Related ArticlesThe importance of a single G in the hairpin loop of the iron responsive element (IRE) in ferritin mRNA for structure: an NMR spectroscopy study.
Noncoding sequences regulate the function of mRNA and DNA. In animal mRNAs, iron responsive elements (IREs) regulate the synthesis of proteins for iron storage, uptake and red cell heme formation. Folding of the IRE was indicated previously by reactivity with chemical and enzymatic probes. 1H- and 31P-NMR spectra now confirm the IRE folding; an atypical 31P-spectrum, differential accessibility of imino protons to solvents, multiple long-range NOEs and heat stable subdomains were observed. Biphasic hyperchromic transitions occurred (52 and 73 degrees C). A G-C base pair occurs in the hairpin loop (HL) (based on dimethylsulfate, RNAse T1 previously used, and changes in NMR imino proton resonances typical of G-C base pairs after G/A substitution). Mutation of the hairpin loop also decreased temperature stability and changed the 31P-NMR spectrum; regulation and protein (IRP) binding were previously shown to change. Alteration of IRE structure shown by NMR spectroscopy, occurred at temperatures used in studies of IRE function, explaining loss of IRP binding. The effect of the HL mutation on the IRE emphasizes the importance of HL structure in other mRNAs, viral RNAs (e.g. HIV-TAR), and ribozymes.
[NMR paper] Bending and adaptability to proteins of the cAMP DNA-responsive element: molecular dy
Bending and adaptability to proteins of the cAMP DNA-responsive element: molecular dynamics contrasted with NMR.
Related Articles Bending and adaptability to proteins of the cAMP DNA-responsive element: molecular dynamics contrasted with NMR.
Biophys J. 2000 Aug;79(2):656-69
Authors: Derreumaux S, Fermandjian S
DNA bending is assumed to play a crucial role during recognition of the cAMP-responsive element (CRE) by transcription factors. However, diverging results have been obtained for the bending direction of the unbound double helix. The...
nmrlearner
Journal club
0
11-19-2010 08:29 PM
[NMR paper] Mechanism of neomycin and Rev peptide binding to the Rev responsive element of HIV-1
Mechanism of neomycin and Rev peptide binding to the Rev responsive element of HIV-1 as determined by fluorescence and NMR spectroscopy.
Related Articles Mechanism of neomycin and Rev peptide binding to the Rev responsive element of HIV-1 as determined by fluorescence and NMR spectroscopy.
Biochemistry. 2000 May 16;39(19):5630-41
Authors: Lacourciere KA, Stivers JT, Marino JP
Rev is an essential HIV-1 regulatory protein that binds the Rev responsive element (RRE) within the env gene of the HIV-1 RNA genome and is involved in transport of...
nmrlearner
Journal club
0
11-18-2010 09:15 PM
[NMR paper] Oxidation of guanines in the iron-responsive element RNA: similar structures from che
Oxidation of guanines in the iron-responsive element RNA: similar structures from chemical modification and recent NMR studies.
Related Articles Oxidation of guanines in the iron-responsive element RNA: similar structures from chemical modification and recent NMR studies.
Chem Biol. 1998 Dec;5(12):679-87
Authors: Ciftan SA, Theil EC, Thorp HH
BACKGROUND: The translation or stability of the mRNAs from ferritin, maconitase, erythroid aminoevulinate synthase and the transferrin receptor is controlled by the binding of two iron regulatory proteins...
nmrlearner
Journal club
0
11-17-2010 11:15 PM
[NMR paper] Structure of an RNA hairpin loop with a 5'-CGUUUCG-3' loop motif by heteronuclear NMR
Structure of an RNA hairpin loop with a 5'-CGUUUCG-3' loop motif by heteronuclear NMR spectroscopy and distance geometry.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Structure 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'),...
nmrlearner
Journal club
0
08-22-2010 05:08 PM
[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),...
nmrlearner
Journal club
0
08-22-2010 03:31 PM
[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....
nmrlearner
Journal club
0
08-22-2010 02:20 PM
[NMR paper] An NMR study of the HIV-1 TAR element hairpin.
An NMR study of the HIV-1 TAR element hairpin.
Related Articles An NMR study of the HIV-1 TAR element hairpin.
Biochemistry. 1993 Nov 23;32(46):12522-30
Authors: Jaeger JA, Tinoco I
The TAR hairpin is an important part of the 5' long terminal repeat of HIV-1 and appears to be recognized by a cellular protein. A 14-base model of the native TAR hairpin 5'-GAGC-GCUC-3' (loop bases in square brackets) has been studied by proton, phosphorus, and natural abundance carbon NMR; these results are compared to other published NMR studies of the TAR...
nmrlearner
Journal club
0
08-22-2010 03:01 AM
[NMR paper] An intrinsic curvature towards the minor groove in the cAMP-responsive element DNA fo
An intrinsic curvature towards the minor groove in the cAMP-responsive element DNA found by combined NMR and molecular modelling studies.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles An intrinsic curvature towards the minor groove in the cAMP-responsive element DNA found by combined NMR and molecular modelling studies.
Eur J Biochem. 1999 Feb;259(3):877-86
Authors: Chaoui M, Derreumaux S, Mauffret O, Fermandjian S
The...