Solution structure of the HIV-1 frameshift inducing stem-loop RNA

Staple, David W.; Butcher, Samuel E.

doi:10.1093/nar/gkg654

Cited by 61 publications

(77 citation statements)

References 31 publications

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“…Further, it is unique in describing RNA dynamics at atomic resolution (Butcher et al 2000;Carlomagno et al 2013;Chowdhury et al 2006;D'Souza et al 2004;Davis et al 2005;Duszczyk et al 2011;Ferner et al 2009;Furtig et al 2003;HouckLoomis et al 2011;Keane et al 2015;Marchanka et al 2015;Sashital et al 2004;Staple and Butcher 2003;Wacker et al 2011). In fact, dynamics ranging from sub nanoseconds to seconds have been found to be essential to understand RNA function Rinnenthal et al 2011).…”

Section: Introductionmentioning

confidence: 99%

19F-labeling of the adenine H2-site to study large RNAs by NMR spectroscopy

et al. 2015

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In comparison to proteins and protein complexes, the size of RNA amenable to NMR studies is limited despite the development of new isotopic labeling strategies including deuteration and ligation of differentially labeled RNAs. Due to the restricted chemical shift dispersion in only four different nucleotides spectral resolution remains limited in larger RNAs. Labeling RNAs with the NMR-active nucleus 19

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Section: Introductionmentioning

confidence: 99%

19F-labeling of the adenine H2-site to study large RNAs by NMR spectroscopy

et al. 2015

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“…[6,7] The frameA C H T U N G T R E N N U N G shift event is induced by two RNA elements between the gag and pol genes in the viral RNA: a heptanucleotide slippery sequence (UUUUUUA) within which the frameA C H T U N G T R E N N U N G shift occurs, and a highly conserved stem-loop structure immediately downstream from the slippery site (Figure 1 A). [1,2,8] We determined the structure of the stem loop of the HIV-1 frameA C H T U N G T R E N N U N G shift site by NMR spectroscopy [9,10] (Figure 1 A, B). The stem loop is highly thermostable, with T m > 90 8C.…”

Section: Introductionmentioning

confidence: 99%

Guanidinoneomycin B Recognition of an HIV‐1 RNA Helix

et al. 2007

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Aminoglycoside antibiotics are small-molecule drugs that bind RNA. The affinity and specificity of aminoglycoside binding to RNA can be increased through chemical modification, such as guanidinylation. Here, we report the binding of guanidinoneomycin B (GNB) to an RNA helix from the HIV-1 frameshift site. The binding of GNB increases the melting temperature (T(m)) of the frameshift-site RNA by at least 10 degrees C, to a point at which a melting transition is not even observed in 2 M urea. A structure of the complex was obtained by using multidimensional heteronuclear NMR spectroscopic methods. We also used a novel paramagnetic-probe assay to identify the site of GNB binding to the surface of the RNA. GNB makes major-groove contacts to two sets of Watson-Crick bases and is in van der Waals contact with a highly structured ACAA tetraloop. Rings I and II of GNB fit into the major groove and form the binding interface with the RNA, whereas rings III and IV are exposed to the solvent and disordered. The binding of GNB causes a broadening of the major groove across the binding site.

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“…Easily measured one-bond 1 H-15 N and 1 H-13 C RDCs provide long-range orientational information that complements the local structural restraints provided by NOE and torsion angle data (Tolman, et al 1995;Bax 2003;Lipsitz and Tjandra 2004). Inclusion of RDC data can significantly improve the precision of DNA and RNA structures (Vermeulen, et al 2000;Padrta, et al 2002;Staple and Butcher 2003;Lipsitz and Tjandra 2004;Davis, et al 2005;Latham, et al 2005;Richards, et al 2006). …”

Section: Introductionmentioning

confidence: 99%

Comparison of alignment tensors generated for native tRNAVal using magnetic fields and liquid crystalline media

et al. 2007

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SummaryResidual dipolar couplings (RDCs) complement standard NOE distance and J-coupling torsion angle data to improve the local and global structure of biomolecules in solution. One powerful application of RDCs is for domain orientation studies, which are especially valuable for structural studies of nucleic acids, where the local structure of a double helix is readily modeled and the orientations of the helical domains can then be determined from RDC data. However, RDCs obtained from only one alignment media generally result in degenerate solutions for the orientation of multiple domains. In protein systems, different alignment media are typically used to eliminate this orientational degeneracy, where the combination of RDCs from two (or more) independent alignment tensors can be used to overcome this degeneracy. It is demonstrated here for native E. coli tRNA Val that many of the commonly used liquid crystalline alignment media result in very similar alignment tensors, which does not eliminate the 4-fold degeneracy for orienting the two helical domains in tRNA. The intrinsic magnetic susceptibility anisotropy (MSA) of the nucleobases in tRNA Val was also used to obtain RDCs for magnetic alignment at 800 and 900 MHz. While these RDCs yield a different alignment tensor, the specific orientation of this tensor combined with the high rhombicity for the tensors in the liquid crystalline media only eliminates two of the four degenerate orientations for tRNA Val . Simulations are used to show that, in optimal cases, the combination of RDCs obtained from liquid crystalline medium and MSA-induced alignment can be used to obtain a unique orientation for two helical domains in tRNA Val .

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Solution structure of the HIV-1 frameshift inducing stem-loop RNA

Cited by 61 publications

References 31 publications

19F-labeling of the adenine H2-site to study large RNAs by NMR spectroscopy

19F-labeling of the adenine H2-site to study large RNAs by NMR spectroscopy

Guanidinoneomycin B Recognition of an HIV‐1 RNA Helix

Comparison of alignment tensors generated for native tRNAVal using magnetic fields and liquid crystalline media

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