CoChat
Sign Up
Cited by 189

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch

Ren, Aiming, Rajashankar, Kanagalaghatta R., Patel, Dinshaw J.·2012·Nature
DOI 10.1038/nature11152PMC PMC3744881
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/nature11152

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

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?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 31

  1. Mironov, A. S. et al. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell 111, 747–756 (2002) · DOI
  2. Winkler, W., Nahvi, A. & Breaker, R. R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419, 952–956 (2002) · DOI
  3. Nudler, E. & Mironov, A. S. The riboswitch control of bacterial metabolism. Trends Biochem. Sci. 29, 11–17 (2004) · DOI
  4. Winkler, W. C. & Breaker, R. R. Regulation of bacterial gene expression by riboswitches. Annu. Rev. Microbiol. 59, 487–517 (2005) · DOI
  5. Serganov, A. & Patel, D. J. Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. Nature Rev. Genet. 8, 776–790 (2007) · DOI
  6. Montange, R. K. & Batey, R. T. Riboswitches: emerging themes in RNA structure and function. Annu. Rev. Biophys. 37, 117–133 (2008) · DOI
  7. Serganov, A. et al. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature 441, 1167–1171 (2006) · DOI
  8. Thore, S., Leinungdut, M. & Ban, N. Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science 312, 1208–1211 (2006) · DOI
  9. Lang, K., Rieder, R. & Micura, R. Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach. Nucleic Acids Res. 35, 5370–5378 (2007) · DOI
  10. Anthony, P. C., Perez, C. F., Garcia-Garcia, C. & Block, S. M. Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer. Proc. Natl Acad. Sci. USA 109, 1485–1489 (2012) · DOI
  11. Mironov, A. S. et al. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell 111, 747–756 (2002) · DOI
  12. Serganov, A., Huang, L. & Patel, D. J. Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch. Nature 458, 233–237 (2009) · DOI
  13. Baker, J. L. et al. Widespread genetic switches and toxicity resistance proteins for fluoride. Science 335, 233–235 (2012) · DOI · Paper page
  14. Mandal, M. et al. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113, 577–586 (2003) · DOI
  15. Batey, R. T., Gilbert, S. D. & Montange, R. K. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432, 411–415 (2004) · DOI
  16. Serganov, A. et al. Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem. Biol. 11, 1729–1741 (2004) · DOI
  17. Mandal, M. et al. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306, 275–279 (2004) · DOI
  18. Huang, L., Serganov, A. & Patel, D. J. Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch. Mol. Cell 40, 774–786 (2010) · DOI
  19. Butler, E. B., Xiong, Y., Wang, J. & Strobel, S. A. Structural basis of cooperative ligand binding by the glycine riboswitch. Chem. Biol. 18, 293–298 (2011) · DOI
  20. Heikinheimo, P. et al. Toward a quantum-mechanical description of metal-assisted phosphoryl transfer in pyrophosphatase. Proc. Natl Acad. Sci. USA 98, 3121–3126 (2001) · DOI · Paper page
  21. Auffinger, P., Hays, F. H., Westhof, E. & Ho, P. S. Halogen bonds in biological molecules. Proc. Natl Acad. Sci. USA 101, 16789–16794 (2004) · DOI
  22. Hanna, R. & Doudna, J. A. Metal ions in ribozyme folding and catalysis. Curr. Opin. Chem. Biol. 4, 166–170 (2000) · DOI
  23. Correll, C. C., Freeborn, B., Moore, P. B. & Steitz, T. A. Metals, motifs and recognition in the crystal structure of a 5S RNA domain. Cell 91, 705–712 (1997) · DOI
  24. Cate, J. H., Hanna, R. L. & Doudna, J. A. A magnesium ion core at the heart of a ribozyme domain. Nature Struct. Biol. 4, 553–558 (1997) · DOI
  25. Cromie, M. J., Shi, Y., Latifi, T. & Groisman, E. A. An RNA sensor for intracellular Mg2+. Cell 125, 71–84 (2006) · DOI
  26. Pikovskaya, O. et al. Preparation and crystallization of riboswitch-ligand complexes. Methods Mol. Biol. 540, 115–128 (2009) · DOI
  27. Pape, T. & Schneider, T. R. HKL2MAP: a graphical user interface for phasing with SHELX programs. J. Appl. Cryst. 37, 843–844 (2004) · DOI
  28. Adams, P. D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D 58, 1948–1954 (2002) · DOI · Paper page
  29. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004) · DOI · Paper page
  30. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240–255 (1997) · DOI
  31. Feig, A. L. & Uhlenbeck, O. C. in The RNA World 2nd edn (eds Gesteland, R. F., Cech, T. R. & Atkins, J. F. ) 287–319 (Cold Spring Harbor Laboratory Press, 1999)

Cited by

Sorted by citations

See all 189

Metadata

Authors
Ren, A., Rajashankar, K. R., & Patel, D. J.
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2012-05-13
Volume
486
Issue
7401
Pages
85-89
ISSN
  • 0028-0836
  • 1476-4687
DOI
10.1038/nature11152
PMC
PMC3744881
Cited by
189
References
1
Language
en
Licence
www.springer.com/tdm (tdm)

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