Systems for the NMR study of modified nucleoside-dependent, metal-ion induced conformational changes in nucleic acids

scientific article published in January 1995

Systems for the NMR study of modified nucleoside-dependent, metal-ion induced conformational changes in nucleic acids is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1016/S0076-6879(95)61014-6
P698PubMed publication ID8569499

P2093author name stringBrown SC
Agris PF
P2860cites workNMR analysis of helix I from the 5S RNA of Escherichia coliQ27642112
Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-GQ27658049
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Properties of pseudouridine N1 imino protons located in the major groove of an A-form RNA duplexQ30985841
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Structural Features that Give Rise to the Unusual Stability of RNA Hairpins Containing GNRA LoopsQ34001168
Summary: the modified nucleosides of RNA.Q34057777
Codon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modificationQ34164307
Ribosome-mediated incorporation of a non-standard amino acid into a peptide through expansion of the genetic codeQ34377933
Synthesis of oligodeoxynucleotides containing 2-thiopyrimidine residues--a new protection schemeQ34822242
Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloopsQ35060336
Small RNA helices as substrates for aminoacylation and their relationship to charging of transfer RNAsQ35320474
Chemical synthesis of biologically active oligoribonucleotides using beta-cyanoethyl protected ribonucleoside phosphoramiditesQ35877792
RNA - ligand interactions:(I) magnesium binding sites in yeast tRNAPheQ36184432
A C-nucleotide base pair: methylpseudouridine-directed incorporation of formycin triphosphate into RNA catalyzed by T7 RNA polymeraseQ67702505
A frequency-time domain 3D COSY-J technique for measurement of1H−31P coupling constants in oligonucleotidesQ67908759
Purification of transfer RNA species by single-step ion-exchange high-performance liquid chromatographyQ67990541
500-MHz proton NMR evidence for two solution structures of the common arm base-paired segment of wheat germ 5S ribosomal RNAQ68766158
Biostructural chemistry of magnesium ion: characterization of the weak binding sites on tRNA(Phe)(yeast). Implications for conformational change and activityQ68882013
Structure of an unmodified tRNA moleculeQ69718436
Letter: Paramagnetic rare earth ion probes of transfer ribonucleic acid structureQ69778298
Nuclear magnetic resonance signal assignments of purified [13C]methyl-enriched yeast phenylalanine transfer ribonucleic acidQ69888558
Nitrogen-15-labeled yeast tRNAPhe: double and two-dimensional heteronuclear NMR of guanosine and uracil ring NH groupsQ70882841
Structural dynamics of transfer ribonucleic aic carbon-13 nuclear magnetic resonance of [13C]methyl-enriched pure speciesQ72694680
Complete nuclear magnetic resonance signal assignments and initial structural studies of [13C]methyl-enriched yeast transfer ribonucleic acidQ72694684
Utilization of an Escherichia coli mutant for carbon-13 enrichment of tRNA for NMR studiesQ36212824
Fluorine-19 nuclear magnetic resonance studies of the structure of 5-fluorouracil-substituted Escherichia coli transfer RNA.Q36463392
Complete assignment of the imino protons of Escherichia coli valine transfer RNA: two-dimensional NMR studies in waterQ36489648
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Nuclear magnetic resonance study of the codon-anticodon interaction in Bombyx mori tRNA(GCCGly).Q38315628
5-Methylcytidine is required for cooperative binding of Mg2+ and a conformational transition at the anticodon stem-loop of yeast phenylalanine tRNA.Q38315754
Free energy via molecular simulation: applications to chemical and biomolecular systemsQ38648060
RNA folding: pseudoknots, loops and bulgesQ38763796
Unusual anticodon loop structure found in E.coli lysine tRNA.Q40398140
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Preparation of 13C and 15N labelled RNAs for heteronuclear multi-dimensional NMR studiesQ40533971
Chemical synthesis of a biologically active natural tRNA with its minor basesQ40534641
Solid phase synthesis of the 5'-half of the initiator t-RNA from B. subtilisQ40537513
Manganese(II) as a paramagnetic probe of the tertiary structure of transfer RNAQ40787042
Magnetic resonance studies of the conformation of enzyme-bound adenylyl(3' → 5')uridine and adenosine 5'-triphosphate on RNA polymerase from Escherichia coliQ40795995
Wobble position modified nucleosides evolved to select transfer RNA codon recognition: A modified-wobble hypothesisQ41149557
Predicting the three-dimensional folding of transfer RNA with a computer modeling protocolQ41768175
Structure of the ribotrinucleoside diphosphate codon UpUpC bound to tRNAPhe from yeast. A time-dependent transferred nuclear Overhauser enhancement study.Q42247846
Aminoacyl-tRNA synthetase and U54 methyltransferase recognize conformations of the yeast tRNA(Phe) anticodon and T stem/loop domainQ42684160
Europium as a fluorescent probe of transfer RNA structureQ43629964
Comparative NMR study of An-bulge loops in DNA duplexes: intrahelical stacking of A, A-A, and A-A-A bulge loopsQ43764795
Multinuclear NMR studies of DNA hairpins. 1. Structure and dynamics of d(CGCGTTGTTCGCG).Q43820812
The T-arm of tRNA is a substrate for tRNA (m5U54)-methyltransferaseQ43978098
The combination of symbolic and numerical computation for three-dimensional modeling of RNA.Q44025473
The crystal and molecular structure of 6-thioguanineQ44138408
Transfer RNA contains sites of localized positive charge: carbon NMR studies of [13C]methyl-enriched Escherichia coli and yeast tRNAPheQ44188669
Recognition of tertiary structure in tRNAs by Rh(phen)2phi3+, a new reagent for RNA structure-function mappingQ44655171
Role of tRNA modification in translational fidelityQ44657710
A magnesium-induced conformational transition in the loop of a DNA analog of the yeast tRNA(Phe) anticodon is dependent on RNA-like modifications of the bases of the stemQ44856353
The role of 5-methylcytidine in the anticodon arm of yeast tRNA(Phe): site-specific Mg2+ binding and coupled conformational transition in DNA analogsQ44856356
Site-selected introduction of modified purine and pyrimidine ribonucleosides into RNA by automated phosphoramidite chemistry.Q44862676
Fluorine-19 NMR studies of the thermal unfolding of 5-fluorouracil-substitutedEscherichia colivaline transfer RNAQ44946293
Conformational analysis of the deoxyribofuranose ring in DNA by means of sums of proton-proton coupling constants: a graphical methodQ45077763
Structure of an unusually stable RNA hairpinQ46105986
An all atom force field for simulations of proteins and nucleic acidsQ46625508
Prevention of translational frameshifting by the modified nucleoside 1-methylguanosine.Q50195341
Conversion of a methionine initiator tRNA into a tryptophan-inserting elongator tRNA in vivoQ52231840
Conformational transitions using molecular dynamics with minimum biasing.Q52392499
Torsion angle approach to nucleic acid distance geometry: TANDYQ52438690
Nucleoside modifications stabilize Mg2+ binding in Escherichia coli tRNA(Val): an imino proton NMR investigation.Q52513396
CHARMM: A program for macromolecular energy, minimization, and dynamics calculationsQ53340989
NMR study of nitrogen-15-labeled Escherichia coli valine transfer RNA.Q54667269
Effects of single-base bulges on intercalator binding to small RNA and DNA hairpins and a ribosomal RNA fragment.Q54733719
NMR studies of ion binding to Escherichia coli tRNAPhe.Q54794766
Two-dimensional hetero-TOCSY-NOESY. Correlation of phosphorus-31 resonances with anomeric and aromatic proton resonances in RNAQ57567810
Modified bases and aminoacylationQ58987884
The automated chemical synthesis of long oligoribuncleotides using 2'-O-silylated ribonucleoside 3'-O-phosphoramidites on a controlled-pore glass support: synthesis of a 43-nucleotide sequence similar to the 3'-half molecule of an Escherichia coli foQ59485876
Determination of nucleic acid backbone conformation by 1H NMRQ67534462
Errors in RNA NOESY distance measurements in chimeric and hybrid duplexes: differences in RNA and DNA proton relaxationQ67534471
P407language of work or nameEnglishQ1860
P304page(s)270-299
P577publication date1995-01-01
P1433published inMethods in EnzymologyQ2076903
P1476titleSystems for the NMR study of modified nucleoside-dependent, metal-ion induced conformational changes in nucleic acids
P478volume261

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cites work (P2860)
Q27732234Design, biological activity and NMR-solution structure of a DNA analogue of yeast tRNA(Phe) anticodon domain
Q44871741Experimental models of protein-RNA interaction: isolation and analyses of tRNA(Phe) and U1 snRNA-binding peptides from bacteriophage display libraries
Q34311978Identification and characterization of metal ion binding sites in RNA.
Q34064391Synthesis and studies on the effect of 2-thiouridine and 4-thiouridine on sugar conformation and RNA duplex stability

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