Gabriele Varani

Representative Publications

H. Walbott, R. Machado-Pinilla, D. Liger, M. Blaud, S. Réty4, P. N. Grozdanov, K. Godin, H. van Tilbeurgh, G. Varani, U. T. Meier, N. Leulliot The H/ACA assembly factor Shq1 functions as an RNA mimic Genes Develop (2011)

Y. Chen and G. Varani Finding the missing code of RNA recognition by PUF proteins Chem. & Biol. 18 (2011)

W. Huang, G.Varani and G. D. Drobny Interactions of Tat Protein Side Chains with TAR RNA Defined with 13C/15N{31P/19F} REDOR NMR J. B. NMR (2011)

M. F. Bardaro and G. Varani Examining the Relationship between RNA Function and Motion using NMR RNA Wires (2011)

Y. Niu, A. J. Jones, H. Wu, G. Varani and J. Cai  γ-AApeptides bind to RNA by mimicking RNA-binding proteins Organic and Biomolecular Chemistry (2011)

R. Stacy, D. W. Begley, I. Phan, B. L. Staker, W. C. Van Voorhis, G. Varani, G. W. Buchko, L. J. Stewart and P. J. Myler Structural genomics of infectious disease drug targets: the SSGCID (2011)

R. P Barnwal and G. Varani Double stranded RNA and end-recognition domains in Encyclopedia of Biophysics (2011)

I. H. Norville, K. O’Shea, M. Sarkar-Tyson, S. Zheng, R. W. Titball, G. Varani and N. J. Harmer The structure of a Burkholderia pseudomallei immunophilin-inhibitor complex reveals new approaches to antimicrobial development Biochem J. 437 413-422 (2011)

M. S. Lalonde, M. A. Lobritz, A. Ratcliff, Z. Athanassiou, Mudit Tyagi, J. A. Robinson, J. Karn, G. Varani and E. J. Arts  Dual inhibition of HIV-1 reverse transcription and mRNA transcription by a conformationally constrained peptidomimetic that binds the Tat-transactivating response element (TAR) in HIV-1 genomic RNA PLOS Pathogens 7e1002038 (2011)

A. Davidson, D. W Begley, C. Lau and G. Varani A small molecule probe induces a conformation in HIV TAR RNA capable of binding drug-like fragments J. Mol Biol. 410 984-996 (2011)

A. Davidson, K. Patora-Komisarska, J. A. Robinson, G. Varani Essential structural requirements for specific recognition of HIV TAR RNA by peptide mimetics of Tat protein Nucleic Acids Res. 39 248-256 (2011)

W. Huang, G.Varani and G. D. Drobny 13C-19F Intermolecular REDOR NMR Study of the Interaction of TAR RNA with Tat Peptides J. Am. Chem. Soc. 132 17643-5 (2010)

P. Emani, G. L. Olsen, D. C. Echodu, G. Varani and G. D. Drobny A slow exchange theory of conformational capture in RNA J. Phys. Chem. B 114 15991-6002 (2010)

T. C. Leeper, X. Qu, C. Lu, C. Moore and G. Varani Recognition of yeast mRNA 3’-end processing signals by Hrp1 and Rna15 proteins J. Mol. Biol. 401 334-349 (2010)

B. M. Lunde, S. L. Reichow, M. Kim, S. Buratowski, A. Meinhart and G. Varani, Recruitment of transcription termination factors by cooperative interactions with the RNA polymerase II C-terminal domain Nature Struct Mol Biol 17 1195-1201(2010)

D. W. Begley, S. Zheng, D. Clem amd G. VaraniFragment-based discovery of novel thymidylate synthase leads by NMR screening and group epitope mapping Chem Bio. And Drug Des. 76 218-233 (2010)

M.-K. Lee, M. Gal, L. Frydman and G. Varani Real-time multidimensional NMR folding the adenine-sensing riboswitch with second resolution PNAS 107 9192-9197 (2010)

G. L. Olsen, M. F. Bardaro, D. C. Echodu, G. P. Drobny and G. Varani Atomic motions of RNA in space and time J. Am. Chem. Soc. 132 303-308 (2010)

Y. Liu, E. Peacey, J. Dickson, C. P. Donahue, S. Zheng, G. Varani and M. S. Wolfe Mitoxantrone Analogues as Ligands for a Stem-Loop Structure of Tau Pre-mRNA 52 6523-6526 J. Med. Chem. (2009)

D. W. Begley and G. Varani Locking our Viral Replication Nature Chem Biol. 5 782-783 (2009)

P. J. Myler, R. Stacy, L. Stewart, B. Staker, W. C. Van Voorhis, G. Varani, G. Buchko The Seattle structural genomics center for infectious diseases (SSGCID) Infect Disord Drug Targets 9 493-506(2009)

G. L. Olsen, M. F. Bardaro, D. C. Echodu, G. P. Drobny and G. Varani Hydration-dependent dynamics in RNA J B NMR 45 133-142 (2009)

A. Davidson, T. C. Leeper, Z. Athanassiou, K. Patora-Komisarska, J. Karn, J. A. Robinson and G.Varani Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein Proc. Natl. Acad. Sci. USA 106 11931-11936 (2009)

K. S. Godin, H. Walbott, N. Leulliot, H. van Tilbeurgh and G. Varani the Box H/Aca snoRNP assembly factor Shq1 is a chaperone protein homologous to Hsp90 co-chaperones that interacts withn the Cbf5 enzyme J. Mol Biol. 390 231-244 (2009)

S. Zheng, Y. Chen, C. Donahue, M. S. Wolfe and G. Varani Structural basis for stabilization of the tau pre-mRNA splicing regulatory element by novatrone (mitoxantrone) Chem Biol 16 557-566(2009)

M. Bardaro, Z. Shajani, K. Patora, J. A. Robinson and G. Varani Binding of small molecule ligands to HIV-1 TAR alters its Motional Landscape Nucleic Acids Res. 37 1529-1540 (2009)

Y. Chen, J. Mandic and G. Varani Cell-free selection of RNA-binding proteins using in vitro compartmentalization Nucleic Acids Res. 36 (2008)

D. Echodu, G. Goobes, Z. Shajani, K. Pederson, G. Meints, G. Varani and G. Furanose Dynamics in the HhaI Methyltransferase Target DNA Studied by Solution and Solid State NMR Relaxation J. Phys. Chem. 112 13934-13944 (2008)

C. M. Gherghe, Z. Shajani, K. A. Wilkinson, G. Varani and K. M. Weeks Strong correlation between SHAPE chemistry and the generalized NMR order parameter in RNA J. Am. Chem. Soc. 130 12244-12245 (2008)

Shajani and G. Varani 13C Relaxation studies of HhaI methyltransferase target DNA reveal a unique motional signature Biochemistry 47, 7617-7625(2008)

S. L. Reichow and G. Varani Nop10 is a Conserved H/ACA snoRNP Molecular adaptor Biochemistry 47 6148-6156 (2008)

J. Liu, D. W. Begley, D. D. Mitchell, C. L. M. J. Verlinde, W. G. J. Hol, G. Varani and E. Fan Multivalent drug design and inhibition of cholera toxin achieved by specific and transient protein-ligand interactions Chem. Biol. and Drug Design 71 408-419 (2008)

Olsen, D. Echodu, Z. Shajani, M. Bardaro, G. Varani and G.Drobny Solid-State Deuterium NMR Studies Reveal us-ns Motions in the HIV-1 TAR RNA Recognition Site  J. Amer. Chem. 130 2896-2897 (2008)

P. Deka, M. E. Bucheli, C. Moore, S. Buratowski and G. Varani Structure of the Yeast SR Protein Npl3 and Interaction with mRNA 3'-End Processing Signals J Mol Biol. (2007)

S. Zheng, R. A. Robertson and G. Varani A knowledge-based potential function predicts the specificity and relative binding energy of RNA-binding proteins FEBS J. (2007)

K. Moele, Z. Athanassiou, K. Patora, A. Davidson, G. Varani, J. R. Robinson Design of beta-Hairpin Peptidomimetics That Inhibit Binding of alpha-Helical HIV-1 Rev Protein to the Rev Response Element RNA Angew Chem Int Ed Engl. 46 9101-9110 (2007)

K. S. Godin and G. Varani How arginine-rich domains coordinate mRNA maturation events RNA Biol. Aug;4 69-75 (2007)

N. Leulliot, K. S. Godin, C. Hoareau-Aveilla, S. Quevillon-Cheruel, G. Varani, Y. Henry, H. Van Tilbeurgh The box H/ACA RNP assembly factor Naf1p contains a domain homologous to Gar1p mediating its interaction with Cbf5p J Mol Biol. 371 1338-1353 (2007)

B. M. Lunde, C. Moore and G. Varani RNA-binding proteins: modular design for efficient function Nat Rev Mol Cell Biol. 8 479-490 (2007)

Z. Shajani, G. Drobny and G. Varani Binding of U1A protein changes RNA dynamics as observed by 13C NMR relaxation studies Biochemistry 46 5875-5883 (2007)

A. L. Watters, P. Deka, C. Corrent, D. Callender, G. Varani, T. Sosnick and D. Baker The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection Cell 128 613-624 (2007)

S. L. Reichow, T. Hamma, A. R. Ferre’-D’ Amare’ and G. Varani The structure and function of small nucleolar ribonucleoproteins Nucleic Acids Res. 35 1452-1464 (2007)

Z. Athanassiou, K. Patora, R. L. Dias, K. Moehle, J. A. Robinson and G. Varani Structure-guided peptidomimetic design leads to nanomolar beta-hairpin inhibitors of the Tat-TAR interaction of bovine immunodeficiency virus Biochemistry 46 741-751 (2007)

G. Dantas, C. Corrent, S. L. Reichow, J. J. Havranek, Z. M. Eletr, N. G. Isern, B. Kuhlman, G. Varani, E. A. Merritt and D. Baker High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design J Mol Biol 366 1209-1221 (2007)

D. G. Murdeppa, C. K. Pang, T. Tsuboi, Y. Endo, F. S. Buckner, G. Varani, P. K. Rathod Cell-free production of functional Plasmodium falciparum dihydrofolate reductase-thymidylate synthase Mol Biochem Parasitol 151 216-219 (2007)

Z. Shajani and G. Varani NMR studies of dynamics in RNA and DNA by 13C relaxation Biopolymers 86 348-359 (2007)

X. Qu, J. M. Perez-Canadillas, S. Agrawal, J. De Baecke, H. Cheng, G. Varani and C. Moore The C-terminal domains of vertebrate CstF-64 and its yeast orthologue Rna15 form a new structure critical for mRNA 3'-end processing J Biol Chem 282 2101-2115 (2007)

T. A. Robertson and G. Varani An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure Proteins 66 359-374 (2007)

P. A. Miller, Z. Shajani, G. A. Meints, D. Caplow, G. Goobes, G. Varani and G. P. Drobny Contrasting views of the internal dynamics of the HhaI methyltransferase target DNA reported by solution and solid-state NMR spectroscopy J Am Chem Soc. 128 15970-15971 (2006)

Z. Shajani, P. Deka and G. Varani Decoding RNA motional codes Trends Biochem Sci 31 421-424 (2006)

H. D. Cho, Y. Chen, G. Varani, A. M. Weiner A model for C74 addition by CCA-adding enzymes: C74 addition, like C75 and A76 addition, does not involve tRNA translocation J Biol Chem 281 9801-9811 (2006)
G. Dantas, A. L. Watters, B. M. Lunde, Z. M. Eletr, N. G. Isern, T. Roseman, J. Lipfert, S. Doniach, M. Tompa, B. Kuhlman, B. L. Stoddard, G. Varani and D. Baker "Mistranslated progeny of a computationally-designed novel-fold protein forms a super-stable symmetric homodimer with zeptomolar affinity" J. Mol. Biology 362 1004-1024 (2006)
S. Reichow and G. Varani RNA switches function" Nature 441 1054-1055 (2006)
Y. Chen, J. Fender, J. D. Legassie, M. B. Jarstfer T. M. Bryan and G. Varani "The structure of stem-loop IV of Tetrahymena telomerase RNA identifies a conformational switch important for enzymatic activity" EMBO J. 25 3156-3166 (2006)
N. Dobson, G. Dantas, D. A. Baker and G. Varani "Complete computational redesign of human U1A protein: thermodynamic stabilization with high-resolution validation of protein structure and dynamics" Structure 14 847-856 (2006)
T. Hamma, S. L. Reichow, G. Varani and A. R. Ferré-D'Amaré "The Dyskerin-Nop10 complex: a conserved molecular bracket at the core of the box H/ACA snoRNP" Nature Struct Mol. Biol. 12 1101-1107 (2005)
T.C. Leeper, Z. Athanassiou, R.L.A. Dias, J.A. Robinson, and G. Varani "TAR RNA recognition by a cyclic peptidomimetic of Tat protein" Biochemistry 44 12362-12372 (2005)
Z. Shajani and G. Varani, "13^C NMR Relaxation Studies of RNA Base and Ribose Nuclei Reveal a Complex Pattern of Motions in the RNA Binding Site for Human U1A Protein" J. Mol. Biol. 349 699-715 (2005)
Y. Chen and G. Varani, "Protein Families and RNA Recognition FEBS J. 272 2088-2097 (2005)
P. Deka, J. M. Perez-Canadillas, R. K. Paranji and G. Varani, "Protein and RNA Dynamics Play a Key Role in Determining the Specific Recognition of GU-rich polyadenylation regulatory elements by human Cstf-64 protein"J. Mol. Biol. 347 719-733 (2005)
T. C. Leeper and G. Varani, "Structure of the enzyme-activating fragment of human telomerase RNA" RNA 11 394-403 (2005)
Y. Chen, T. Kortemme, T. Robertson, D. Baker and G. Varani, "A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminated decoys." Nucleic Acids Res. 32 5147-5162 (2004)
C. Detering and G. Varani "Validation of automated docking programs for docking and database" J. Med. Chem. 47 4188-4201 (2004)
"A new α-helical extension promotes RNA-binding by the dsRBD of Rnt1p RNAse III" Nicolas Leulliot, Sophie Quevillon-Cheruel, Marc Graille, Herman van Tilbeurgh Thomas L Leeper, Thomas E Edwards, Snorri Sigurdsson, Natasha Rozenkrants Roland J. Nagel, Katherine S Godin, Manuel Ares, Jr., Gabriele Varani EMBO J 23 2468-2477 (2004)
"Structural Mimicry of Retroviral Tat Proteins by Constrained β-Hairpin Peptidomimetics: Ligands with High Affinity and Selectivity for Viral TAR RNA Regulatory Elements" Zafiria Athanassiou, Ricardo L. A. Dias, Kerstin Moehle, Neil Dobson, Gabriele Varani and John A. Robinson J. Am. Chem. Soc. 126 6906-6913 (2004)
B. Davis, M. Afshar, G. Varani, A. I. H. Murchie, J. Karn, G. Lentzen, M. Drysdale, J. Bower, A. J. Potter, I. D. Starkey, T. Swarbrick, and F. Aboul-ela. "Rational Design of Inhibitors of HIV-1 TAR RNA Through the Stabilization of Electrostatic Hot Spots" J. Mol. Biol. 336 343-356 (2004)
B. Kuhlman, G. Dantas, G. C. Ireton, G. Varani, B. L. Stoddard & D. Baker. "Design of a Novel Globular Protein Fold with Atomic Level Accuracy" Science 302 1364-1368 (2003)
C.-J. Park, S.-H. Bae, G. Varani, M.-K. Lee and B.-S. Choi "Differential Recognition of Viral Promoter Structures by RNA-Dependent RNA Polymerase from Influenza Virus" Nucleic Acid Res. 31 2824-2832 (2003) (with cover)
J-M. Perez-Canadillas and G. Varani "Recognition of GU-rich polyadenylation regulatory elements by human Cstf-64 protein" EMBO J. 22 2821-2830 (2003)
T. L. Leeper, N. Leulliot and G. Varani "The solution structure of an essential stem-loop of human telomerase RNA" Nucleic Acids Res. 31 2614-2621 (2003)
J. Greatorex, J. Gallego, G. Varani and A. "Lever Structure and stability of wild-type and mutant RNA internal loops from the SL-1 domain of the HIV-1 packaging signal" J. Mol. Biol. 322 543- (2002)
J. A. Collier, J. Gallego, R. Klinck, P. T. Cole, S. J. Harris, G. P. Harrison, F. Aboul-Ela, G. Varani, S. Walker: "A conserved RNA structure within the HCV IRES eIF3-binding site." Nat Struct Biol. 9 375-380 (2002)
J. Gallego and G. Varani "Targeting RNA with Small-Molecule Drugs: Therapeutic Opportunities and Chemical Challenges." Acc. Chem. Res. 34 836-843 (2001)
N. Leulliot and G. Varani "Current Topics in RNA-Protein Recognition: Control of Specificity and Biological Function through Induced Fit and Conformation Capture." Biochemistry 40, 7947-7955 (2001)
L. Varani, S. I. Gunderson, T. Mittermaier, L. Kay, D. Neuhaus, I. Mattaj and G. Varani "The NMR Structure of the 40 kDa Human U1A Ternary Complex Reveals the Basis of Cooperativity in U1A Inhibition of Poly(A) Polymerase" Nature Struct. Biol. 7 329-335 (2000) (with Cover, News and Views)
A. Zeffman, S. Hassard, A. Lever and G. Varani "Structure of a Conserved RNA Internal Loop from the HIV-1 Encapsidation Signal and Interaction with gag Protein", J. Mol. Biol. 297 877-893 (2000).
A. Ramos, S. Grunert, M. Proktor, M. Bycroft, D. St Johnston & G. Varani. "Structural basis for RNA Recognition by Drosophila Staufen Double-Stranded RNA-Binding Domains" EMBO J 19, 997-1009 (2000)
A. Mittermaier, L. Varani, D. Muhandiram, L. E. Kay and G. Varani. "Changes in sidechain and backbone dynamics identify determinants of specificity in RNA recognition by human U1A protein." J. Mol. Biol 294 967-979 (1999) (cover)
K-Y. Chang, G. Varani, S. Bhattacharya, H. Choi and W. H. McClain "Correlation between RNA Deformability and tRNA Aminoacylation" PNAS USA 96 11764-11769 (1999)
L. Varani, M. G. Spillantini, B. Ghetti, A. Klug, M. Goedert and G. Varani "Structure of Tau Exon 10 Splicing Regulatory Element RNA and Disruption by Frontotemporal Dementian and Parkinsonism Linked to Chromosome Mutations." PNAS USA 96, 8229-8234 (1999)
A. Ramos and G. Varani "A New Method to Detect Long-Range Protein-RNA Contacts: NMR Detection of Electron-Proton Relaxation Induced by Nitroxide Spin-Labelled RNA" J. Am. Chem. Soc. 120 10992-10993 (1998)
G. Varani and K. Nagai "RNA Recognition by RNP Proteins during RNA Processing and Maturation" Ann. Rev. Biophys. Biomol. Struct. 27 407-445 (1998)
F. H.-T. Allain, P. W. A. Howe, D. Neuhaus and G. Varani "Structural Basis for the RNA-Binding Specificity of Human U1A Protein" EMBO Journal 16 5764-5774 (1997)
K-Y. Chang and G. Varani "Nucleic Acids Structure and Recognition" Nature Struct. Biol. 4 854-859 (1997)
F. Hamy, G. Heizmann, E. Felder, G. Varani, F. Aboul-Ela, J. Lazdins, M. Walker, J. Karn and T. Klimkait "Identification of an Inhibitor of the Tat/TAR RNA Interaction that Effectively Suppresses HIV Replication" PNAS USA 94, 3548-3553 (1997)
F.-H. T. Allain, C. C. Gubser, P. W. A. Howe, K. Nagai, D. Neuhaus and G. Varani, "RNP Interaction Specificity Determined by RNA Folding during Complex Formation." Nature 380 646-650 (1996)
G. Varani, F. Aboul-ela and F. H.-T. Allain "NMR Investigations of RNA Structure" Prog. NMR Spectroscopy 29 51-127 (1996)
F. Aboul-ela, J. Karn and G. Varani, "The Structure of the Human Immunodeficiency Virus Type-1 TAR RNA Reveals Principles of RNA Recognition by Tat Protein." J. Mol. Biol. 253, 313-332 (1995) (cover)
G. Varani, "Exceptionally Stable Nucleic Acid Hairpins."Ann. Rev. Biophys. Biomol. Structure 24, 379-404 (1995)
P. W. A. Howe, K. Nagai, D. Neuhaus and G. Varani, "NMR Studies of U1 snRNA Recognition by the N-Terminal RNP Domain of the Human U1A Protein."EMBO J 13, 3873-3881 (1994)

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