Anne M. Baranger - Publications

Affiliations: 
University of California, Berkeley, Berkeley, CA 
Area:
RNA Recognition By Proteins and Small Molecules
Website:
http://chemistry.berkeley.edu/faculty/chem/baranger

48 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Guzman I, Ghaemi Z, Baranger A, Luthey-Schulten Z, Gruebele M. Native conformational dynamics of the spliceosomal U1A protein. The Journal of Physical Chemistry. B. 119: 3651-61. PMID 25659967 DOI: 10.1021/Jp511760M  1
2014 Wong CH, Nguyen L, Peh J, Luu LM, Sanchez JS, Richardson SL, Tuccinardi T, Tsoi H, Chan WY, Chan HY, Baranger AM, Hergenrother PJ, Zimmerman SC. Targeting toxic RNAs that cause myotonic dystrophy type 1 (DM1) with a bisamidinium inhibitor. Journal of the American Chemical Society. 136: 6355-61. PMID 24702247 DOI: 10.1021/Ja5012146  1
2013 Jahromi AH, Fu Y, Miller KA, Nguyen L, Luu LM, Baranger AM, Zimmerman SC. Developing bivalent ligands to target CUG triplet repeats, the causative agent of myotonic dystrophy type 1. Journal of Medicinal Chemistry. 56: 9471-81. PMID 24188018 DOI: 10.1021/Jm400794Z  1
2013 Jahromi AH, Nguyen L, Fu Y, Miller KA, Baranger AM, Zimmerman SC. A novel CUG(exp)·MBNL1 inhibitor with therapeutic potential for myotonic dystrophy type 1. Acs Chemical Biology. 8: 1037-43. PMID 23480597 DOI: 10.1021/Cb400046U  1
2012 Wong CH, Richardson SL, Ho YJ, Lucas AM, Tuccinardi T, Baranger AM, Zimmerman SC. Investigating the binding mode of an inhibitor of the MBNL1·RNA complex in myotonic dystrophy type 1 (DM1) leads to the unexpected discovery of a DNA-selective binder. Chembiochem : a European Journal of Chemical Biology. 13: 2505-9. PMID 23097190 DOI: 10.1002/Cbic.201200602  1
2012 Warui DM, Baranger AM. Identification of small molecule inhibitors of the HIV-1 nucleocapsid-stem-loop 3 RNA complex. Journal of Medicinal Chemistry. 55: 4132-41. PMID 22480197 DOI: 10.1021/Jm2007694  1
2012 Fu Y, Ramisetty SR, Hussain N, Baranger AM. MBNL1-RNA recognition: contributions of MBNL1 sequence and RNA conformation. Chembiochem : a European Journal of Chemical Biology. 13: 112-9. PMID 22106026 DOI: 10.1002/Cbic.201100487  1
2011 Wong CH, Fu Y, Ramisetty SR, Baranger AM, Zimmerman SC. Selective inhibition of MBNL1-CCUG interaction by small molecules toward potential therapeutic agents for myotonic dystrophy type 2 (DM2). Nucleic Acids Research. 39: 8881-90. PMID 21768123 DOI: 10.1093/Nar/Gkr415  1
2011 Anunciado D, Dhar A, Gruebele M, Baranger AM. Multistep kinetics of the U1A-SL2 RNA complex dissociation. Journal of Molecular Biology. 408: 896-908. PMID 21419778 DOI: 10.1016/J.Jmb.2011.02.054  1
2011 Kormos BL, Pieniazek SN, Beveridge DL, Baranger AM. U1A protein-stem loop 2 RNA recognition: prediction of structural differences from protein mutations. Biopolymers. 95: 591-606. PMID 21384338 DOI: 10.1002/Bip.21616  1
2011 Benitex Y, Baranger AM. Control of the stability of a protein-RNA complex by the position of fluorine in a base analogue. Journal of the American Chemical Society. 133: 3687-9. PMID 21361282 DOI: 10.1021/Ja102601H  1
2010 Ramisetty SR, Baranger AM. Cooperative binding of a quinoline derivative to an RNA stem loop containing a dangling end. Bioorganic & Medicinal Chemistry Letters. 20: 3134-7. PMID 20400307 DOI: 10.1016/J.Bmcl.2010.03.090  1
2009 Arambula JF, Ramisetty SR, Baranger AM, Zimmerman SC. A simple ligand that selectively targets CUG trinucleotide repeats and inhibits MBNL protein binding. Proceedings of the National Academy of Sciences of the United States of America. 106: 16068-73. PMID 19805260 DOI: 10.1073/Pnas.0901824106  1
2009 Warui DM, Baranger AM. Identification of specific small molecule ligands for stem loop 3 ribonucleic acid of the packaging signal Psi of human immunodeficiency virus-1. Journal of Medicinal Chemistry. 52: 5462-73. PMID 19691339 DOI: 10.1021/Jm900599V  1
2009 Ong HC, Arambula JF, Rao Ramisetty S, Baranger AM, Zimmerman SC. Molecular recognition of a thymine bulge by a high affinity, deazaguanine-based hydrogen-bonding ligand. Chemical Communications (Cambridge, England). 668-70. PMID 19322416 DOI: 10.1039/B817733N  1
2008 Zhao Y, Knee JL, Baranger AM. Characterization of two adenosine analogs as fluorescence probes in RNA. Bioorganic Chemistry. 36: 271-7. PMID 18707751 DOI: 10.1016/J.Bioorg.2008.06.003  1
2008 Anunciado D, Agumeh M, Kormos BL, Beveridge DL, Knee JL, Baranger AM. Characterization of the dynamics of an essential helix in the U1A protein by time-resolved fluorescence measurements. The Journal of Physical Chemistry. B. 112: 6122-30. PMID 18293956 DOI: 10.1021/Jp076896C  1
2007 Benitex Y, Baranger AM. Recognition of essential purines by the U1A protein. Bmc Biochemistry. 8: 22. PMID 17980039 DOI: 10.1186/1471-2091-8-22  1
2007 Yan Z, Sikri S, Beveridge DL, Baranger AM. Identification of an aminoacridine derivative that binds to RNA tetraloops. Journal of Medicinal Chemistry. 50: 4096-104. PMID 17665894 DOI: 10.1021/Jm070305P  1
2007 Yan Z, Rao Ramisetty S, Bolton PH, Baranger AM. Selective recognition of RNA helices containing dangling ends by a quinoline derivative. Chembiochem : a European Journal of Chemical Biology. 8: 1658-61. PMID 17654628 DOI: 10.1002/Cbic.200700261  1
2007 Kormos BL, Benitex Y, Baranger AM, Beveridge DL. Affinity and specificity of protein U1A-RNA complex formation based on an additive component free energy model. Journal of Molecular Biology. 371: 1405-19. PMID 17603075 DOI: 10.1016/J.Jmb.2007.06.003  1
2007 Kormos BL, Baranger AM, Beveridge DL. A study of collective atomic fluctuations and cooperativity in the U1A-RNA complex based on molecular dynamics simulations. Journal of Structural Biology. 157: 500-13. PMID 17194603 DOI: 10.1016/J.Jsb.2006.10.022  1
2006 Kormos BL, Baranger AM, Beveridge DL. Do collective atomic fluctuations account for cooperative effects? Molecular dynamics studies of the U1A-RNA complex. Journal of the American Chemical Society. 128: 8992-3. PMID 16834346 DOI: 10.1021/Ja0606071  1
2006 Zhao Y, Kormos BL, Beveridge DL, Baranger AM. Molecular dynamics simulation studies of a protein-RNA complex with a selectively modified binding interface. Biopolymers. 81: 256-69. PMID 16278830 DOI: 10.1002/Bip.20408  1
2006 Beveridge DL, Dixit SB, Kormos BL, Baranger AM, Jayaram B. Molecular dynamics simulations and free energy calculations on protein-nucleic acid complexes Computational Studies of Rna and Dna. 211-234. DOI: 10.1007/978-1-4020-4851-3_8  1
2004 Yan Z, Baranger AM. Binding of an aminoacridine derivative to a GAAA RNA tetraloop. Bioorganic & Medicinal Chemistry Letters. 14: 5889-93. PMID 15501063 DOI: 10.1016/J.Bmcl.2004.09.021  1
2003 Zhao Y, Baranger AM. Design of an adenosine analogue that selectively improves the affinity of a mutant U1A protein for RNA. Journal of the American Chemical Society. 125: 2480-8. PMID 12603136 DOI: 10.1021/Ja021267W  1
2002 Tuite JB, Shiels JC, Baranger AM. Substitution of an essential adenine in the U1A-RNA complex with a non-polar isostere. Nucleic Acids Research. 30: 5269-75. PMID 12466552 DOI: 10.1093/Nar/Gkf636  1
2002 Pitici F, Beveridge DL, Baranger AM. Molecular dynamics simulation studies of induced fit and conformational capture in U1A-RNA binding: do molecular substates code for specificity? Biopolymers. 65: 424-35. PMID 12434430 DOI: 10.1002/Bip.10251  1
2002 Gayle AY, Baranger AM. Inhibition of the U1A-RNA complex by an aminoacridine derivative. Bioorganic & Medicinal Chemistry Letters. 12: 2839-42. PMID 12270158 DOI: 10.1016/S0960-894X(02)00636-4  1
2002 Shiels JC, Tuite JB, Nolan SJ, Baranger AM. Investigation of a conserved stacking interaction in target site recognition by the U1A protein. Nucleic Acids Research. 30: 550-8. PMID 11788718 DOI: 10.1093/Nar/30.2.550  1
2001 Shiels JC, Jerkovic B, Baranger AM, Bolton PH. RNA-DNA hybrids containing damaged DNA are substrates for RNase H. Bioorganic & Medicinal Chemistry Letters. 11: 2623-6. PMID 11551764 DOI: 10.1016/S0960-894X(01)00527-3  1
2001 Blakaj DM, McConnell KJ, Beveridge DL, Baranger AM. Molecular dynamics and thermodynamics of protein-RNA interactions: mutation of a conserved aromatic residue modifies stacking interactions and structural adaptation in the U1A-stem loop 2 RNA complex. Journal of the American Chemical Society. 123: 2548-51. PMID 11456923 DOI: 10.1021/Ja005538J  1
2000 Luchansky SJ, Nolan SJ, Baranger AM. Contribution of RNA conformation to the stability of a high-affinity RNA-protein complex [9] Journal of the American Chemical Society. 122: 7130-7131. DOI: 10.1021/Ja000837U  1
1999 Nolan SJ, Shiels JC, Tuite JB, Cecere KL, Baranger AM. Recognition of an essential adenine at a protein-RNA interface: Comparison of the contributions of hydrogen bonds and a stacking interaction [6] Journal of the American Chemical Society. 121: 8951-8952. DOI: 10.1021/Ja991617N  1
1998 Baranger AM. Accessory factor-bZIP-DNA interactions. Current Opinion in Chemical Biology. 2: 18-23. PMID 9667910 DOI: 10.1016/S1367-5931(98)80031-8  1
1996 Hanna TA, Baranger AM, Bergman RG. Reactivity of Zirconocene Azametallacyclobutenes: Insertion of Aldehydes, Carbon Monoxide, and Formation of alpha,beta-Unsaturated Imines. Formation and Trapping of [Cp(2)Zr=O] in a [4 + 2] Retrocycloaddition(1). The Journal of Organic Chemistry. 61: 4532-4541. PMID 11667377 DOI: 10.1021/Jo9521561  1
1996 Hanna TA, Baranger AM, Bergman RG. Addition of Organic 1,3-Dipolar Compounds across a Heterobinuclear Bond between Earl), and Late Transition Metals: Mechanism of Nitrogen Loss from an Organoazido Complex To Form a Bridging Imido Complex Angewandte Chemie (International Edition in English). 35: 653-655.  1
1996 Hanna TA, Baranger AM, Bergman RG. Reactivity of zirconocene azametallacyclobutenes: Insertion of aldehydes, carbon monoxide, and formation of α,β-unsaturated imines. Formation and trapping of [Cp2Zr=O] in a [4 + 2] retrocycloaddition Journal of Organic Chemistry. 61: 4532-4541.  1
1995 Baranger AM, Palmer CR, Hamm MK, Giebler HA, Brauweiler A, Nyborg JK, Schepartz A. Mechanism of DNA-binding enhancement by the human T-cell leukaemia virus transactivator Tax. Nature. 376: 606-8. PMID 7637812 DOI: 10.1038/376606A0  1
1995 Baranger AM, Hanna TA, Bergman RG. Transfer of oxygen and sulfur from organic molecules to a Zr-Ir bond. Evidence for an unusually rapid atom abstraction reaction Journal of the American Chemical Society. 117: 10041-10046.  1
1995 Hanna TA, Baranger AM, Walsh PJ, Bergman RG. Formation of α,β-unsaturated imines and successful trapping of oxozirconocene in a [4 + 2] azaoxametallacyclohexene retrocycloaddition Journal of the American Chemical Society. 117: 3292-3293.  1
1995 Hanna TA, Baranger AM, Bergman RG. Reaction of carbon dioxide and heterocumulenes with an unsymmetrical metal-metal bond. Direct addition of carbon dioxide across a zirconium-iridium bond and stoichiometric reduction of carbon dioxide to formate Journal of the American Chemical Society. 117: 11363-11364.  1
1994 Baranger AM, Bergman RG. Cooperative reactivity in the interactions of X-H bonds with a zirconium-iridium bridging imido complex Journal of the American Chemical Society. 116: 3822-3835.  1
1993 Baranger AM, Hollander FJ, Bergman RG. Synthesis of an early-late heterobimetallic imido complex: Cooperative reactivity with N-H, O-H, and S-H bonds and formation of a novel aminophosphine complex Journal of the American Chemical Society. 115: 7890-7891.  1
1993 Baranger AM, Walsh PJ, Bergman RG. Variable regiochemistry in the stoichiometric and catalytic hydroamination of alkynes by imidozirconium complexes caused by an unusual dependence of the rate law on alkyne structure and temperature Journal of the American Chemical Society. 115: 2753-2763.  1
1992 Walsh PJ, Baranger AM, Bergman RG. Stoichiometric and catalytic hydroamination of alkynes and allene by zirconium bisamides Cp2Zr(NHR)2 Journal of the American Chemical Society. 114: 1708-1719.  1
1988 Becker MM, Lesser D, Kurpiewski M, Baranger A, Jen-Jacobson L. 'Ultraviolet footprinting' accurately maps sequence-specific contacts and DNA kinking in the EcoRI endonuclease-DNA complex Proceedings of the National Academy of Sciences of the United States of America. 85: 6247-6251. PMID 2842760 DOI: 10.1073/Pnas.85.17.6247  1
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