Related ArticlesStructure of an RNA hairpin loop with a 5'-CGUUUCG-3' loop motif by heteronuclear NMR spectroscopy and distance geometry.
Biochemistry. 1997 Nov 18;36(46):13989-4002
Authors: Sich C, Ohlenschläger O, Ramachandran R, Görlach M, Brown LR
Structural features of a 19-nucleotide RNA hairpin loop (5'-GGCGUACGUUUCGUACGCC-3'), a loop motif which occurs in eukaryotic 18S rRNA, have been derived using multidimensional heteronuclear NMR spectroscopy in combination with local conformational analysis and torsion angle distance geometry followed by restrained energy minimization. A method to obtain both the 3JC4'P3' and 3JC4'P5' coupling constants from a set of spin-echo difference constant time HSQC spectra is introduced, and it is shown how these couplings can be assigned to the backbone angles beta and epsilon. A total of 280 distance constraints as well as 132 homo- and heteronuclear three-bond scalar coupling constants were derived from the NMR data. The structure which has been determined is a pentaloop rather than a triloop with no base pairing between G8 and C12. G8 is pointed to the minor groove where it forms a base triplet with C7-G13 that is further stabilized by hydrogen bonding to the 2'-hydroxyl group of C7. C12 is directed to the major groove where its conformation is stabilized by hydrogen bonding between O2 and HO2'. The NMR data suggest two possible, interconverting conformations with stacking of bases U10-G8 or U11-C7. Overall, the loop provides a variety of interaction sites for RNA or protein interactions.
[NMR paper] NMR structures of loop B RNAs from the stem-loop IV domain of the enterovirus interna
NMR structures of loop B RNAs from the stem-loop IV domain of the enterovirus internal ribosome entry site: a single C to U substitution drastically changes the shape and flexibility of RNA.
Related Articles NMR structures of loop B RNAs from the stem-loop IV domain of the enterovirus internal ribosome entry site: a single C to U substitution drastically changes the shape and flexibility of RNA.
Biochemistry. 2004 May 18;43(19):5757-71
Authors: Du Z, Ulyanov NB, Yu J, Andino R, James TL
The 5'-untranslated region of positive-strand RNA viruses...
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[NMR paper] NMR structure of the 3' stem-loop from human U4 snRNA.
NMR structure of the 3' stem-loop from human U4 snRNA.
Related Articles NMR structure of the 3' stem-loop from human U4 snRNA.
Nucleic Acids Res. 2002 Oct 15;30(20):4371-9
Authors: Comolli LR, Ulyanov NB, Soto AM, Marky LA, James TL, Gmeiner WH
The NMR structure of the 3' stem-loop (3'SL) from human U4 snRNA was determined to gain insight into the structural basis for conservation of this stem-loop sequence from vertebrates. 3'SL sequences from human, rat, mouse and chicken U4 snRNA each consist of a 7 bp stem capped by a UACG tetraloop. No...
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[NMR paper] NMR structure of the second intracellular loop of the alpha 2A adrenergic receptor: e
NMR structure of the second intracellular loop of the alpha 2A adrenergic receptor: evidence for a novel cytoplasmic helix.
Related Articles NMR structure of the second intracellular loop of the alpha 2A adrenergic receptor: evidence for a novel cytoplasmic helix.
Biochemistry. 2002 Mar 19;41(11):3596-604
Authors: Chung DA, Zuiderweg ER, Fowler CB, Soyer OS, Mosberg HI, Neubig RR
A major, unresolved question in signal transduction by G protein coupled receptors (GPCRs) is to understand how, at atomic resolution, a GPCR activates a G protein. A...
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[NMR paper] NMR structure of stem-loop SL2 of the HIV-1 psi RNA packaging signal reveals a novel
NMR structure of stem-loop SL2 of the HIV-1 psi RNA packaging signal reveals a novel A-U-A base-triple platform.
Related Articles NMR structure of stem-loop SL2 of the HIV-1 psi RNA packaging signal reveals a novel A-U-A base-triple platform.
J Mol Biol. 2000 May 26;299(1):145-56
Authors: Amarasinghe GK, De Guzman RN, Turner RB, Summers MF
The genome of the human immunodeficiency virus type-1 (HIV-1) contains a stretch of approximately 120 nucleotides known as the psi-site that is essential for RNA packaging during virus assembly. These...
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[NMR paper] A hairpin-loop conformation in tandem repeat sequence of the ice nucleation protein r
A hairpin-loop conformation in tandem repeat sequence of the ice nucleation protein revealed by NMR spectroscopy.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles A hairpin-loop conformation in tandem repeat sequence of the ice nucleation protein revealed by NMR spectroscopy.
FEBS Lett. 1997 Jun 9;409(2):227-31
Authors: Tsuda S, Ito A, Matsushima N
The 1H-NMR spectrum of a synthetic 24-residue peptide (A1-G-V-D-S-S-L-I-A-G-Y-G-S-T-Q-T-S-G-S-D-S-A-L-T24; INP24),...
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[NMR paper] A hairpin-loop conformation in tandem repeat sequence of the ice nucleation protein r
A hairpin-loop conformation in tandem repeat sequence of the ice nucleation protein revealed by NMR spectroscopy.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles A hairpin-loop conformation in tandem repeat sequence of the ice nucleation protein revealed by NMR spectroscopy.
FEBS Lett. 1997 Jun 9;409(2):227-31
Authors: Tsuda S, Ito A, Matsushima N
The 1H-NMR spectrum of a synthetic 24-residue peptide (A1-G-V-D-S-S-L-I-A-G-Y-G-S-T-Q-T-S-G-S-D-S-A-L-T24; INP24),...
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[NMR paper] A model of the iron responsive element RNA hairpin loop structure determined from NMR
A model of the iron responsive element RNA hairpin loop structure determined from NMR and thermodynamic data.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles A model of the iron responsive element RNA hairpin loop structure determined from NMR and thermodynamic data.
Biochemistry. 1996 Oct 22;35(42):13586-96
Authors: Laing LG, Hall KB
The iron responsive element (IRE) is a conserved RNA structure that is found in the 5' UTR of ferritin mRNA and in the 3' UTR of transferrin receptor mRNA....
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[NMR paper] The importance of a single G in the hairpin loop of the iron responsive element (IRE)
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.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles 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
Authors: Sierzputowska-Gracz H, McKenzie RA, Theil EC
Noncoding sequences...