Investigation of adenosine base ionization in the hairpin ribozyme by nucleotide analog interference mapping

RNA

Volumn 7, Issue 10, 2001, Pages 1454-1463

  Ryder, Sean P ^a   Oyelere, Adegboyega K ^a   Padilla, Jenifer L ^a   Klostermeier, Dagmar ^b   Millar, David P ^b   Strobel, Scott A ^a  

^a YALE UNIVERSITY   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

FRET; pKa perturbation; Reaction mechanism; RNA catalysis

Indexed keywords

ADENOSINE; NUCLEOTIDE DERIVATIVE; RIBOZYME;

ACID BASE BALANCE; ARTICLE; CATALYST; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME MECHANISM; IONIZATION; PRIORITY JOURNAL; PROTEIN DEGRADATION; RNA STRUCTURE;

ADENOSINE; BASE SEQUENCE; CATALYSIS; NUCLEIC ACID CONFORMATION; NUCLEOTIDES; RNA, CATALYTIC; TRANSCRIPTION, GENETIC;

EID: 0034757632     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (34)

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3. Ribbons
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8. Inter-domain cross-linking and molecular modelling of the hairpin ribozyme
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10. Use of cis- and trans-ribozymes to remove 5′ and 3′ heterogeneities from milligrams of in vitro transcribed RNA
11. Crystal structure of a hepatitis delta virus ribozyme
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14. Formycin A and its N-methyl analogues, specific inhibitors of E. Coli purine nucleoside phosphorylase (PNP): Induced tautomeric shifts on binding to enzyme, and enzyme-ligand fluorescence resonance energy transfer
15. Helical junctions as determinants for RNA folding: Origin of tertiary structure stability of the hairpin ribozyme
16. Nucleosides and nucleotides. 184. Synthesis and conformational investigation of antifixed 3-deaza-3-halopurine ribonucleotides
17. The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone
18. An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis
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21. Protein structure, ribonuclease-S and nucleotide interactions
22. Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis
23. Chemical probing of RNA by nucleotide analog interference mapping
24. Nucleotide analog interference mapping of the hairpin ribozyme: Implications for secondary and tertiary structure formation
25. Base and sugar requirements for RNA cleavage of essential nucleoside residues in internal loop B of the hairpin ribozyme: Implications for secondary structure
26. X-ray crystallographic studies of alanine-65 variants of carbonic anhydrase II reveal the structural basis of compromised proton transfer in catalysis
27. Defining the chemical groups essential for Tetrahymena group I intron function by nucleotide analog interference mapping
28. Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction
29. Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer
30. Fluorescence studies of nucleotides and polynucleotides
31. Fluorescence emission properties of 8-azapurines and their nucleosides, and application to the kinetics of the reverse synthetic reaction of purine nucleoside phosphorylase
32. The role of essential pyrimidines in the hairpin ribozyme-catalysed reaction