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A Conserved Hairpin Structure Predicted for the Poly(A) Signal of Human and Simian Immunodeficiency Viruses
Open accessAbstract
A comparative sequence analysis of part of the RNA genome containing the poly(A) signal of different groups of immunodeficiency viruses, including human types 1 and 2, simian types mandrill, african green monkey, and sykes, reveals the conservation of certain structural features despite the divergence in sequence. In all cases, the AAUAAA signal was found to be flanked by nucleotide segments that can basepair, thus forming a hairpin structure with the poly(A) signal in the single-stranded loop. The fact that both this stem-loop structure and its thermodynamic stability are well conserved suggests a biological function for this structure motif [corrected]. Consistent with this idea, we demonstrate that stabilization or destabilization of the stem region does severely inhibit the replication potential of the HIV-1 virus.
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In HIV-1, the polyA signal forms a stem-loop motif that could facilitate suppression of the polyA signal at the 5′ end of the transcript.
“Structure prediction and biochemical approaches suggest that in HIV-1, the polyA signal forms a stem-loop motif that could facilitate suppression of the polyA signal at the 5′ end of the transcript (Berkhout et al. 1995, Das et al. 1999, Klasens et al. 1999).”
From Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication (2026) · cites this paper as Berkhout et al. 1995
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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
“Structure prediction and biochemical approaches suggest that in HIV-1, the polyA signal forms a stem-loop motif that could facilitate suppression of the polyA signal at the 5 end of the transcript (Berkhout et al. 1995 , Das et al. 1999 , Klasens et al. 1999 ).”
Metadata
- Authors
- Berkhout, B., Klaver, B., & Das, A. T.
- Affiliations
- Amsterdam UMC Location University of Amsterdam (NL)
- Venue
- Virology
- Publisher
- Elsevier BV
- Published
- 1995-02
- Volume
- 207
- Issue
- 1
- Pages
- 276-281
- ISSN
- 0042-6822 (ISSN-L)
- OpenAlex
- W2007550065
- Cited by
- 57
- References
- 0
- Citations by year
- 2025: 1 · 2024: 1 · 2023: 1 · 2021: 2 · 2020: 2 · 2019: 1 · 2018: 1 · 2017: 1 · 2015: 1 · 2014: 1 · 2013: 1 · 2012: 3
- FWCI
- 1.49
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Virology (publishedVersion)
- PubMed (publishedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Pure Amsterdam UMC (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- polyadenylation signal, HIV-1, simian immunodeficiency virus, hairpin structure, stem-loop structure, RNA secondary structure, thermodynamic stability, viral RNA genome, HIV-1 replication, sequence conservation
- MeSH terms
- Algorithms, Animals, Base Composition, Base Sequence, Cell Line, Humans, Molecular Sequence Data, Mutation, Nucleic Acid Conformation, Phylogeny, Poly A, Primates, RNA, Messenger, RNA, Viral, Genetic Variation, Virus Replication, Simian Immunodeficiency Virus, HIV-1, HIV-2, Sequence Alignment
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