Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
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Arthur Pardi

TitleProfessor
InstitutionUniversity of Colorado Boulder
DepartmentChemistry & Biochemistry
Phone303/492-6263

     Bibliographic 
     selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Warner LR, Gatzeva-Topalova PZ, Doerner PA, Pardi A, Sousa MC. Flexibility in the Periplasmic Domain of BamA Is Important for Function. Structure. 2017 Jan 03; 25(1):94-106.
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    2. Xiao Y, Warner LR, Latham MP, Ahn NG, Pardi A. Structure-Based Assignment of Ile, Leu, and Val Methyl Groups in the Active and Inactive Forms of the Mitogen-Activated Protein Kinase Extracellular Signal-Regulated Kinase 2. Biochemistry. 2015 Jul 21; 54(28):4307-19.
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    3. Xiao Y, Liddle JC, Pardi A, Ahn NG. Dynamics of protein kinases: insights from nuclear magnetic resonance. Acc Chem Res. 2015 Apr 21; 48(4):1106-14.
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    4. Rudolph J, Xiao Y, Pardi A, Ahn NG. Slow inhibition and conformation selective properties of extracellular signal-regulated kinase 1 and 2 inhibitors. Biochemistry. 2015 Jan 13; 54(1):22-31.
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    5. Dodevski I, Nucci NV, Valentine KG, Sidhu GK, O'Brien ES, Pardi A, Wand AJ. Optimized reverse micelle surfactant system for high-resolution NMR spectroscopy of encapsulated proteins and nucleic acids dissolved in low viscosity fluids. J Am Chem Soc. 2014 Mar 05; 136(9):3465-74.
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    6. Xiao Y, Lee T, Latham MP, Warner LR, Tanimoto A, Pardi A, Ahn NG. Phosphorylation releases constraints to domain motion in ERK2. Proc Natl Acad Sci U S A. 2014 Feb 18; 111(7):2506-11.
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    7. Dallmann A, Simon B, Duszczyk MM, Kooshapur H, Pardi A, Bermel W, Sattler M. Efficient detection of hydrogen bonds in dynamic regions of RNA by sensitivity-optimized NMR pulse sequences. Angew Chem Int Ed Engl. 2013 Sep 27; 52(40):10487-90.
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    8. 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 05; 411(1):83-95.
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    9. Gatzeva-Topalova PZ, Warner LR, Pardi A, Sousa MC. Structure and flexibility of the complete periplasmic domain of BamA: the protein insertion machine of the outer membrane. Structure. 2010 Nov 10; 18(11):1492-501.
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    10. Lee SW, Zhao L, Pardi A, Xia T. Ultrafast dynamics show that the theophylline and 3-methylxanthine aptamers employ a conformational capture mechanism for binding their ligands. Biochemistry. 2010 Apr 06; 49(13):2943-51.
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    11. Grishaev A, Yao L, Ying J, Pardi A, Bax A. Chemical shift anisotropy of imino 15N nuclei in Watson-Crick base pairs from magic angle spinning liquid crystal NMR and nuclear spin relaxation. J Am Chem Soc. 2009 Jul 15; 131(27):9490-1.
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    12. Farjon J, Boisbouvier J, Schanda P, Pardi A, Simorre JP, Brutscher B. Longitudinal-relaxation-enhanced NMR experiments for the study of nucleic acids in solution. J Am Chem Soc. 2009 Jun 24; 131(24):8571-7.
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    13. Latham MP, Zimmermann GR, Pardi A. NMR chemical exchange as a probe for ligand-binding kinetics in a theophylline-binding RNA aptamer. J Am Chem Soc. 2009 Apr 15; 131(14):5052-3.
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    14. Walton TA, Sandoval CM, Fowler CA, Pardi A, Sousa MC. The cavity-chaperone Skp protects its substrate from aggregation but allows independent folding of substrate domains. Proc Natl Acad Sci U S A. 2009 Feb 10; 106(6):1772-7.
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    15. Latham MP, Pardi A. Measurement of imino 1H-1H residual dipolar couplings in RNA. J Biomol NMR. 2009 Feb; 43(2):121-9.
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    16. Grishaev A, Ying J, Canny MD, Pardi A, Bax A. Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data. J Biomol NMR. 2008 Oct; 42(2):99-109.
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    17. Boots JL, Canny MD, Azimi E, Pardi A. Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme. RNA. 2008 Oct; 14(10):2212-22.
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    18. Douglas JT, Latham MP, Armstrong GS, Bendiak B, Pardi A. High-resolution pyrimidine- and ribose-specific 4D HCCH-COSY spectra of RNA using the filter diagonalization method. J Biomol NMR. 2008 Aug; 41(4):209-19.
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    19. Lee JH, Jucker F, Pardi A. Imino proton exchange rates imply an induced-fit binding mechanism for the VEGF165-targeting aptamer, Macugen. FEBS Lett. 2008 Jun 11; 582(13):1835-9.
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    20. Latham MP, Hanson P, Brown DJ, Pardi A. Comparison of alignment tensors generated for native tRNA(Val) using magnetic fields and liquid crystalline media. J Biomol NMR. 2008 Feb; 40(2):83-94.
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    21. Ying J, Grishaev A, Latham MP, Pardi A, Bax A. Magnetic field induced residual dipolar couplings of imino groups in nucleic acids from measurements at a single magnetic field. J Biomol NMR. 2007 Oct; 39(2):91-6.
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    22. Downey CD, Crisman RL, Randolph TW, Pardi A. Influence of hydrostatic pressure and cosolutes on RNA tertiary structure. J Am Chem Soc. 2007 Aug 01; 129(30):9290-1.
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    23. Lee JH, Pardi A. Thermodynamics and kinetics for base-pair opening in the P1 duplex of the Tetrahymena group I ribozyme. Nucleic Acids Res. 2007; 35(9):2965-74.
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    24. Canny MD, Jucker FM, Pardi A. Efficient ligation of the Schistosoma hammerhead ribozyme. Biochemistry. 2007 Mar 27; 46(12):3826-34.
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    25. Downey CD, Fiore JL, Stoddard CD, Hodak JH, Nesbitt DJ, Pardi A. Metal ion dependence, thermodynamics, and kinetics for intramolecular docking of a GAAA tetraloop and receptor connected by a flexible linker. Biochemistry. 2006 Mar 21; 45(11):3664-73.
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    26. Lee JH, Canny MD, De Erkenez A, Krilleke D, Ng YS, Shima DT, Pardi A, Jucker F. A therapeutic aptamer inhibits angiogenesis by specifically targeting the heparin binding domain of VEGF165. Proc Natl Acad Sci U S A. 2005 Dec 27; 102(52):18902-7.
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    27. Latham MP, Brown DJ, McCallum SA, Pardi A. NMR methods for studying the structure and dynamics of RNA. Chembiochem. 2005 Sep; 6(9):1492-505.
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    28. Van Melckebeke H, Pardi A, Boisbouvier J, Simorre JP, Brutscher B. Resolution-enhanced base-type-edited HCN experiment for RNA. J Biomol NMR. 2005 Aug; 32(4):263-71.
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    29. Hodak JH, Downey CD, Fiore JL, Pardi A, Nesbitt DJ. Docking kinetics and equilibrium of a GAAA tetraloop-receptor motif probed by single-molecule FRET. Proc Natl Acad Sci U S A. 2005 Jul 26; 102(30):10505-10.
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    30. Vermeulen A, McCallum SA, Pardi A. Comparison of the global structure and dynamics of native and unmodified tRNAval. Biochemistry. 2005 Apr 26; 44(16):6024-33.
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    31. Canny MD, Jucker FM, Kellogg E, Khvorova A, Jayasena SD, Pardi A. Fast cleavage kinetics of a natural hammerhead ribozyme. J Am Chem Soc. 2004 Sep 08; 126(35):10848-9.
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    32. Jucker FM, Phillips RM, McCallum SA, Pardi A. Role of a heterogeneous free state in the formation of a specific RNA-theophylline complex. Biochemistry. 2003 Mar 11; 42(9):2560-7.
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    33. McCallum SA, Pardi A. Refined solution structure of the iron-responsive element RNA using residual dipolar couplings. J Mol Biol. 2003 Feb 28; 326(4):1037-50.
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    34. Bondensgaard K, Mollova ET, Pardi A. The global conformation of the hammerhead ribozyme determined using residual dipolar couplings. Biochemistry. 2002 Oct 01; 41(39):11532-42.
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    35. Sibille N, Pardi A, Simorre JP, Blackledge M. Refinement of local and long-range structural order in theophylline-binding RNA using (13)C-(1)H residual dipolar couplings and restrained molecular dynamics. J Am Chem Soc. 2001 Dec 12; 123(49):12135-46.
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    36. Hoogstraten CG, Wank JR, Pardi A. Active site dynamics in the lead-dependent ribozyme. Biochemistry. 2000 Aug 15; 39(32):9951-8.
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    37. Mollova ET, Pardi A. NMR solution structure determination of RNAs. Curr Opin Struct Biol. 2000 Jun; 10(3):298-302.
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    38. Zimmermann GR, Wick CL, Shields TP, Jenison RD, Pardi A. Molecular interactions and metal binding in the theophylline-binding core of an RNA aptamer. RNA. 2000 May; 6(5):659-67.
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    39. Hansen MR, Hanson P, Pardi A. Pf1 filamentous phage as an alignment tool for generating local and global structural information in nucleic acids. J Biomol Struct Dyn. 2000; 17 Suppl 1:365-9.
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    40. Hansen MR, Hanson P, Pardi A. Filamentous bacteriophage for aligning RNA, DNA, and proteins for measurement of nuclear magnetic resonance dipolar coupling interactions. Methods Enzymol. 2000; 317:220-40.
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    41. Shields TP, Mollova E, Ste Marie L, Hansen MR, Pardi A. High-performance liquid chromatography purification of homogenous-length RNA produced by trans cleavage with a hammerhead ribozyme. RNA. 1999 Sep; 5(9):1259-67.
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    42. Hansen MR, Simorre JP, Hanson P, Mokler V, Bellon L, Beigelman L, Pardi A. Identification and characterization of a novel high affinity metal-binding site in the hammerhead ribozyme. RNA. 1999 Aug; 5(8):1099-104.
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    43. Zhou H, Vermeulen A, Jucker FM, Pardi A. Incorporating residual dipolar couplings into the NMR solution structure determination of nucleic acids. Biopolymers. 1999-2000; 52(4):168-80.
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    44. Hansen MR, Mueller L, Pardi A. Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions. Nat Struct Biol. 1998 Dec; 5(12):1065-74.
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    45. Legault P, Hoogstraten CG, Metlitzky E, Pardi A. Order, dynamics and metal-binding in the lead-dependent ribozyme. J Mol Biol. 1998 Nov 27; 284(2):325-35.
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    46. Hoogstraten CG, Legault P, Pardi A. NMR solution structure of the lead-dependent ribozyme: evidence for dynamics in RNA catalysis. J Mol Biol. 1998 Nov 27; 284(2):337-50.
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    47. Hoogstraten CG, Pardi A. Measurement of carbon-phosphorus J coupling constants in RNA using spin-echo difference constant-time HCCH-COSY. J Magn Reson. 1998 Jul; 133(1):236-40.
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    48. Zimmermann GR, Shields TP, Jenison RD, Wick CL, Pardi A. A semiconserved residue inhibits complex formation by stabilizing interactions in the free state of a theophylline-binding RNA. Biochemistry. 1998 Jun 23; 37(25):9186-92.
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    49. Simorre JP, Legault P, Baidya N, Uhlenbeck OC, Maloney L, Wincott F, Usman N, Beigelman L, Pardi A. Structural variation induced by different nucleotides at the cleavage site of the hammerhead ribozyme. Biochemistry. 1998 Mar 24; 37(12):4034-44.
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    50. Hoogstraten CG, Pardi A. Improved distance analysis in RNA using network-editing techniques for overcoming errors due to spin diffusion. J Biomol NMR. 1998 Jan; 11(1):85-95.
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    51. Addess KJ, Basilion JP, Klausner RD, Rouault TA, Pardi A. Structure and dynamics of the iron responsive element RNA: implications for binding of the RNA by iron regulatory binding proteins. J Mol Biol. 1997 Nov 21; 274(1):72-83.
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    52. Burke DH, Hoffman DC, Brown A, Hansen M, Pardi A, Gold L. RNA aptamers to the peptidyl transferase inhibitor chloramphenicol. Chem Biol. 1997 Nov; 4(11):833-43.
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    53. Uhlenbeck OC, Pardi A, Feigon J. RNA structure comes of age. Cell. 1997 Sep 05; 90(5):833-40.
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    54. Zimmermann GR, Jenison RD, Wick CL, Simorre JP, Pardi A. Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA. Nat Struct Biol. 1997 Aug; 4(8):644-9.
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    55. Simorre JP, Legault P, Hangar AB, Michiels P, Pardi A. A conformational change in the catalytic core of the hammerhead ribozyme upon cleavage of an RNA substrate. Biochemistry. 1997 Jan 21; 36(3):518-25.
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    56. Jucker FM, Heus HA, Yip PF, Moors EH, Pardi A. A network of heterogeneous hydrogen bonds in GNRA tetraloops. J Mol Biol. 1996 Dec 20; 264(5):968-80.
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    57. Baeyens KJ, De Bondt HL, Pardi A, Holbrook SR. A curved RNA helix incorporating an internal loop with G.A and A.A non-Watson-Crick base pairing. Proc Natl Acad Sci U S A. 1996 Nov 12; 93(23):12851-5.
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    58. Simorre JP, Zimmermann GR, Mueller L, Pardi A. Correlation of the guanosine exchangeable and nonexchangeable base protons in 13C-/15N-labeled RNA with an HNC-TOCSY-CH experiment. J Biomol NMR. 1996 Mar; 7(2):153-6.
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    59. Simorre JP, Zimmermann GR, Pardi A, Farmer BT, Mueller L. Triple resonance HNCCCH experiments for correlating exchangeable and nonexchangeable cytidine and uridine base protons in RNA. J Biomol NMR. 1995 Dec; 6(4):427-32.
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    60. Jucker FM, Pardi A. Solution structure of the CUUG hairpin loop: a novel RNA tetraloop motif. Biochemistry. 1995 Nov 07; 34(44):14416-27.
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    61. Zimmermann GR, Legault P, Selsted ME, Pardi A. Solution structure of bovine neutrophil beta-defensin-12: the peptide fold of the beta-defensins is identical to that of the classical defensins. Biochemistry. 1995 Oct 17; 34(41):13663-71.
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    62. Legault P, Jucker FM, Pardi A. Improved measurement of 13C, 31P J coupling constants in isotopically labeled RNA. FEBS Lett. 1995 Apr 03; 362(2):156-60.
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    63. Jucker FM, Pardi A. GNRA tetraloops make a U-turn. RNA. 1995 Apr; 1(2):219-22.
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    64. Pardi A. Multidimensional heteronuclear NMR experiments for structure determination of isotopically labeled RNA. Methods Enzymol. 1995; 261:350-80.
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    65. Pardi A. Ribozyme revealed. Nat Struct Biol. 1994 Dec; 1(12):846-9.
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    66. Skalicky JJ, Selsted ME, Pardi A. Structure and dynamics of the neutrophil defensins NP-2, NP-5, and HNP-1: NMR studies of amide hydrogen exchange kinetics. Proteins. 1994 Sep; 20(1):52-67.
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    67. Aboul-ela F, Nikonowicz EP, Pardi A. Distinguishing between duplex and hairpin forms of RNA by 15N-1H heteronuclear NMR. FEBS Lett. 1994 Jun 27; 347(2-3):261-4.
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    68. Jenison RD, Gill SC, Pardi A, Polisky B. High-resolution molecular discrimination by RNA. Science. 1994 Mar 11; 263(5152):1425-9.
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    69. Farmer BT, Müller L, Nikonowicz EP, Pardi A. Unambiguous through-bond sugar-to-base correlations for purines in 13C,15N-labeled nucleic acids: the HsCsNb,HsCs(N)bCb, and HbNbCb experiments. J Biomol NMR. 1994 Jan; 4(1):129-33.
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    70. Legault P, Pardi A. 31P chemical shift as a probe of structural motifs in RNA. J Magn Reson B. 1994 Jan; 103(1):82-6.
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    71. Skalicky JJ, Metzler WJ, Ciesla DJ, Galdes A, Pardi A. Solution structure of the calcium channel antagonist omega-conotoxin GVIA. Protein Sci. 1993 Oct; 2(10):1591-603.
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    72. Nikonowicz EP, Pardi A. An efficient procedure for assignment of the proton, carbon and nitrogen resonances in 13C/15N labeled nucleic acids. J Mol Biol. 1993 Aug 20; 232(4):1141-56.
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    73. Pardi A, Legault P, Nikonowicz EP. Structural studies of catalytic RNAs by heteronuclear multi-dimensional NMR. Nucleic Acids Symp Ser. 1993; (29):116.
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    74. Zhang XL, Selsted ME, Pardi A. NMR studies of defensin antimicrobial peptides. 1. Resonance assignment and secondary structure determination of rabbit NP-2 and human HNP-1. Biochemistry. 1992 Nov 24; 31(46):11348-56.
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    75. Pardi A, Zhang XL, Selsted ME, Skalicky JJ, Yip PF. NMR studies of defensin antimicrobial peptides. 2. Three-dimensional structures of rabbit NP-2 and human HNP-1. Biochemistry. 1992 Nov 24; 31(46):11357-64.
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    76. Nikonowicz EP, Sirr A, Legault P, Jucker FM, Baer LM, Pardi A. Preparation of 13C and 15N labelled RNAs for heteronuclear multi-dimensional NMR studies. Nucleic Acids Res. 1992 Sep 11; 20(17):4507-13.
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    77. Hertel KJ, Pardi A, Uhlenbeck OC, Koizumi M, Ohtsuka E, Uesugi S, Cedergren R, Eckstein F, Gerlach WL, Hodgson R, et al. Numbering system for the hammerhead. Nucleic Acids Res. 1992 Jun 25; 20(12):3252.
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    78. Nikonowicz EP, Pardi A. Three-dimensional heteronuclear NMR studies of RNA. Nature. 1992 Jan 09; 355(6356):184-6.
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    79. Huang LH, Cheng H, Pardi A, Tam JP, Sweeney WV. Sequence-specific 1H NMR assignments, secondary structure, and location of the calcium binding site in the first epidermal growth factor like domain of blood coagulation factor IX. Biochemistry. 1991 Jul 30; 30(30):7402-9.
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    80. Heus HA, Pardi A. Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science. 1991 Jul 12; 253(5016):191-4.
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    81. Heus HA, Pardi A. Nuclear magnetic resonance studies of the hammerhead ribozyme domain. Secondary structure formation and magnesium ion dependence. J Mol Biol. 1991 Jan 05; 217(1):113-24.
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    82. Kominos D, Bassolino DA, Levy RM, Pardi A. Analysis of side-chain conformational distributions in neutrophil peptide-5 NMR structures. Biopolymers. 1990 Dec; 29(14):1807-22.
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    83. Metzler WJ, Wang C, Kitchen DB, Levy RM, Pardi A. Determining local conformational variations in DNA. Nuclear magnetic resonance structures of the DNA duplexes d(CGCCTAATCG) and d(CGTCACGCGC) generated using back-calculation of the nuclear Overhauser effect spectra, a distance geometry algorithm and constrained molecular dynamics. J Mol Biol. 1990 Aug 05; 214(3):711-36.
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    84. Heus HA, Uhlenbeck OC, Pardi A. Sequence-dependent structural variations of hammerhead RNA enzymes. Nucleic Acids Res. 1990 Mar 11; 18(5):1103-8.
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    85. Levy RM, Bassolino DA, Kitchen DB, Pardi A. Solution structures of proteins from NMR data and modeling: alternative folds for neutrophil peptide 5. Biochemistry. 1989 Nov 28; 28(24):9361-72.
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    86. Metzler WJ, Hare DR, Pardi A. Limited sampling of conformational space by the distance geometry algorithm: implications for structures generated from NMR data. Biochemistry. 1989 Aug 22; 28(17):7045-52.
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    87. Pardi A, Galdes A, Florance J, Maniconte D. Solution structures of alpha-conotoxin G1 determined by two-dimensional NMR spectroscopy. Biochemistry. 1989 Jun 27; 28(13):5494-501.
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    88. Pardi A, Hare DR, Wang C. Determination of DNA structures by NMR and distance geometry techniques: a computer simulation. Proc Natl Acad Sci U S A. 1988 Dec; 85(23):8785-9.
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    89. Pardi A, Hare DR, Selsted ME, Morrison RD, Bassolino DA, Bach AC. Solution structures of the rabbit neutrophil defensin NP-5. J Mol Biol. 1988 Jun 05; 201(3):625-36.
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    90. Bach AC, Selsted ME, Pardi A. Two-dimensional NMR studies of the antimicrobial peptide NP-5. Biochemistry. 1987 Jul 14; 26(14):4389-97.
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    91. Pardi A, Billeter M, Wüthrich K. Calibration of the angular dependence of the amide proton-C alpha proton coupling constants, 3JHN alpha, in a globular protein. Use of 3JHN alpha for identification of helical secondary structure. J Mol Biol. 1984 Dec 15; 180(3):741-51.
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    92. Pardi A, Wagner G, Wüthrich K. Protein conformation and proton nuclear-magnetic-resonance chemical shifts. Eur J Biochem. 1983 Dec 15; 137(3):445-54.
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    93. Pardi A, Morden KM, Patel DJ, Tinoco I. Kinetics for exchange of the imino protons of the d(C-G-C-G-A-A-T-T-C-G-C-G) double helix in complexes with the antibiotics netropsin and/or actinomycin. Biochemistry. 1983 Mar 01; 22(5):1107-13.
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    94. Pardi A, Morden KM, Patel DJ, Tinoco I. Kinetics for exchange of imino protons in the d(C-G-C-G-A-A-T-T-C-G-C-G) double helix and in two similar helices that contain a G . T base pair, d(C-G-T-G-A-A-T-T-C-G-C-G), and an extra adenine, d(C-G-C-A-G-A-A-T-T-C-G-C-G). Biochemistry. 1982 Dec 07; 21(25):6567-74.
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    95. Pardi A, Tinoco I. Kinetics for exchange of imino protons in deoxyribonucleic acid, ribonucleic acid, and hybrid oligonucleotide helices. Biochemistry. 1982 Sep 14; 21(19):4686-93.
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    96. Dahl KS, Pardi A, Tinoco I. Structural effects on the circular dichroism of ethidium ion-nucleic acid complexes. Biochemistry. 1982 May 25; 21(11):2730-7.
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    97. Patel DJ, Pardi A, Itakura K. DNA conformation, dynamics, and interactions in solution. Science. 1982 May 07; 216(4546):581-90.
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    98. Pardi A, Martin FH, Tinoco I. Comparative study of ribonucleotide, deoxyribonucleotide, and hybrid oligonucleotide helices by nuclear magnetic resonance. Biochemistry. 1981 Jul 07; 20(14):3986-96.
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