Structural features of the trans-activation response RNA element of equine infectious anemia virus.
Abstract: A 25-nucleotide RNA with the sequence of the trans-activation response (TAR) element of equine infectious anemia virus (EIAV) was analyzed by biochemical methods and by one- and two-dimensional NMR spectroscopy. NMR, nuclease probing, and polyacrylamide gel migration rates show that the RNA consists of an A-helical stem capped by two non-Watson-Crick U-G base pairs and a compact four-nucleotide loop. The loop is stabilized by base stacking, with loop nucleotides C12 and C15 stacked upon U11 and G16, respectively. Near the 5' end of the molecule, the stem contains a bulge at nucleotide C2, most likely a result of base pairing between G1 and C25. A method for distinguishing RNA stem-loops from palindromic dimers is described and was used to confirm that the EIAV TAR RNA has a stem-loop structure at conditions used for NMR spectroscopy. RNase A and RNase T1 cleavage patterns are consistent with the structural features derived from the NMR data.
Publication Date: 1993-02-02 PubMed ID: 8381023DOI: 10.1021/bi00055a015Google Scholar: Lookup
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- Journal Article
- Research Support
- Non-U.S. Gov't
- Research Support
- U.S. Gov't
- Non-P.H.S.
Summary
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This study looks at the structural features of a specific RNA sequence in the equine infectious anemia virus (EIAV) using various biochemical methods and spectroscopy techniques.
Objective of the Research
- The main objective of the research was to investigate the structural features of a 25-nucleotide RNA with the sequence of the trans-activation response (TAR) element belonging to the equine infectious anemia virus (EIAV). The researchers wanted to gain a deeper understanding of the particular structure that this element RNA assumes.
Methods Used
- Several techniques were used to conduct this investigation, including biochemical methods, one- and two-dimensional NMR spectroscopy, nuclease probing, and polyacrylamide gel migration rates.
- A method was also described for distinguishing RNA stem-loops from palindromic dimers to ensure the RNA element had a specific stem-loop structure at conditions used for NMR spectroscopy.
Results and Findings
- The analysis revealed that the RNA sequence consists of an A-helical stem capped by two non-Watson-Crick U-G base pairs and a compact four-nucleotide loop.
- The compact four-nucleotide loop is held together by base stacking, with its loop nucleotides C12 and C15 stacked upon U11 and G16 respectively.
- The research also found that near the 5′ end of the molecule, the stem contains a bulge at the C2 nucleotide, which is mainly due to base pairing between G1 and C25.
Implications of the Research
- The RNase A and RNase T1 cleavage patterns are consistent with the structural features derived from the NMR data.
- This research provides useful insights about the molecular structure of the TAR RNA in EIAV, which is crucial for understanding the virus and could potentially contribute to the development of novel treatment strategies.
Cite This Article
APA
Hoffman DW, Colvin RA, Garcia-Blanco MA, White SW.
(1993).
Structural features of the trans-activation response RNA element of equine infectious anemia virus.
Biochemistry, 32(4), 1096-1104.
https://doi.org/10.1021/bi00055a015 Publication
Researcher Affiliations
- Department of Microbiology, Duke University Medical Center, Durham, North Carolina 27710.
MeSH Terms
- Base Composition
- Base Sequence
- DNA, Viral
- Electrophoresis, Polyacrylamide Gel
- HIV Long Terminal Repeat
- HIV-1 / genetics
- Infectious Anemia Virus, Equine / genetics
- Magnetic Resonance Spectroscopy
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA, Viral / chemistry
- Ribonucleases / metabolism
- Sequence Homology, Nucleic Acid
- Transcriptional Activation / genetics
Citations
This article has been cited 6 times.- Qi X, Wang X, Wang S, Lin Y, Jiang C, Ma J, Zhao L, Lv X, Shen R, Wang F, Kong X, Su Z, Zhou J. Genomic analysis of an effective lentiviral vaccine-attenuated equine infectious anemia virus vaccine EIAV FDDV13.. Virus Genes 2010 Aug;41(1):86-98.
- Holland JA, Hoffman DW. Structural features and stability of an RNA triple helix in solution.. Nucleic Acids Res 1996 Jul 15;24(14):2841-8.
- Howe PW, Nagai K, Neuhaus D, Varani G. NMR studies of U1 snRNA recognition by the N-terminal RNP domain of the human U1A protein.. EMBO J 1994 Aug 15;13(16):3873-81.
- Sierzputowska-Gracz H, McKenzie RA, Theil EC. The importance of a single G in the hairpin loop of the iron responsive element (IRE) in ferritin mRNA for structure: an NMR spectroscopy study.. Nucleic Acids Res 1995 Jan 11;23(1):146-53.
- Gao X, Jeffs PW. Sequence-dependent conformational heterogeneity of a hybrid DNA.RNA dodecamer duplex.. J Biomol NMR 1994 May;4(3):367-84.
- Hoffman DW, White SW. NMR analysis of the trans-activation response (TAR) RNA element of equine infectious anemia virus.. Nucleic Acids Res 1995 Oct 25;23(20):4058-65.
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