by nucleocapsid protein during reverse transcription of the retroviral genome
24. Human immunodeficiency virus nucleocapsid protein stimulates strand transfer from internal regions of heteropolymeric RNA templates
25. 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
26. Evidence for a unique mechanism of strand transfer from the transactivation response region of HIV-1
27. Interactions between HIV-1 nucleocapsid protein and viral DNA may have important functions in the viral life cycle
28. Recombinant HIV-1 nucleocapsid protein accelerates HIV-1 reverse transcriptase catalyzed DNA strand transfer reactions and modulates RNase H activity
29. Human immunodeficiency virus nucleocapsid protein accelerates strand transfer of the terminally redundant sequences involved in reverse transcription
30. Strict conservation of the retroviral nucleocapsid protein zinc-finger is strongly influenced by its role in viral infection processes: Characterization of HIV-1 particles containing mutant nucleocapsid zinc- coordinating sequences
31. Role of the N-terminal zinc-finger of human immunodeficiency virus type 1 nucleocapsid protein in virus structure and replication
32. The human immunodeficiency virus type 1 Gag polyprotein has nucleic acid chaperone activity: Possible role in dimerization of genomic RNA and placement of tRNA on the primer binding site
33. Influence of human immunodeficiency virus nucleocapsid protein on synthesis and strand transfer by the reverse transcriptase in vitro
34. Functional sites in the 5′ region of human immunodeficiency virus type 1 RNA form defined structural domains
35. Human immunodeficiency virus type 1 nucleocapsid protein can prevent self-priming of minus-strand strong stop DNA by promoting the annealing of short oligonucleotides to hairpin sequences
36. Possible roles of HIV-1 nucleocapsid protein in the specificity of proviral DNA synthesis and in its variability
37. Molecular requirements for human immunodeficiency virus type 1 plus-strand transfer: Analysis in reconstituted and endogenous reverse transcription systems
38. Role of post-transcriptional modifications of primer tRNALys,3 in the fidelity and efficacy of plus strand DNA transfer during HIV-1 reverse transcription
39. Human immunodeficiency virus type 1 nucleocapsid protein reduces reverse transcriptase pausing at a secondary structure near the murine leukemia virus polypurine tract
40. Effect of human immunodeficiency virus type 1 (HIV-1) nucleocapsid protein on HIV-1 reverse transcriptase activity in vitro
41. A mechanism for plus-strand transfer enhancement by the HIV-1 nucleocapsid protein during reverse transcription
42. Mechanism for nucleic acid chaperone activity of HIV-1 nucleocapsid protein revealed by single molecule stretching
43. HIV-1 nucleocapsid protein zinc finger structures induce tRNA(Lys,3) structural changes but are not critical for primer/template annealing
44. Heteronuclear NMR studies of the interaction of tRNA(Lys)3 with HIV-1 nucleocapsid protein
45. A single mode of DNA base-pair opening drives imino proton exchange
46. Kinetics and energetics of base-pair opening in 5′-d(CGCGAATTCGCG)-3′ and a substituted dodecamer containing G·T mismatches
47. Terminal base-pairs of oligodeoxynucleotides: Imino proton exchange and fraying
48. Evidence from base-pair kinetics for two types of adenine tract structures in solution: Their relation to DNA curvature
49. Ordered aggregation of ribonucleic acids by the human immunodeficiency virus type 1 nucleocapsid protein
50. Recombinant human immunodeficiency virus type 1 nucleocapsid (NCp7) protein unwinds tRNA
51. The annealing of tRNA3Lys to human immunodeficiency virus type 1 primer binding site is critically dependent on the NCp7 zinc-fingers structure
52. The effect of mutations in the HIV-1 nucleocapsid protein on strand transfer in cell-free reverse transcription reactions
53. Binding of the HIV-1 nucleocapsid protein to the primer tRNA(3Lys), in vitro, is essentially not specific
54. Sequence-specific binding of human immunodeficiency virus type 1 nucleocapsid protein to short oligonucleotides
55. Nucleic acid sequence discrimination by the HIV-1 nucleocapsid protein NCp7: A fluorescence study
56. Exciton interaction in molecular beacons: A sensitive sensor for short range modifications of the nucleic acid structure
57. Aggregation of polyA-HIV-1 nucleocapsid protein NCp7 complexes and properties of the aggregates
58. Conformational transitions monitored for single molecules in solution
59. Fast interactions between Rh6G and dGTP in water studied by fluorescence correlation spectoscopy
60. Fluorescence characteristics of 5-carboxytetra-methylrhodamine linked covalently to the 5′ end of oligonucleotides: Multiple conformers of single-stranded and double-stranded dye-DNA complexes
61. Intra-tRNA distance measurements for nucleocapsid proteindependent tRNA unwinding during priming of HIV reverse transcription
62. Interaction of retroviral nucleocapsid proteins with transfer RNAPhe: A lead ribozyme and 1H NMR study
63. Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility
64. Ratiometric analysis of single-molecule fluorescence resonance energy transfer using logical combinations of thresold criteria: A study of 12-mer DNA
65. Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules
66. Conformational fluctuations in single DNA molecules
67. Kinetics of conformational fluctuations in DNA hairpin-loops
68. The effect of cross-links on the conformational dynamics of duplex DNA
69. DNA lesions. A thermodynamic perspective
70. Influence of the oxidatively damaged adduct 8-oxodeoxyguanosine on the conformation, energetics, and thermodynamic stability of a DNA duplex
71. Proton exchange and internal motions in two chromomycin dimer-DNA oligomer complexes
72. Zinc finger structures in the human immunodeficiency virus type 1 nucleocapsid protein facilitate efficient minus- and plus-strand transfer
73. First large scale chemical synthesis of the 72 amino acid HIV-1 nucleocapsid protein NCp7 in an active form
74. Negative electrospray ionization mass spectrometry of synthetic and chemically modified oligonucleotides
75. Determination of the absolute quantum yield of fluorescence solutions
76. Absolute luminescence yield of cresyl violet. A standard for the red
77. Analyzing the distribution of decay constants in pulse-fluorimetry using the maximum entropy method
78. Maximum entropy method of data analysis in time-resolved spectroscopy
79. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics