Cited by 307HIV Research and TreatmentRNA and protein synthesis mechanismsRNA Research and Splicing

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 access

Clever, J, Sassetti, C, Parslow, T G·1995·Journal of Virology

DOI 10.1128/jvi.69.4.2101-2109.1995PMC PMC188876

Open this paper in CoChat — free account

Abstract

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.

Integrity signals

Registry

Crossref · 10.1128/jvi.69.4.2101-2109.1995

Cites

54 of 54 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

On Finding All Suboptimal Foldings of an RNA Molecule
Zuker, M. (1989) · Science · doi:10.1126/science.2468181 · Cited by 1,998
Construction of a retrovirus packaging mutant and its use to produce helper-free defective retrovirus
Mann, R., Mulligan, R. C., & Baltimore, D. (1983) · Cell · doi:10.1016/0092-8674(83)90344-6 · Cited by 1,776
Human Retroviruses and Aids - 1999
KUIKEN, C. L., & Foley, B. T. (1999) · doi:10.2172/1186019 · Cited by 952
RNA Structure Prediction
Turner, D. H., Sugimoto, N., & Freier, S. M. (1988) · Annual Review of Biophysics and Biophysical Chemistry · doi:10.1146/annurev.bb.17.060188.001123 · Cited by 647
Mutations of RNA and protein sequences involved in human immunodeficiency virus type 1 packaging result in production of noninfectious virus
Aldovini, A., & Young, R. A. (1990) · Journal of Virology · doi:10.1128/jvi.64.5.1920-1926.1990 · Cited by 548
Evidence that the packaging signal of Moloney murine leukemia virus extends into the gag region
Bender, M. A., Palmer, T. D., Gelinas, R. E., & Miller, A. D. (1987) · Journal of Virology · doi:10.1128/jvi.61.5.1639-1646.1987 · Cited by 410
Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro
Skripkin, E., Paillart, J. C., Marquet, R., Ehresmann, B., & Ehresmann, C. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.11.4945 · Cited by 401
Noninfectious human immunodeficiency virus type 1 mutants deficient in genomic RNA
Gorelick, R. J., Nigida, S. M., Bess, J. W., Arthur, L. O., Henderson, L. E., & Rein, A. R. (1990) · Journal of Virology · doi:10.1128/jvi.64.7.3207-3211.1990 · Cited by 386
[17] Predicting optimal and suboptimal secondary structure for RNA
Jaeger, J. A., Turner, D. H., & Zuker, M. (1990) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(90)83019-6 · Cited by 382
Identification of a sequence required for efficient packaging of human immunodeficiency virus type 1 RNA into virions
Lever, A. M. L., Göttlinger, H. G., Haseltine, W. A., & Sodroski, J. (1989) · Journal of Virology · doi:10.1128/jvi.63.9.4085-4087.1989 · Cited by 375

Show all 54 references

Sorted by citations

Items 201–300 of 307

Structural Dynamics of Retroviral Genome and the Packaging
Miyazaki, Y., Miyake, A., Nomaguchi, M., & Adachi, A. (2011) · Frontiers in Microbiology · doi:10.3389/fmicb.2011.00264 · Cited by 23
“…and Panganiban, 1992; Kim et al., 1994; Luban and Goff, 1994; Parolin et al., 1994; Berkowitz et al., 1995; McBride and Panganiban, 1996, 1997; McBride et al., 1997; Harrison et al., 1998; Helga-Maria et al., 1999; Clever et al., 2002; Russell et al., 2002; Sakuragi et al., 2003, 2007).”
BackgroundMethod
Transduction of Human Immunodeficiency Virus Type 1 Vectors Lacking Encapsidation and Dimerization Signals
Laham-Karam, N., & Bacharach, E. (2007) · Journal of Virology · doi:10.1128/jvi.00653-07 · Cited by 20
“Each of the four stem-loops (SL1 to SL4) appears to have substantial ability to bind HIV Gag, and the same is true for multiple stem-loops consisting of two, three, or four of these stem-loops in tandem (2, 4, 12, 16, 23, 74).”
Background
Co-packaging of sense and antisense RNAs: a novel strategy for blocking HIV-1 replication
Ding, S. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.13.3270 · Cited by 22
Initiation of HIV-1 Gag lattice assembly is required for recognition of the viral genome packaging signal
Lei, X., Gonçalves-Carneiro, D., Zang, T. M., & Bieniasz, P. D. (2023) · eLife · doi:10.7554/elife.83548 · Cited by 22
In Vivo SELEX of Single-Stranded Domains in the HIV-1 Leader RNA
van Bel, N., Das, A. T., & Berkhout, B. (2013) · Journal of Virology · doi:10.1128/jvi.02942-13 · Cited by 22
Identification of Peptide Ligands for Target RNA Structures Derived from the HIV‐1 Packaging Signal ψ by Screening Phage‐Displayed Peptide Libraries
Pustowka, A., Dietz, J., Ferner, J., Baumann, M. J., Landersz, M., Königs, C., Schwalbe, H., & Dietrich, U. (2003) · ChemBioChem · doi:10.1002/cbic.200300681 · Cited by 21
Footprinting and circular dichroism studies on paromomycin binding to the packaging region of human immunodeficiency virus type-1
McPike, M. P., Goodisman, J., & Dabrowiak, J. C. (2002) · Bioorganic & Medicinal Chemistry · doi:10.1016/s0968-0896(02)00220-1 · Cited by 21
Design, biochemical, biophysical and biological properties of cooperative antisense oligonucleotides
Kandimalla, E. R., Manning, A. N., Lathan, C. S., Byrn, R. A., & Agrawal, S. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.17.3578 · Cited by 21
RNA Binding Domain of Jamestown Canyon Virus S Segment RNAs
Ogg, M. M., & Patterson, J. L. (2007) · Journal of Virology · doi:10.1128/jvi.01492-07 · Cited by 20
Induced Degradation of Tat by Nucleocapsid (NC) via the Proteasome Pathway and Its Effect on HIV Transcription
Hong, H., Lee, S., & Myung, H. (2013) · Viruses · doi:10.3390/v5041143 · Cited by 20
“This domain binds to the packaging signal (psi) at 5' LTR of the viral genomic RNA for encapsidation [8–10].”
Background
Monomer−Dimer Equilibrium Constants of RNA in the Dimer Initiation Site of Human Immunodeficiency Virus Type 1
Shubsda, M. F., McPike, M. P., Goodisman, J., & Dabrowiak, J. C. (1999) · Biochemistry · doi:10.1021/bi990744t · Cited by 20
Deletion Mutagenesis Downstream of the 5′ Long Terminal Repeat of Human Immunodeficiency Virus Type 1 Is Compensated for by Point Mutations in both the U5 Region and gag Gene
Liang, C., Rong, L., Russell, R., & Wainberg, M. (2000) · Journal of Virology · doi:10.1128/jvi.74.14.6251-6261.2000 · Cited by 23
The Simian Immunodeficiency Virus 5′ Untranslated Leader Sequence Plays a Role in Intracellular Viral Protein Accumulation and in RNA Packaging
Patel, J. G., Wang, S.-W., Izmailova, E. S., & Aldovini, A. (2003) · Journal of Virology · doi:10.1128/jvi.77.11.6284-6292.2003 · Cited by 19
Randomization and in vivo selection reveal a GGRG motif essential for packaging human immunodeficiency virus Type 2 RNA
Baig, T. T., Lanchy, J.-M., & Lodmell, J. S. (2009) · Journal of Virology · doi:10.1128/jvi.01521-08 · Cited by 21
“In vitro studies have suggested that the HIV-1 packaging signal is composed of at least four stem-loops located both upstream and downstream of SD (6, 11).”
Background
HIV-2 Genome Dimerization Is Required for the Correct Processing of Gag: a Second-Site Reversion in Matrix Can Restore Both Processes in Dimerization-Impaired Mutant Viruses
L’Hernault, A., Weiß, E. U., Greatorex, J. S., & Lever, A. M. L. (2012) · Journal of Virology · doi:10.1128/jvi.00124-12 · Cited by 18
“In human immunodeficiency virus type 1 (HIV-1), the cis-acting elements required for genome dimerization and encapsidation overlap and have been mapped to four stem-loops (SL-1 to SL-4) located in the 5= leader of the genome, suggesting that the two processes may be linked (6, 7, 12, 13, 28, 39, 50, 54).”
Background
Comparative Structural Effects of HIV-1 Gag and Nucleocapsid Proteins in Binding to and Unwinding of the Viral RNA Packaging Signal
Bell, N. M., Kenyon, J. C., Balasubramanian, S., & Lever, A. M. L. (2012) · Biochemistry · doi:10.1021/bi2017969 · Cited by 18
HIV-1 vector systems.
Srinivasakumar, N. (2001) · Somatic Cell and Molecular Genetics · doi:10.1023/a:1021074613196 · Cited by 18
RNA Aptamers that Bind the Nucleocapsid Protein Contain Pseudoknots
Kim, M. Y., & Jeong-Yu, S. (2003) · Molecules and Cells · doi:10.1016/s1016-8478(23)13821-0 · Cited by 18
Packaging Cell System for Lentivirus Vectors: Preparation and Use
Srinivasakumar, N. (2003) · Humana Press eBooks · doi:10.1385/1-59259-141-8:275 · Cited by 17
Mechanisms and Factors That Drive Extensive Human Immunodeficiency Virus Type-1 Hypervariability: An Overview
Yaseen, M. M., Abuharfeil, N. M., Alqudah, M. A. Y., & Yaseen, M. M. (2017) · Viral Immunology · doi:10.1089/vim.2017.0065 · Cited by 17
Deletion of stem-loop 3 is compensated by second-site mutations within the Gag protein of human immunodeficiency virus type 1.
Rong, L., Russell, R., Hu, J., Laughrea, M., Wainberg, M., & Liang, C. (2003) · Virology · doi:10.1016/s0042-6822(03)00405-7 · Cited by 21
“We hypothesize that the involvement of SL3 in RNA dimerization may be related to its NC-binding activity (Berkowitz et al., 1993, 1994; Clever et al., 1995; Sakaguchi et al., 1993).”
BackgroundInfluential
Steady-State Kinetics of Ricin A-Chain Reaction with the Sarcin−Ricin Loop and with HIV-1 Ψ-RNA Hairpins Evaluated by Direct Infusion Electrospray Ionization Mass Spectrometry
Fabris, D. (2000) · Journal of the American Chemical Society · doi:10.1021/ja0019676 · Cited by 17
In Vitro Studies on tRNA Annealing and Reverse Transcription with Mutant HIV-1 RNA Templates
Beerens, N., & Berkhout, B. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.20.15474 · Cited by 17
A Phylogenetic Survey on the Structure of the HIV-1 Leader RNA Domain That Encodes the Splice Donor Signal
Mueller, N., Das, A. T., & Berkhout, B. (2016) · Viruses · doi:10.3390/v8070200 · Cited by 14
Identification of conserved RNA secondary structures at influenza B and C splice sites reveals similarities and differences between influenza A, B, and C
Dela-Moss, L. I., Moss, W. N., & Turner, D. H. (2014) · BMC Research Notes · doi:10.1186/1756-0500-7-22 · Cited by 20
“RNA structure is also used for start codon selection and viral replication [14], for packaging signals [15], for RNA editing [16], and for many more functions.”
RNA Regulatory Elements in the Genomes of Simple Retroviruses
Banks, J. D., BEEMON, K. L., & Linial, M. L. (1997) · Seminars in Virology · doi:10.1006/smvy.1997.0122 · Cited by 16
Sequestering the 5′‐cap for viral RNA packaging
Ding, P., & Summers, M. F. (2022) · BioEssays · doi:10.1002/bies.202200104 · Cited by 16
Current perspectives on RNA secondary structure probing
Kenyon, J., Prestwood, L., & Lever, A. M. L. (2014) · Biochemical Society Transactions · doi:10.1042/bst20140084 · Cited by 17
Characterization of the Inhibition Mechanism of HIV-1 Nucleocapsid Protein Chaperone Activities by Methylated Oligoribonucleotides
Avilov, S., Boudier, C., Gottikh, M., Darlix, J., & Mély, Y. (2011) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.05614-11 · Cited by 15
“At each temperature used, the experimentally determined quantities of heat were corrected for the heat of dilution measured by performing a control experiment in which NC(11-55) was titrated into the buffer alone.”
BackgroundMethodInfluential
Potential inhibition of HIV-1 encapsidation by oligoribonucleotide–dendrimer nanoparticle complexes
Parboosing, R., Chonco, L., de la Mata, J., Govender, T., Maguire, G. E. M., & Kruger, G. (2017) · International Journal of Nanomedicine · doi:10.2147/ijn.s114446 · Cited by 14
Mutations in matrix and SP1 repair the packaging specificity of a Human Immunodeficiency Virus Type 1 mutant by reducing the association of Gag with spliced viral RNA
Ristic, N., & Chin, M. P. S. (2010) · Retrovirology · doi:10.1186/1742-4690-7-73 · Cited by 17
“The primary recognition sites for NC are the four SLs in the 5′ UTR of the HIV-1 genome [7,11-16].”
BackgroundResultInfluential
SL1 revisited: functional analysis of the structure and conformation of HIV-1 genome RNA
Sakuragi, S., Yokoyama, M., Shioda, T., Sato, H., & Sakuragi, J.-I. (2016) · Retrovirology · doi:10.1186/s12977-016-0310-9 · Cited by 14
The bifurcated stem loop 4 (SL4) is crucial for efficient packaging of mouse mammary tumor virus (MMTV) genomic RNA
Mustafa, F., Vivet‐Boudou, V., Jabeen, A., Ali, L. M., Kalloush, R. M., Marquet, R., & Rizvi, T. A. (2018) · RNA Biology · doi:10.1080/15476286.2018.1486661 · Cited by 15
“The case of human immunodeficiency virus type 1 (HIV-1) may somewhat be similar to MMTV: the 5ʹ UTR in HIV-1 implicated in RNA packaging folds into several stem loops, SL1-4 [39,40] of which SL1 harbors a GC-rich 6-nt pal sequence in the form of a loop that has been shown to function as the DIS [41,42].”
Background
Molecular biology of human immunodeficiency virus Type-1
Joshi, S., & Joshi, R. L. (1996) · Transfusion Science · doi:10.1016/0955-3886(96)00004-5 · Cited by 14
Nucleomimetic strategy for the inhibition of HIV-1 nucleocapsid protein NCp7 activities
Druillennec, S., Meudal, H., Roques, B. P., & Fournié‐Zaluski, M. (1999) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/s0960-894x(99)00052-9 · Cited by 14
The T12I mutation within the SP1 region of Gag restricts packaging of spliced viral RNA into human immunodeficiency virus type 1 with mutated RNA packaging signals and mutated nucleocapsid sequence
Roy, B. B., Russell, R. S., Turner, D., & Liang, C. (2005) · Virology · doi:10.1016/j.virol.2005.09.011 · Cited by 17
Molecular determinants of HIV-1 NCp7 chaperone activity in maturation of the HIV-1 dimerization initiation site
Aduri, R., Briggs, K. T., Gorelick, R. J., & Marino, J. P. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1350 · Cited by 12
Development of a Cell-Based Assay Probing the Specific Interaction between the Human Immunodeficiency Virus Type 1 Nucleocapsid and Psi RNA In Vivo
Jang, S.-I., Kim, Y. H., Paik, S., & You, J.-C. (2007) · Journal of Virology · doi:10.1128/jvi.00414-07 · Cited by 10
“However, studies of NC function with respect to the interaction with RNA have thus far relied on either mutational studies using a proviral DNA clone (1, 18, 25) in vivo or in vitro analyses such as nitrocellulose filter binding (10, 13), or gel mobility assays (7, 12, 29) using purified recombinant Gag or NC protein.”
Method
Hydrophobic Amino Acids in the Human Immunodeficiency Virus Type 1 p2 and Nucleocapsid Proteins Can Contribute to the Rescue of Deleted Viral RNA Packaging Signals
Rong, L., Russell, R. S., Hu, J., Guan, Y., Kleiman, L., Liang, C., & Wainberg, M. A. (2001) · Journal of Virology · doi:10.1128/jvi.75.16.7230-7243.2001 · Cited by 12
Fluorescence and nucleic acid binding properties of bovine leukemia virus nucleocapsid protein
Morcock, D. R., Katakam, S. B., Kane, B., & Casas‐Finet, J. R. (2002) · Biophysical Chemistry · doi:10.1016/s0301-4622(02)00070-4 · Cited by 11
A Small Molecule, Lys-Ala-7-amido-4-methylcoumarin, Facilitates RNA Dimer Maturation of a Stem−Loop 1 Transcript in Vitro: Structure−Activity Relationship of the Activator
Chung, J., Mujeeb, A., Jiang, Y., Guilbert, C., Pendke, M., Wu, Y., & James, T. L. (2008) · Biochemistry · doi:10.1021/bi800230m · Cited by 10
Role of Purine-Rich Regions in Mason-Pfizer Monkey Virus (MPMV) Genomic RNA Packaging and Propagation
Ali, L. M., Pitchai, F. N. N., Vivet‐Boudou, V., Chameettachal, A., Jabeen, A., Pillai, V. N., Mustafa, F., Marquet, R., & Rizvi, T. A. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.595410 · Cited by 10
Examination of specific binding activity of aptamer RNAs to the HIV-NC by using a cell-based in vivo assay for protein-RNA interaction.
Jeong, Y. Y., Kim, S. H., Jang, S.-I., & You, J.-C. (2008) · BMB Reports · doi:10.5483/bmbrep.2008.41.7.511 · Cited by 10
“enable it to encapsulate selectively the viral genomic RNA among many different cellular RNAs (4, 11-13).”
Background
NMR Studies of Retroviral Genome Packaging
Boyd, P. S., Brown, J. B., Brown, J. D., Catazaro, J., Chaudry, I., Ding, P., Dong, X., Marchant, J., O’Hern, C., Singh, K., et al. (2020) · Viruses · doi:10.3390/v12101115 · Cited by 10
Functional Investigations of Retroviral Protein—Ribonucleic Acid Complexes by Nanospray Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
Fabris, D., Chaudhari, P. D., Hagan, N., & Turner, K. B. (2007) · European Journal of Mass Spectrometry · doi:10.1255/ejms.839 · Cited by 9
Visualization of Retroviral Gag-Genomic RNA Cellular Interactions Leading to Genome Encapsidation and Viral Assembly: An Overview
Bernacchi, S. (2022) · Viruses · doi:10.3390/v14020324 · Cited by 8
Encapsidation Determinants Located Downstream of the Major Splice Donor in the Maedi-Visna Virus Leader Region
Bjarnadóttir, H., Guðmundsson, B., Guðnason, J. F., & Jónsson, J. J. (2006) · Journal of Virology · doi:10.1128/jvi.01284-06 · Cited by 8
“extend into the proximal gag gene (5, 15, 26).”
Background
A Stretch of Unpaired Purines in the Leader Region of Simian Immunodeficiency Virus (SIV) Genomic RNA is Critical for its Packaging into Virions
Pillai, V. N., Ali, L. M., Prabhu, S., Krishnan, A., Chameettachal, A., Pitchai, F. N. N., Mustafa, F., & Rizvi, T. A. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167293 · Cited by 9
Inhibition of HIV Type 1 RNA Dimerization by Antisense DNA Corresponding to the 17-Nucleotide Sequence Downstream from the Splice Donor Site of HIV Type 1 RNA
Zhang, S., Hara, H., Kaji, H. K., & Kaji, A. (1997) · AIDS Research and Human Retroviruses · doi:10.1089/aid.1997.13.865 · Cited by 8
Molecular Dynamics Simulation for Probing the Flexibility of the 35 Nucleotide SL1 Sequence Kissing Complex from HIV-1Lai Genomic RNA
Mazier, S., & Genest, D. (2007) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2007.10507135 · Cited by 8
Probing the RNA Binding Surface of the HIV-1 Nucleocapsid Protein by Site-Directed Mutagenesis
Ouyang, W., Okaine, S., McPike, M. P., Lin, Y., & Borer, P. N. (2013) · Biochemistry · doi:10.1021/bi400125z · Cited by 8
Inhibition of HIV-1 Replication by Oligonucleotide Analogues Directed to the Packaging Signal and Trans-Activating Response Region
Brown, D. E., Arzumanov, A. A., Syed, S., Gait, M. J., & Lever, A. M. L. (2006) · Antiviral chemistry & chemotherapy · doi:10.1177/095632020601700101 · Cited by 8
Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging
Krishnan, A., Ali, L. M., Prabhu, S. G., Pillai, V. N., Chameettachal, A., Vivet-Boudou, V., Bernacchi, S., Mustafa, F., Marquet, R., & Rizvi, T. A. (2024) · RNA · doi:10.1261/rna.079840.123 · Cited by 6
“…structure level, these sequences assume higher order structural motifs found to be important for gRNA packaging among various retroviruses (Clever et al. 1995; Zeffman et al. 2000; D ’ Souza and Summers 2004, 2005; Mustafa et al. 2004, 2018; Lever 2007; Kenyon et al. 2008, 2011; Jaballah…”
Background
Binding of human immunodeficiency virus type 1 nucleocapsid protein to psi-RNA-SL3.
Shubsda, M. F., Kirk, C. A., Goodisman, J., & Dabrowiak, J. C. (2000) · Biophysical Chemistry · doi:10.1016/s0301-4622(00)00188-5 · Cited by 9
“When the virus is budding the correct RNA must be selected from a pool of competing cellular RNAs for insertion into the virus particle [10-13].”
Background
Cu(II)-Based Paramagnetic Probe to Study RNA–Protein Interactions by NMR
Seebald, L. M., DeMott, C. M., Ranganathan, S., Asare‐Okai, P. N., Glazunova, A., Chen, A. A., Shekhtman, A. G., & Royzen, M. (2017) · Inorganic Chemistry · doi:10.1021/acs.inorgchem.6b02286 · Cited by 6
Development of a Novel Competitive qRT-PCR Assay to Measure Relative Lentiviral Packaging Efficiency
Vamva, E., Lever, A. M. L., Vink, C. A., & Kenyon, J. C. (2020) · Molecular Therapy — Methods & Clinical Development · doi:10.1016/j.omtm.2020.09.010 · Cited by 7
Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR
Seebald, L. M., DeMott, C. M., Ranganathan, S., Asare‐Okai, P. N., Glazunova, A., Chen, A. A., Shekhtman, A. G., & Royzen, M. (2017) · Journal of Inorganic Biochemistry · doi:10.1016/j.jinorgbio.2017.02.024 · Cited by 6
Cellular Trafficking Mechanisms in the Assembly and Release of HIV
Giese, S., & Marsh, M. (2013) · Springer eBooks · doi:10.1007/978-1-4614-7729-7_2 · Cited by 6
Partial Restoration of Replication of Simian Immunodeficiency Virus by Point Mutations in either the Dimerization Initiation Site (DIS) or Gag Region after Deletion Mutagenesis within the DIS
Guan, Y., Diallo, K., Detorio, M., Whitney, J., Liang, C., & Wainberg, M. (2001) · Journal of Virology · doi:10.1128/jvi.75.23.11920-11923.2001 · Cited by 5
“The secondary structure of the HIV-1 leader sequence, located downstream of U5, includes four stem-loop RNA motifs, termed SL1, SL2, SL3, and SL4 (5, 13).”
Background
Upstream of N-Ras (Unr/CSDE1) Interacts with NCp7 and Gag, Modulating HIV-1 IRES-Mediated Translation Initiation
Taha, N., Zgheib, S., Sharma, K. K., Humbert, N., Boutant, E., Didier, P., Mély, Y., & Réal, É. (2022) · Viruses · doi:10.3390/v14081798 · Cited by 7
Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication
Jehad, M. A., Ali, L. M., Pillai, V. N., Prabhu, S. G., Mustafa, F., & Rizvi, T. A. (2026) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaf066 · Cited by 5
HIV-1 Packaging Visualised by In-Gel SHAPE
D’Souza, A. R., Jayaraman, D., Long, Z., Zeng, J., Prestwood, L. J., Chan, C., Kappei, D., Lever, A. M. L., & Kenyon, J. C. (2021) · Viruses · doi:10.3390/v13122389 · Cited by 4
Introduction to Retroviruses
Goff, S. P. (2004) · Elsevier eBooks · doi:10.1016/b978-012764051-8/50006-8 · Cited by 4
Functional Analysis of RNA Signals in the HIV-1 Genome by Forced Evolution
Berkhout, B., & Das, A. T. (1999) · Springer eBooks · doi:10.1007/978-94-011-4485-8_19 · Cited by 4
Three-Dimensional RNA Structure-Based Drug Discovery
James, T. L., Lind, K. E., Filikov, A. V., & Mujeeb, A. (2000) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2000.10506622 · Cited by 3
HIV-1 Gag binds specifically to RNA stem-loops in the 5' leader sequence.
Maddison, B., Marya, P. K., & Heaphy, S. (1998) · Biochimica et Biophysica Acta · doi:10.1016/s0167-4781(98)00080-3 · Cited by 2
Insight into the intrinsic flexibility of the SL1 stem‐loop from genomic RNA of HIV‐1 as probed by molecular dynamics simulation
Mazier, S., & Genest, D. (2007) · Biopolymers · doi:10.1002/bip.20888 · Cited by 3
RNA ‐centric world of retroviruses: unravelling the molecular strategies of genomic RNA packaging
Jehad, M. A., Prabhu, S., Ali, L. M., Pillai, V. N., Mustafa, F., & Rizvi, T. A. (2026) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1002/brv.70188 · Cited by 2
MMTV RNA packaging requires an extended long-range interaction for productive Gag binding to packaging signals
Prabhu, S. G., Pillai, V. N., Ali, L. M., Vivet-Boudou, V., Chameettachal, A., Bernacchi, S., Mustafa, F., Marquet, R., & Rizvi, T. A. (2024) · PLOS Biology · doi:10.1371/journal.pbio.3002827 · Cited by 2
Expression and Purification of HIV-I p15NC Protein inEscherichia coli
Ozturk, D., & Erickson-Viitanen, S. (1998) · Protein Expression and Purification · doi:10.1006/prep.1998.0934 · Cited by 2
The human cellular protein NoL12 is a specific partner of the HIV-1 nucleocapsid protein NCp7
Zgheib, S., Taha, N., Zeiger, M., Glushonkov, O., Lequeu, T., Anton, H., Didier, P., Boutant, E., Mély, Y., & Réal, É. (2023) · Journal of Virology · doi:10.1128/jvi.00040-23 · Cited by 3
Evaluation of global HIV/SIV envelope gp120 RNA structure and evolution within and among infected hosts
Magalis, B. R., Pond, S. L. K., Summers, M. F., & Salemi, M. (2018) · Virus Evolution · doi:10.1093/ve/vey018 · Cited by 2
“…probability scales or multiple models that satisfied or partially satisfied the chemical probing data (Harrison and Lever 1992; Baudin 1993; Clever, Sassetti, and Parslow 1995; McBride and Panganiban 1996; Clever, Miranda, and Parslow 2002; Abbink and Berkhout 2003; Damgaard et al. 2004;…”
Background
A novel role for gag as a cis-acting element regulating RNA structure, dimerization and packaging in HIV-1 lentiviral vectors
Vamva, E., Griffiths, A., Vink, C. A., Lever, A. M. L., & Kenyon, J. C. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab1206 · Cited by 3
An Intact U5-Leader Stem Is Important for Efficient Replication of Simian Immunodeficiency Virus
Guan, Y., Diallo, K., Whitney, J. B., Liang, C., & Wainberg, M. A. (2001) · Journal of Virology · doi:10.1128/jvi.75.23.11924-11929.2001 · Cited by 2
“These include two critical stem-loop structures in the R region, i.e., the TAR and poly(A) hairpins, the U5-IR stem-loop and the U5-leader stem in the PBS region, and four distinct stem-loop structures in the region downstream of the PBS (2, 5, 9 , 13, 22).”
Background
Structural changes in the SL5 and SL6 leader sequences of HIV-1 RNA following interactions with the viral mGag protein
Roldán, A., Liang, C., & Wainberg, M. A. (2010) · Virus Research · doi:10.1016/j.virusres.2010.09.005 · Cited by 1
A Nucleic Acid Switch Triggered by the HIV-1 Nucleocapsid Protein
DeCiantis, C. L., Jensen, D. K., Hudson, B. S., & Borer, P. N. (2007) · Biochemistry · doi:10.1021/bi700031j · Cited by 1
Steric Block High Affinity Oligonucleotide Analogues: A New Tool for Mapping RNA-Protein Binding Sites
Brown, D., Joy, E. A., Greatorex, J. S., Gait, M. J., & Lever, A. M. L. (2008) · Nucleosides Nucleotides & Nucleic Acids · doi:10.1080/15257770701795961 · Cited by 1
Functional Analysis of the Murine Sarcoma Virus RNA Packaging Sequence
Izmailova, E. S., & Aldovini, A. (2002) · Journal of Virology · doi:10.1128/jvi.76.9.4643-4648.2002 · Cited by 1
“This process, termed RNA packaging, depends upon specific sequences in the unspliced viral RNA and in the Gag polyprotein (2, 6, 19, 32, 36).”
Background
STUDIES OF THE DIMERIZATION AND PACKAGING SIGNALS IN HIV-2 RNA
Baig, T. T. (2008) · The Mathematics Enthusiast · Cited by 1
Packaging of the HIV-1 RNA Genome
Chen, J., Nikolaitchik, O. A., Dilley, K. A., & Hu, W.-S. (2013) · Springer eBooks · doi:10.1007/978-1-4614-7729-7_3
Cis–Acting RNA Elements of Human Immunodeficiency Virus
Ps, M. (2012) · InTech eBooks · doi:10.5772/25916
Etude structurale par RMN des changements conformationnels de la séquence SL1 de l'ARN de l'isolat VIH-1 laï
Kieken, F. (2004) · HAL
Evolutionary analyses of HIV-1 protein-coding sequences : adaptation to host cytotoxic immune responses and purifying selection at synonymous sites
Ngandu, N. K. (2009) · Open University of Cape Town (University of Cape Town)
HIV-1 Packing to Leave
Cullen, B. R. (2014) · Cell · doi:10.1016/j.cell.2014.11.008
“…requirements for selective recruitment of an RNA into HIV-1 virions has previously identified a structured RNA element called ‘‘psi’’ (‘‘c’’), located in the viral RNA 50 UTR, that is selectively bound by NC and that greatly facilitates genomic RNA packaging (Clever et al., 1995; Lu et al., 2011).”
Background
Mutations designed to alter the stability of a putative RNA duplex in the HIV-1 pol gene
Tjøtta, E., Hungnes, O., & Grinde, B. (1999) · Archives of Virology · doi:10.1007/s007050050628
“The latter functions, however, appear to be independent of sequences in the central part of the genome [4, 11], suggesting that they should not be affected by the mutations.”
Background
The effect of alpha-HGA on HIV-1 replication
Youssefi, M. (2009) · Figshare
Synonymous site conservation in the HIV-1
Mayrose, I., Stern, A., Burdelova, E. O., Sabo, Y., Laham-Karam, N., Zamostiano, R., Bacharach, E., & Pupko, T. (2013)
Structure and Dynamics in Viral RNA Packaging
Dieckmann, T., & Zumwalt, M. (2008) · WORLD SCIENTIFIC eBooks · doi:10.1142/9789812790859_0008
Gene Therapy for HIV-1 Infection
Arbuthnot, P. B. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-410518-8.00008-9
Etude structurale par RMN des changements
Kieken, F. (2004)
Virus-host interactions in the early stages of the Equine Hepacivirus (EqHV) lifecycle
Lattimer, J. (2017) · White Rose eTheses Online (University of Leeds, The University of Sheffield, University of York)
Estimating Chronic Wasting Disease infectivity in cell culture
Schmädicke, A.-C. (2011) · doi:10.53846/goediss-1119
Sequence-based Predictors for Identification of Nucleosome Positioning and Transmembrane Proteins
Tahir, M. (2017)
Analysis of the Relationship between the Structure and Function of the HIV-1 Rev Response Element (RRE)
Sherpa, C. (2014) · doi:10.18130/v3p821
Mechanisms by which HIV-1 Nef disrupts the intracellular trafficking of host proteins
Leonard, J. A. (2011) · Deep Blue (University of Michigan)
HIV-1 5'UTR RNA structures: connections to infectious lifecycle and potential therapeutic applications
Staller, S. (2021) · MOspace Institutional Repository (University of Missouri) · doi:10.32469/10355/91021
Programmable Antivirals and Just-in-Time Vaccines: Biosecurity Implications of Viral RNA Secondary Structure Targeting
Pannu, J., & Glenn, J. S. (2022) · Health Security · doi:10.1089/hs.2022.0098
Etude des mécanismes contrôlant la spécificité d'encapsidation des ARN dans le VIH-1
Didierlaurent, L. (2010) · theses.fr (ABES) · doi:10.70675/6af45cb6z95b9z414cz94fbzdcd9c17fde4a
Etudes de deux protéines chaperonnes des acides nucléiques de virus de l’immunodéficience humaine type 1 : Vif et la protéine nucléocapside
Sleiman, D. (2013) · theses.fr (ABES) · doi:10.70675/3b4db089z564az4d55z8f18ze353af99cbe5
Novel potent antiviral molecules targeting the nucleocapsid protein of the HIV-1 virus
Basta, B. (2012) · theses.fr (ABES) · doi:10.70675/151cc823z1197z4e3azbfd9z27dadc35fe11

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
DOI: 10.1128/jvi.69.4.2101-2109.1995
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
Licence: journals.asm.org/non-commercial-tdm-license (tdm)
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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

RNA secondary structure and binding sites for gag gene products in the 5’ packaging signal of human immunodeficiency virus type 1

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks