Publications

2011

Warner LR, Varga K, Lange OF, Baker SL, Baker D, Sousa MC, Pardi A. Structure
of the BamC Two-Domain Protein Obtained by Rosetta with a Limited NMR Data Set. J
Mol Biol. 2011 Aug 5;411(1):83-95. Epub 2011 May 23. PubMed PMID: 21624375.
Structure of the BamC Two-Domain Protein Obtained by Rosetta with a Limited NMR Data Set. Warner LR, Varga K, Lange OF, Baker SL, Baker D, Sousa MC, Pardi A. JMol Biol. 2011 Aug 5;411(1):83-95.

2010

Structure and flexibility of the complete periplasmic domain of BamA: the protein insertion machine of the outer membrane. Gatzeva-Topalova PZ, Warner LR, Pardi A, Sousa MC. Structure. 2010 Nov 10;18(11):1492-501.

Ultrafast dynamics show that the theophylline and 3-methylxanthine aptamers employ a conformational capture mechanism for binding their ligands. Lee SW, Zhao L, Pardi A, Xia T. Biochemistry. 2010 Apr 6;49(13):2943-51.

2009

Chemical shift anisotropy of imino 15N nuclei in Watson-Crick base pairs from magic angle spinning liquid crystal NMR and nuclear spin relaxation. Grishaev A, Yao L, Ying J, Pardi A, Bax A. J AM Chem Soc. 2009 Jul 15;131(27):9490-1.

Longitudinal-relaxation-enhanced NMR experiments for the study of nucleic acids in solution. Farjon J, Boisbouvier J, Schanda P, Pardi A, Simorre JP, Brutscher B. J Am Chem Soc. 2009 Jun 24;131(24):8571-7.

NMR chemical exchange as a probe for ligand-binding kinetics in a theophylline-binding RNA aptamer. Latham MP, Zimmermann GR, Pardi A. J Am Chem Soc. 2009 Apr 15;131(14):5052-3.

The cavity-chaperone Skp protects its substrate from aggregation but allows independent folding of substrate domains. Walton TA, Sandoval CM, Fowler CA, Pardi A, Sousa MC. Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1772-7.

Measurement of imino 1H-1H residual dipolar couplings in RNA. Latham MP, Pardi A. J Biomol NMR. 2009 Feb;43(2):121-9.

2008

Solution structure of tRNA Val from refinement of homology model against residual dipolar coupling and SAXS data. Grishaev A, Ying J, Canny MD, Pardi A, Bax A. J Biomol NMR. 2008 Oct;42(2):99-109.

Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme. Boots JL, Canny MD, Azimi E, Pardi A. RNA. 2008 Oct;14(10):2212-22.

High-resolution pyrimidine- and ribose-specific 4D HCCH-COSY spectra of RNA using the filter diagonalization method. Douglas JT, Latham MP, Armstrong GS, Bendiak B, Pardi A.

Imino proton exchange rates imply an induced-fit binding mechanism for the VEGF165-targeting aptamer, Macugen. Lee JH, Jucker F, Pardi A. FEBS Lett. 2008 Jun 11;582(13):1835-9.

Comparison of alignment tensors generated for native tRNA(Val) using magnetic fields and liquid crystalline media. Latham MP, Hanson P, Brown DJ, Pardi A. J Biomol NMR. 2008 Feb;40(2):83-94.

2007

Magnetic field induced residual dipolar couplings of imino groups in nucleic acids from measurements at a single magnetic field. Ying J, Grishaev A, Latham MP, Pardi A, Bax A. (2007) J Biomol NMR. 39 91-6

Influence of hydrostatic pressure and cosolutes on RNA tertiary structure. Downey CD, Crisman RL, Randolph TW, Pardi A. (2007) J Am Chem Soc. 129 9290-1

Thermodynamics and kinetics for base-pair opening in the P1 duplex of the Tetrahymena group I ribozyme. Lee JH, Pardi A. (2007) Nucleic Acids Res. 35 2965–74

Efficient ligation of the Schistosoma hammerhead ribozyme. Canny MD, Jucker FM, Pardi A. (2007) Biochemistry 46 3826-34

2006

Metal ion dependence, thermodynamics, and kinetics for intramolecular docking of a GAAA tetraloop and receptor connected by a flexible linker. Downey CD, Fiore JL, Stoddard CD, Hokas JH, Nesbitt DJ, Pardi A. (2006) Biochemistry 45 3664-73.

2005

A therapeutic aptamer inhibits angiogenesis by specifically targeting the heparin binding domain of VEGF165. Lee JH, Canny MD, De Erkenez A, Krilleke D, Ng YS, Shima DT, Pardi A, Jucker F. (2005) Proc Natl Acad Sci USA 102 18902-7

 Resolution-enhanced base-type-edited HCN experiment for RNA. Van Melckebeke H, Pardi A, Boisbouvier J, Simorre JP, Brutscher B. (2005) J Biomol NMR. 32 263-71


NMR Methods for Studying the Structure and Dynamics of RNA
. Latham M, Brown DJ, McCallum SA, Pardi A. (2005)ChemBioChem. 6 1492-505

 Docking kinetics and equilibrium of a GAAA tetraloop-receptor motif probed by single-molecule FRET. Hodak JH, Downey CD, Fiore JL, Pardi A, Nesbitt DJ. (2005) Proc Natl Acad Sci USA 102 10505-10

 Comparison of the global structure and dynamics of native and unmodified tRNAval. Vermeulen A, McCallum SA, Pardi A. (2005)Biochemistry 44 6024-33

2004

Fast cleavage kinetics of a natural hammerhead ribozyme. Canny MD, Jucker FM, Kellogg E, Khvorova A, Jayasena SD, Pardi A. (2004) J Am Chem Soc. 126 10848-9

2003

Role of a heterogeneous free state in the formation of a specific RNA-theophylline complex. Jucker FM, Phillips RM, McCallum SA, Pardi A. (2003) Biochemistry 42 2560-7

 Refined Solution Structure of the Iron-responsive Element RNA Using Residual Dipolar Couplings. McCallum SA, Pardi A. (2003) J Mol Biol. 326 1037-50

2002

The global conformation of the hammerhead ribozyme determined using residual dipolar couplings. Bondensgaard K, Mollova ET, Pardi A. (2002) Biochemistry 41 11532-42

2001

Refinement of local and long-range structural order in theophylline-binding RNA using (13)C-(1)H residual dipolar couplings and restrained molecular dynamics. Sibille N, Pardi A, Simorre JP, Blackledge M. (2001) J Am Chem Soc. 123 12135-46

Incorporating residual dipolar couplings into the NMR solution structure determination of nucleic acids. Zhou H, Vermeulen A, Jucker FM, Pardi A. (2001) Biopolymers 52 168-80

2000

Active site dynamics in the lead-dependent ribozyme. Hoogstraten CG, Wank JR, Pardi A. (2000) Biochemistry 39 9951-8
 NMR solution structure determination of RNAs. Mollova ET, Pardi A. (2000) Curr Opin Struct Biol. 10 298-302
 Determining DNA Global Structure and DNA Bending by Application of NMR Residual Dipolar Couplings. Vermeulen A, Zhou H, and Pardi A. (2000) J Am Chem Soc. 122 9638-47
 Global Structure of RNA Determined with Residual Dipolar Couplings. Mollova ET, Hansen MR, and Pardi A. (2000) J Am Chem Soc. 122 11561-2
 Molecular interactions and metal binding in the theophylline-binding core of an RNA aptamer. Zimmermann GR, Wick CL, Shields TP, Jenison RD, Pardi A. (2000) RNA 6 659-67

1999

 High-Performance liquid chromatography purification of homogeneous-length RNA produced by trans cleavage with a hammerhead ribozyme. Shields TP, Mollova ET, Ste. Marie L, Hansen MR, and Pardi A. (1999) RNA 5 1259-67

 Identification and characterization of a novel high affinity metal-binding site in the hammerhead ribozyme. Hansen MR, Simorre JP, Hanson P, Mokler V, Bellon L, Beigelman L, and Pardi A. (1999) RNA 5 1099-1104

1998

 Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions. Hansen MR, Mueller L, Pardi A.(1998) Nat Struct Biol. 5 1065-74

 Observation of Long-Range 1H-1H Distances in Solution by Dipolar Coupling Interactions. Hansen MR, Rance M, and Pardi A. (1998) J Am Chem Soc. 120 11210-11

 NMR solution structure of the lead-dependent ribozyme: evidence for dynamics in RNA catalysis. Hoogstraten CG, Legault P, Pardi A. (1998) J Mol Biol. 284 337-50

 Order, dynamics and metal-binding in the lead-dependent ribozyme. Legault P, Hoogstraten CG, Metlitzky E, Pardi A. J Mol Biol. 1998 Nov 27;284(2):325-35.

 Measurement of carbon-phosphorus J coupling constants in RNA using spin-echo difference constant-time HCCH-COSY. Hoogstraten CG, Pardi A. (1998) J Magn Reson. 133 236-40

 A semiconserved residue inhibits complex formation by stabilizing interactions in the free state of a theophylline-binding RNA. Zimmermann GR, Shields TP, Jenison RD, Wick CL, Pardi A. (1998) Biochemistry 37 9186-92

 Structural variation induced by different nucleotides at the cleavage site of the hammerhead ribozyme. Simorre JP, Legault P, Baidya N, Uhlenbeck OC, Maloney L, Wincott F, Usman N, Beigelman L, Pardi A. (1998) Biochemistry 37 4034-44

1997

 RNA aptamers to the peptidyl transferase inhibitor chloramphenicol. Burke DH, Hoffman DC, Brown A, Hansen M, Pardi A, and Gold L. (1997) Chemistry & Biology 4 833-43

 Structure and dynamics of the iron responsive element RNA: implications for binding of the RNA by iron regulatory binding proteins. Addess KJ, Basilion JP, Klausner RD, Rouault TA, Pardi A. (1997) J Mol Biol. 274 72-83

 Unusual Dynamics and pKa Shift at the Active Site of a Lead-Dependent Ribozyme, Legault P, and Pardi A. (1997) J Am Chem Soc. 119 6621-6628

1996

 Triple-Resonance Experiments for Assignment of Adenine Base Resonances in 13C/15N-Labeled RNA. Simorre JP, Zimmermann GR, Mueller L, and Pardi A. J Am Chem Soc. 118 5316-17