The DOI matches its Crossref record; 54 of the 54 references it cites were found in a registry or an index.
RNA secondary structure and binding sites for gag gene products in the 5’ packaging signal of human immunodeficiency virus type 1
Open accessAbstract
The selective encapsidation of retroviral RNA requires sequences in the Gag protein, as well as a cis-acting RNA packaging signal (psi site) near the 5' end of the genomic transcript. Gag protein of human immunodeficiency virus type 1 (HIV-1) has recently been found to bind specifically to the HIV-1 psi element in vitro. Here we report studies aimed at mapping features within the genetically defined psi locus that are required for binding of HIV-1 Gag or of its processed nucleocapsid derivative. The full-length HIV-1 Gag (p55) and nucleocapsid (p15) sequences were expressed as glutathione S-transferase (GST) fusion proteins in Escherichia coli. In a gel shift assay containing excess competitor tRNA, affinity-purified GST-p15 and GST-p55 proteins bound to a 206-nucleotide psi RNA element spanning the major splice donor and gag start codons but did not bind to antisense psi transcripts. Quantitative filter-binding assays revealed that both GST-p55 and GST-p15 bound to this RNA sequence with identical affinities (apparent Kd congruent to 5 x 10(-8) M), indicating that all major determinants of psi binding affinity reside within the nucleocapsid portion of Gag. Chemical and RNase accessibility mapping, coupled with computerized sequence analysis, suggested a model for psi RNA structure comprising four independent stem-loops. Filter-binding studies revealed that RNAs corresponding to three of these hypothetical stem-loops can each function as a independent Gag binding site and that each is bound with approximately fourfold-lower apparent affinity than the full-length psi locus. Interaction of Gag with these regions is likely to play a major role in directing HIV-1 RNA encapsidation in vivo.
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In the citing paper
“These structured motifs often include stem-loops, bulges, and unpaired purine-rich sequences that serve as high-affinity Gag binding sites”
From Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication (2026) · cites this paper as Clever et al. 1995
In the citing paper
“Structure–function studies across diverse retroviruses, including HIV-1, MMTV, MPMV, and FIV, have consistently demonstrated that RNA packaging elements form complex secondary and tertiary structures.”
From Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication (2026) · cites this paper as Clever et al. 1995
Citations
Cites
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Evidence that the packaging signal of Moloney murine leukemia virus extends into the gag region
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[17] Predicting optimal and suboptimal secondary structure for RNA
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Cited by
Sorted by citations
HIV-1 Gag proteins: diverse functions in the virus life cycle
Freed, E. O. (1998) · Virology · doi:10.1006/viro.1998.9398 · Cited by 717
“In HIV-1, this domain has been predicted to fold into four stem-loops (SL1–SL4) with SL3 being particularly well conserved among virus isolates (Clever et al., 1995).”
BackgroundStructure of the HIV-1 Nucleocapsid Protein Bound to the SL3 Ψ-RNA Recognition Element
De Guzman, R. N., Wu, Z. R., Stalling, C. C., Pappalardo, L., Borer, P. N., & Summers, M. F. (1998) · Science · doi:10.1126/science.279.5349.384 · Cited by 659
Structural biology of HIV 1 1Edited by P. E. Wright
Turner, B. G., & Summers, M. F. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2354 · Cited by 470
“The HIV-1 -site contains four stemloops (SL1-SL4) that are important for ef®cient encapsidation (Clever et al., 1995; Clever & Parslow, 1997; Harrison & Lever, 1992; Hayashi et al., 1992, 1993; McBride & Panganiban, 1996; Sakaguchi et al., 1993).”
BackgroundWilkinson, K. A., Gorelick, R. J., Vasa, S. M., Guex, N., Rein, A. R., Mathews, D. H., Giddings, M. C., & Weeks, K. M. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060096 · Cited by 428
Levin, J. G., Guo, J., Rouzina, I. F., & Musier‐Forsyth, K. (2005) · Progress in nucleic acid research and molecular biology · doi:10.1016/s0079-6603(05)80006-6 · Cited by 367
Metadata
- Authors
- Clever, J., Sassetti, C., & Parslow, T. G.
- Affiliations
- University of California, San Francisco (US)
- ORCID
- Sassetti, C
- Venue
- Journal of Virology
- Publisher
- American Society for Microbiology
- Published
- 1995-04
- Volume
- 69
- Issue
- 4
- Pages
- 2101-2109
- ISSN
- 0022-538X (ISSN-L)
- 1098-5514
- PMC
- PMC188876
- OpenAlex
- W2122273986
- Cited by
- 307
- References
- 54
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 2 · 2023: 3 · 2022: 6 · 2021: 9 · 2020: 4 · 2018: 7 · 2017: 9 · 2016: 7 · 2015: 4 · 2014: 10 · 2013: 12 · 2012: 13
- FWCI
- 6.52
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Virology (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (5r01ai029313-06, 5r01gm037036-03)
- National Institute of General Medical Sciences (GM37036)
- National Institute of Allergy and Infectious Diseases (AI-07395, AI29313, T32AI007395)
- Topics
- Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- HIV-1, RNA secondary structure, Gag protein, RNA-protein interactions, RNA encapsidation, stem-loop structure, binding affinity, retroviral RNA
- MeSH terms
- Base Sequence, Molecular Sequence Data, Nucleic Acid Conformation, Protein Binding, RNA, Viral, HIV-1, Gene Products, gag, DNA Primers
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