ArticleProceedings of the National Academy of Sciences of the United States of America2015
Targeted binding of nucleocapsid protein transforms the folding landscape of HIV-1 TAR RNA.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 44 citations in OpenAlex.
- Article
- Dynamics of viral self-assembly, viral genome packaging, and virus-cell interactions studied by optical tweezers.European biophysics journal : EBJ · 2026Review
- Effect of TAR hairpin stabilization on HIV-1 reverse transcription.Journal of virology · 2026Article
- Single-molecule analysis reveals low-temperature misfolding in HIV-1 TAR RNA.Scientific reports · 2026Article
- Mechanism of SARS-CoV-2 Nucleocapsid Protein Phosphorylation-Induced Functional Switch.Viruses · 2026Article
- Specific Nucleic Acid Chaperone Activity of HIV-1 Nucleocapsid Protein Deduced from Hairpin Unfolding.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Force-induced melting and S-DNA pathways for DNA overstretching exhibit distinct kinetics.Nucleic acids research · 2025Article
- A Method for the Sensitive Detection of Base Pairing and Stacking Energies for Damaged and Noncanonical Sequences from Single Molecule Unfolding Experiments.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Optical Tweezers to Study Viruses.Sub-cellular biochemistry · 2024Review
- Structural domains of SARS-CoV-2 nucleocapsid protein coordinate to compact long nucleic acid substrates.Nucleic acids research · 2023Article
- Human FACT subunits coordinate to catalyze both disassembly and reassembly of nucleosomes.Cell reports · 2022Article
- Single-molecule mechanical studies of chaperones and their clients.Biophysics reviews · 2022Review
- POTATO: Automated pipeline for batch analysis of optical tweezers data.Biophysical journal · 2022Article
- RNA Structural Requirements for Nucleocapsid Protein-Mediated Extended Dimer Formation.Viruses · 2022Article
- Overview of the Nucleic-Acid Binding Properties of the HIV-1 Nucleocapsid Protein in Its Different Maturation States.Viruses · 2020Review
- Nucleocapsid Protein Precursors NCp9 and NCp15 Suppress ATP-Mediated Rescue of AZT-Terminated Primers by HIV-1 Reverse Transcriptase.Antimicrobial agents and chemotherapy · 2020Article
- The nucleic acid chaperone activity of the HIV-1 Gag polyprotein is boosted by its cellular partner RPL7: a kinetic study.Nucleic acids research · 2020Article
- Significant Differences in RNA Structure Destabilization by HIV-1 GagDp6 and NCp7 Proteins.Viruses · 2020Article
- HIV-1 Nucleocapsid Protein Unfolds Stable RNA G-Quadruplexes in the Viral Genome and Is Inhibited by G-Quadruplex Ligands.ACS infectious diseases · 2019Article
- Exosomal packaging of trans-activation response element (TAR) RNA by HIV-1 infected cells: a pro-malignancy message delivery to cancer cells.Molecular biology reports · 2019Review
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
Abstract
Retroviral nucleocapsid (NC) proteins are nucleic acid chaperones that play a key role in the viral life cycle. During reverse transcription, HIV-1 NC facilitates the rearrangement of nucleic acid secondary structure, allowing the transactivation response (TAR) RNA hairpin to be transiently destabilized and annealed to a cDNA hairpin. It is not clear how NC specifically destabilizes TAR RNA but does not strongly destabilize the resulting annealed RNA-DNA hybrid structure, which must be formed for reverse transcription to continue. By combining single-molecule optical tweezers measurements with a quantitative mfold-based model, we characterize the equilibrium TAR stability and unfolding barrier for TAR RNA. Experiments show that adding NC lowers the transition state barrier height while also dramatically shifting the barrier location. Incorporating TAR destabilization by NC into the mfold-based model reveals that a subset of preferential protein binding sites is responsible for the observed changes in the unfolding landscape, including the unusual shift in the transition state. We measure the destabilization induced at these NC binding sites and find that NC preferentially targets TAR RNA by binding to specific sequence contexts that are not present on the final annealed RNA-DNA hybrid structure. Thus, specific binding alters the entire RNA unfolding landscape, resulting in the dramatic destabilization of this specific structure that is required for reverse transcription.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.