Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription

RNA

Volumn 7, Issue 8, 2001, Pages 1097-1114

  Berkhout, Ben ^a   Vastenhouw, Nadine L ^a   Klasens, Bianca I F ^a   Huthoff, Hendrik ^a  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

DNA structure; HIV 1 retrovirus; Reverse transcription; RNA DNA duplex formation; Strand transfer

Indexed keywords

ARTICLE; BASE PAIRING; DNA STRUCTURE; DNA SYNTHESIS; DNA TEMPLATE; ENZYME DEGRADATION; ENZYME RELEASE; GENETIC COMPLEMENTATION; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR INTERACTION; NONHUMAN; NUCLEIC ACID HYBRIDIZATION; PRIORITY JOURNAL; REVERSE TRANSCRIPTION; TANDEM REPEAT; VIRUS GENOME;

BASE SEQUENCE; DNA; DNA, COMPLEMENTARY; DNA, SINGLE-STRANDED; DOSE-RESPONSE RELATIONSHIP, DRUG; GENE DELETION; HIV-1; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; POLY A; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RIBONUCLEASE H, CALF THYMUS; RNA; RNA-DIRECTED DNA POLYMERASE; TEMPERATURE; TRANSCRIPTION, GENETIC;

EID: 0034903425     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838201002035     Document Type: Article

References (83)

1. Transactivation of the minus-strand DNA transfer by nucleocapsid protein during reverse transcription of the retroviral genome
2. Cis elements and trans-acting factors required for minus-strand DNA transfer during reverse transcription of the genomic RNA of murine leukemia virus
3. Secondary structure model for the last two domains of single-stranded RNA phage Qβ
4. The native structure of the HIV-1 RNA genome is required for the first strand-transfer of reverse transcription
5. Trans activation of human immunodeficiency virus type 1 is sequence specific for both the single-stranded bulge and loop of the trans-acting-responsive hairpin: A quantitative analysis
6. Forced evolution of a regulatory RNA helix in the HIV-1 genome
7. The leader of the HIV-1 RNA genome forms a compactly folded tertiary structure
8. Requirements for DNA strand transfer during reverse transcription in mutant HIV-1 virions
9. Effects on DNA synthesis and translocation caused by mutations in the RNase H domain of Moloney murine leukemia virus reverse transcriptase
10. DNA aptamers selected against the HIV-1 TAR RNA element form RNA/DNA kissing complexes
11. Effect of RNA secondary structure on polyadenylation site selection
12. In vitro evidence for the interaction of tRNALys3 with U3 during the first strand transfer of HIV-1 reverse transcription
13. Mutations in HIV reverse transcriptase which alter RNase H activity and decrease strand transfer efficiency are suppressed by HIV nucleocapsid protein
14. Binding of RNA template to a complex of HIV-1 reverse transcriptase/primer/template
15. Roles of ribonuclease H in reverse transcription
16. The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement
17. Characterization of the Jembrana disease virus tat gene and the cis- and trans-regulatory elements in its long terminal repeat
18. Utilization of nonviral sequences for minus-strand DNA transfer and gene reconstitution during retroviral replication
19. Genetic dissociation of the encapsidation and reverse transcription functions in the 5′R region of human immunodeficiency virus type 1
20. Unwinding-like activity associated with avian retrovirus RNA-directed DNA polymerase
21. The secondary structure of the R region of a murine leukemia virus is important for stimulation of long terminal repeat driven gene expression
22. Effects of homology length in the repeat region on minus-strand DNA transfer and retroviral replication
23. Cis elements and trans-acting factors involved in the RNA dimerization of the human immunodeficiency virus HIV-1
24. First glimpses at structure-function relationships of the nucleocapsid protein of retroviruses
25. Trans-activation of the 5′ to 3′ viral DNA strand transfer by nucleocapsid protein during reverse transcription of HIV-1 RNA
26. The 5′ and 3′ TAR elements of the human immunodeficiency virus exert effects at several points in the virus life cycle
27. A conserved hairpin motif in the R-U5 region of the human immunodeficiency virus type 1 RNA genome is essential for replication
28. Kinetic analysis of strand transfer from internal regions of heteropolymeric RNA templates by human immunodeficiency virus reverse transcriptase
29. Polymerization and RNase H activities of the reverse transcriptases of avian myeloblastosis, human immunodeficiency, and Moloney murine leukemia viruses are functionally uncoupled
30. In vitro selection identifies key determinants for loop-loop interactions: RNA aptamers selective for the TAR RNA element of HIV-1
31. Characterization of intracellular reverse transcription complexes of Moloney murine leukemia virus
32. When retroviral reverse transcriptase reach the end of their RNA templates
33. Inhibitors of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase
34. Similarities and differences in the RNase H activities of human immunodeficiency virus type 1 reverse transcriptase and Moloney murine leukemia virus reverse transcriptase
35. A detailed model of reverse transcription and tests of crucial aspects
36. Dimer initiation sequence of HIV-1 LAI genomic RNA: NMR solution structure of the extended duplex
37. Human immunodeficiency virus type 1 reverse transcriptase: Spatial and temporal relationship between the polymerase and RNase H activities
38. Human immunodeficiency virus type 1 nucleocapsid protein proMoles efficient strand transfer and specific viral DNA synthesis by inhibiting TAR-dependent self-priming from minus-strand strong-stop DNA
39. Actinomycin D inhibits human immunodeficiency virus type 1 minus-strand transfer in in vitro and endogenous reverse transcription assays
40. The human immunodeficiency virus type 1 TAR RNA upper stem-loop plays distinct roles in reverse transcription and RNA packaging
41. A critical role for the TAR element in promoting efficient human immunodeficiency virus type 1 reverse transcription
42. RNA chaperones and the RNA folding problem
43. Retroviral recombination and reverse transcription
44. Two alternating structures for the HIV-1 leader RNA
45. The mechanism of Actinomycin D-mediated inhibition of HIV-1 reverse transcription
46. One retroviral RNA is sufficient for synthesis of viral DNA
47. Evidence for a unique mechanism of strand transfer from the transactivation region of HIV-1
48. Premature strand transfer by the HIV-1 reverse transcriptase during strong-stop DNA synthesis
49. Evolution of a disrupted TAR RNA hairpin structure in the HIV-1 virus
50. Determination of the site of first strand transfer during Moloney murine leukemia virus reverse transcription and identification of strand transfer-associated reverse transcriptase errors
51. Analysis of the nucleic acid annealing activities of nucleocapsid protein from HIV-1
52. Reverse transcription of retroviral genomes: Mutations in the terminal repeat sequences
53. Template switching by reverse transcriptase during DNA synthesis
54. Novel endogenous type C retroviruses in baboons: Complete sequence, providing evidence for baboon endogenous virus gag-pol ancestry
55. Genotype, serum level of hepatitis C virus RNA and liver histology as predictors of response to interferon-alpha therapy in patients with chronic hepatitis C
56. Dissecting RNA recombination in vitro: Role of RNA sequences and the viral replicase
57. Surface plasmon resonance kinetic studies of the HIV TAR RNA kissing hairpin complex and its stabilization by 2-thiouridine modification
58. Recombination during reverse transcription: An evaluation of the role of the nucleocapsid protein
59. Copy-choice recombination by reverse transcriptases: Reshuffling of genetic markers mediated by RNA chaperones
60. Sequences in the 5′ and 3′R elements of human immunodeficiency virus type 1 critical for efficient reverse transcription
61. 5-Azacytidine and RNA secondary structure increase the retrovirus mutation rate
62. Recombinant HIV-1 nucleocapsid protein accelerates HIV-1 reverse transcriptase catalyzed DNA strand transfer reactions and modulates RNase H activity
63. Mechanism of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase
64. Utilization of nonviral sequences for minus-strand DNA transfer and gene reconstitution during retroviral replication
65. Nucleic-acid-chaperone activity of retroviral nucleocapsid proteins: Significance for viral replication
66. Influence of human immunodeficiency virus nucleocapsid protein on synthesis and strand transfer by the reverse transcriptase in vitro
67. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
68. Thermodynamics and NMR of internal GT mismatches in DNA
69. Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro
70. Abortive reverse transcription by mutants of Moloney murine leukemia virus deficient in the reverse transcriptase-associated RNase H function
71. Strong-stop strand transfer during reverse transcription
72. Reverse transcriptase and the generation of retroviral DNA
73. Evolution of functional structures of RNA
74. Cis-acting elements required for strong stop acceptor template selection during Moloney murine leukemia virus reverse transcription
75. R region sequences in the long terminal repeat of a murine retrovirus specifically increase expression of unspliced RNAs
76. DNA strand exchange and selective DNA annealing promoted by the human immunodeficiency virus type 1 nucleocapsid protein
77. Single-stranded bacteriophages
78. The first strand transfer during HIV-1 reverse transcription can occur either intramolecularly or intermolecularly
79. Strand transfer mediated by human immunodeficiency virus reverse transcriptase in vitro is promoted by pausing and results in misincorporation
80. Human immunodeficiency virus type I nucleocapsid protein reduces reverse transcriptase pausing at a secondary structure near the Murine Leukemia Virus polypurine tract
81. Utilization of nonhomologous minus-strand DNA transfer to generate recombinant retroviruses
82. Human immunodeficiency virus nucleocapsid protein accelerates strand transfer of the terminally redundant sequences involved in reverse transcription
83. On finding all suboptimal foldings of an RNA molecule