Search results for: Arthur Pardi

Items from 21 to 36 out of 36 results

article

Fast Cleavage Kinetics of a Natural Hammerhead Ribozyme

Marella D. Canny, Fiona M. Jucker, Elizabeth Kellogg, Anastasia Khvorova, more

Journal of the American Chemical Society > 2004 > 126 > 35 > 10848 - 10849

article

Role of a Heterogeneous Free State in the Formation of a Specific RNA−Theophylline Complex ^†

Fiona M. Jucker, Rebecca M. Phillips, Scott A. McCallum, Arthur Pardi

Biochemistry > 2003 > 42 > 9 > 2560 - 2567

article

Refined Solution Structure of the Iron-responsive Element RNA Using Residual Dipolar Couplings

Scott A. McCallum, Arthur Pardi

Journal of Molecular Biology > 2003 > 326 > 4 > 1037-1050

The iron-responsive element (IRE) is a 30nt RNA motif located in the non-coding regions of mRNAs of proteins involved in iron regulation. In humans, the IRE plays a direct role in the control of iron levels by post-transcriptional regulation of the ferritin and transferrin receptor proteins through highly specific recognition by IRE-binding proteins. The IRE fold is representative of many RNA motifs...

article

The Global Conformation of the Hammerhead Ribozyme Determined Using Residual Dipolar Couplings ^†

Kent Bondensgaard, Emilia T. Mollova, Arthur Pardi

Biochemistry > 2002 > 41 > 39 > 11532 - 11542

article

Refinement of Local and Long-Range Structural Order in Theophylline-Binding RNA Using ¹³ C− ¹ H Residual Dipolar Couplings and Restrained Molecular Dynamics

Nathalie Sibille, Arthur Pardi, Jean-Pierre Simorre, Martin Blackledge

Journal of the American Chemical Society > 2001 > 123 > 49 > 12135 - 12146

article

NMR solution structure determination of RNAs

Emilia T Mollova, Arthur Pardi

Current Opinion in Structural Biology > 2000 > 10 > 3 > 298-302

During the past several years, there have been significant advances in NMR solution structure determination of macromolecules. The ability to easily measure residual dipolar couplings, to directly detect NH...N hydrogen bonding interactions and to study much larger macromolecules by the application of heteronuclear experiments that select narrow lines in 2D and 3D spectra of isotopically labeled molecules...

article

NMR solution structure of the lead-dependent ribozyme: evidence for dynamics in RNA catalysis11Edited by I. Tinoco

Charles G Hoogstraten, Pascale Legault, Arthur Pardi

Journal of Molecular Biology > 1998 > 284 > 2 > 337-350

The NMR solution structure of a lead-dependent ribozyme, known as the leadzyme, is presented. This ribozyme is among the smallest of the known catalytic RNAs, with an active site consisting of a six-nucleotide asymmetric internal loop. This loop has a roughly double-helical structure, including a protonated adenine-cytosine wobble base-pair, that positions the cytosine base 5′ to the cleavage site...

article

Order, dynamics and metal-binding in the lead-dependent ribozyme11Edited by I. Tinoco

Pascale Legault, Charles G. Hoogstraten, Elana Metlitzky, Arthur Pardi

Journal of Molecular Biology > 1998 > 284 > 2 > 325-335

The in vitro selected lead-dependent ribozyme is among the smallest and simplest of the known catalytic RNA motifs and has a unique metal ion specificity for divalent lead. The conformation and dynamics of this ribozyme are analyzed here by NMR and chemical probing experiments. Complete assignments of the ¹H, ¹³C, and ¹⁵N resonances have been made, and the NMR chemical shift changes in the presence...

article

Measurement of Carbon-PhosphorusJCoupling Constants in RNA Using Spin-Echo Difference Constant-Time HCCH-COSY

Charles G. Hoogstraten, Arthur Pardi

Journal of Magnetic Resonance > 1998 > 133 > 1 > 236-240

We report a novel NMR technique for the measurement of carbon-phosphorus coupling constants in RNA oligomers. This method, spin-echo difference constant-time HCCH-COSY, takes advantage of the well-dispersed H1' and C1' resonances to analyze couplings involving the more poorly dispersed ribose carbon and phosphorus resonances. The technique was applied to analysis of the ³ J _C ₂ ...

article

Improved distance analysis in RNA using network-editing techniques for overcoming errors due to spin diffusion

Charles G. Hoogstraten, Arthur Pardi

Journal of Biomolecular NMR > 1998 > 11 > 1 > 85-95

Multispin magnetization transfer, or spin diffusion, is a significant source of error in NOESY-derived distance measurements for the determination of nucleic acid solution structures. The BD-NOESY and CBD-NOESY experiments, which allow the measurement of interproton distances with greatly reduced contributions from spin diffusion, have been adapted to structural analysis in RNA oligonucleotides. The...

article

Structure and dynamics of the iron responsive element RNA: implications for binding of the RNA by iron regulatory binding proteins

Kenneth J. Addess, James P. Basilion, Richard D. Klausner, Tracey A. Rouault, more

Journal of Molecular Biology > 1997 > 274 > 1 > 72-83

The iron responsive element (IRE) is a ~30 nucleotide RNA hairpin that is located in the 5' untranslated region of all ferritin mRNAs and in the 3' untranslated region of all transferrin receptor mRNAs. The IREs are bound by two related IRE-binding proteins (IRPs) which help control intracellular levels of iron by regulating the expression of both ferritin and transferrin receptor genes. Multi-dimensional...

article

RNA aptamers to the peptidyl transferase inhibitor chloramphenicol

Donald H. Burke, David C. Hoffman, Analisa Brown, Mark Hansen, more

Chemistry & Biology > 1997 > 4 > 11 > 833-843

Background: The problem of how macromolecules adopt specific shapes to recognize small molecules in their environment is readily addressed through in vitro selections (the SELEX protocol). RNA-antibiotic interactions are particularly attractive systems for study because they provide an opportunity to expand our understanding of molecular recognition by RNA and to facilitate ribosomal modeling. Specifically,...

article

RNA Structure Comes of Age

Olke C. Uhlenbeck, Arthur Pardi, Juli Feigon

Cell > 1997 > 90 > 5 > 833-840

article

A Network of Heterogeneous Hydrogen Bonds in GNRA Tetraloops

Fiona M. Jucker, Hans A. Heus, Ping F. Yip, Ellen H.M. Moors, more

Journal of Molecular Biology > 1996 > 264 > 5 > 968-980

RNA hairpin loops containing a GNRA consensus sequence are the most frequently occurring hairpins in a variety of prokaryotic and eukaryotic RNAs. These tetraloops play important functional roles in RNA folding, in RNA – RNA tertiary interactions and as protein binding sites. Homo and heteronuclear NMR spectroscopy have been used to determine the structures of the most abundant members of the GNRA...

article

Improved measurement of ¹ ³ C, ³ ¹ P J coupling constants in isotopically labeled RNA

Pascale Legault, Fiona M. Jucker, Arthur Pardi

FEBS Letters > 1995 > 362 > 2 > 156-160

3J _C _P coupling constants have been measured in a 99% ¹ ³ C, ¹ ⁵ N labeled lead-dependent ribozyme, known as the leadzyme. These coupling constants were determined by analysis of the intensity of individual crosspeaks in a spin-echo difference constant time HSQC experiment. This procedure permits improved measurement of the ³ J _C ₂ _P ...

article

Distinguishing between duplex and hairpin forms of RNA by ¹ ⁵ N ¹ H heteronuclear NMR

Fareed Aboul-ela, Edward P. Nikonowicz, Arthur Pardi

FEBS Letters > 1994 > 347 > 2-3 > 261-264

A general method is described for distinguishing RNA hairpins from RNA duplexes by application of two-dimensional filtered nuclear Overhauser enhancement spectra on a 1:1 mixture of unlabeled and 99% ¹ ⁵ N-labeled molecules. The method is applied to the RNA dodecamer rGGCGCUUGCGUC which can form an intramolecular hairpin under low salt conditions and a duplex in high salt. This procedure...

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INFONA - science communication portal

Search results for: Arthur Pardi

Fast Cleavage Kinetics of a Natural Hammerhead Ribozyme

Role of a Heterogeneous Free State in the Formation of a Specific RNA−Theophylline Complex ^†

Refined Solution Structure of the Iron-responsive Element RNA Using Residual Dipolar Couplings

The Global Conformation of the Hammerhead Ribozyme Determined Using Residual Dipolar Couplings ^†

Refinement of Local and Long-Range Structural Order in Theophylline-Binding RNA Using ¹³ C− ¹ H Residual Dipolar Couplings and Restrained Molecular Dynamics

NMR solution structure determination of RNAs

NMR solution structure of the lead-dependent ribozyme: evidence for dynamics in RNA catalysis11Edited by I. Tinoco

Order, dynamics and metal-binding in the lead-dependent ribozyme11Edited by I. Tinoco

Measurement of Carbon-PhosphorusJCoupling Constants in RNA Using Spin-Echo Difference Constant-Time HCCH-COSY

Improved distance analysis in RNA using network-editing techniques for overcoming errors due to spin diffusion

Structure and dynamics of the iron responsive element RNA: implications for binding of the RNA by iron regulatory binding proteins

RNA aptamers to the peptidyl transferase inhibitor chloramphenicol

RNA Structure Comes of Age

A Network of Heterogeneous Hydrogen Bonds in GNRA Tetraloops

Improved measurement of ¹ ³ C, ³ ¹ P J coupling constants in isotopically labeled RNA

Distinguishing between duplex and hairpin forms of RNA by ¹ ⁵ N ¹ H heteronuclear NMR

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