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    Alan Frankel, PhD

    TitleProfessor
    SchoolUCSF School of Medicine
    DepartmentBiochemistry and Biophysics
    Address600 16th Street
    San Francisco CA 94158
    Phone415-476-9994

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       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Nakamura RL, Landt SG, Mai E, Nejim J, Chen L, Frankel AD. A cell-based method for screening RNA-protein interactions: identification of constitutive transport element-interacting proteins. PLoS One. 2012; 7(10):e48194.
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      2. D'Orso I, Jang GM, Pastuszak AW, Faust TB, Quezada E, Booth DS, Frankel AD. Transition step during assembly of HIV Tat:P-TEFb transcription complexes and transfer to TAR RNA. Mol Cell Biol. 2012 Dec; 32(23):4780-93.
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      3. Faust T, Frankel A, D'Orso I. Transcription control by long non-coding RNAs. Transcription. 2012 Mar-Apr; 3(2):78-86.
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      4. Fernandes J, Jayaraman B, Frankel A. The HIV-1 Rev response element: an RNA scaffold that directs the cooperative assembly of a homo-oligomeric ribonucleoprotein complex. RNA Biol. 2012 Jan; 9(1):6-11.
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      5. Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ. Global landscape of HIV-human protein complexes. Nature. 2012 Jan 19; 481(7381):365-70.
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      6. Fahey ME, Bennett MJ, Mahon C, Jäger S, Pache L, Kumar D, Shapiro A, Rao K, Chanda SK, Craik CS, Frankel AD, Krogan NJ. GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. BMC Bioinformatics. 2011; 12:298.
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      7. Wang H, Ma X, Yeh YS, Zhu Y, Daugherty MD, Frankel AD, Musier-Forsyth K, Barbara PF. Comparative analysis of RNA/protein dynamics for the arginine-rich-binding motif and zinc-finger-binding motif proteins encoded by HIV-1. Biophys J. 2010 Nov 17; 99(10):3454-62.
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      8. Pastuszak AW, Joachimiak MP, Blanchette M, Rio DC, Brenner SE, Frankel AD. An SF1 affinity model to identify branch point sequences in human introns. Nucleic Acids Res. 2011 Mar; 39(6):2344-56.
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      9. Daugherty MD, Liu B, Frankel AD. Structural basis for cooperative RNA binding and export complex assembly by HIV Rev. Nat Struct Mol Biol. 2010 Nov; 17(11):1337-42.
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      10. Jäger S, Gulbahce N, Cimermancic P, Kane J, He N, Chou S, D'Orso I, Fernandes J, Jang G, Frankel AD, Alber T, Zhou Q, Krogan NJ. Purification and characterization of HIV-human protein complexes. Methods. 2011 Jan; 53(1):13-9.
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      11. Daugherty MD, Booth DS, Jayaraman B, Cheng Y, Frankel AD. HIV Rev response element (RRE) directs assembly of the Rev homooligomer into discrete asymmetric complexes. Proc Natl Acad Sci U S A. 2010 Jul 13; 107(28):12481-6.
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      12. D'Orso I, Frankel AD. RNA-mediated displacement of an inhibitory snRNP complex activates transcription elongation. Nat Struct Mol Biol. 2010 Jul; 17(7):815-21.
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      13. Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, König R, Bandyopadhyay S, Ideker T, Goff SP, Krogan NJ, Frankel AD, Young JA, Chanda SK. Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog. 2009 May; 5(5):e1000437.
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      14. D'Orso I, Frankel AD. Tat acetylation modulates assembly of a viral-host RNA-protein transcription complex. Proc Natl Acad Sci U S A. 2009 Mar 3; 106(9):3101-6.
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      15. Daugherty MD, D'Orso I, Frankel AD. A solution to limited genomic capacity: using adaptable binding surfaces to assemble the functional HIV Rev oligomer on RNA. Mol Cell. 2008 Sep 26; 31(6):824-34.
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      16. D'Orso I, Grunwell JR, Nakamura RL, Das C, Frankel AD. Targeting tat inhibitors in the assembly of human immunodeficiency virus type 1 transcription complexes. J Virol. 2008 Oct; 82(19):9492-504.
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      17. Mokdad A, Frankel AD. ISFOLD: structure prediction of base pairs in non-helical RNA motifs from isostericity signatures in their sequence alignments. J Biomol Struct Dyn. 2008 Apr; 25(5):467-72.
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      18. Mills NL, Daugherty MD, Frankel AD, Guy RK. An alpha-helical peptidomimetic inhibitor of the HIV-1 Rev-RRE interaction. J Am Chem Soc. 2006 Mar 22; 128(11):3496-7.
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      19. Landt SG, Ramirez A, Daugherty MD, Frankel AD. A simple motif for protein recognition in DNA secondary structures. J Mol Biol. 2005 Sep 2; 351(5):982-94.
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      20. Calabro V, Frankel AD. Viral RNA gymnastics. Nat Chem Biol. 2005 Jul; 1(2):67-8.
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      21. Landt SG, Tipton AR, Frankel AD. Localized influence of 2'-hydroxyl groups and helix geometry on protein recognition in the RNA major groove. Biochemistry. 2005 May 3; 44(17):6547-58.
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      22. Calabro V, Daugherty MD, Frankel AD. A single intermolecular contact mediates intramolecular stabilization of both RNA and protein. Proc Natl Acad Sci U S A. 2005 May 10; 102(19):6849-54.
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      23. Xie B, Calabro V, Wainberg MA, Frankel AD. Selection of TAR RNA-binding chameleon peptides by using a retroviral replication system. J Virol. 2004 Feb; 78(3):1456-63.
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      24. Cheng AC, Frankel AD. Ab initio interaction energies of hydrogen-bonded amino acid side chain[bond]nucleic acid base interactions. J Am Chem Soc. 2004 Jan 21; 126(2):434-5.
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      25. Das C, Edgcomb SP, Peteranderl R, Chen L, Frankel AD. Evidence for conformational flexibility in the Tat-TAR recognition motif of cyclin T1. Virology. 2004 Jan 5; 318(1):306-17.
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      26. Das C, Frankel AD. Sequence and structure space of RNA-binding peptides. Biopolymers. 2003 Sep; 70(1):80-5.
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      27. Cheng AC, Chen WW, Fuhrmann CN, Frankel AD. Recognition of nucleic acid bases and base-pairs by hydrogen bonding to amino acid side-chains. J Mol Biol. 2003 Apr 4; 327(4):781-96.
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      28. Walberer BJ, Cheng AC, Frankel AD. Structural diversity and isomorphism of hydrogen-bonded base interactions in nucleic acids. J Mol Biol. 2003 Apr 4; 327(4):767-80.
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      29. Xie B, Wainberg MA, Frankel AD. Replication of human immunodeficiency viruses engineered with heterologous Tat-transactivation response element interactions. J Virol. 2003 Feb; 77(3):1984-91.
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      30. Peled-Zehavi H, Horiya S, Das C, Harada K, Frankel AD. Selection of RRE RNA binding peptides using a kanamycin antitermination assay. RNA. 2003 Feb; 9(2):252-61.
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      31. Cheng AC, Calabro V, Frankel AD. Design of RNA-binding proteins and ligands. Curr Opin Struct Biol. 2001 Aug; 11(4):478-84.
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      32. Peled-Zehavi H, Berglund JA, Rosbash M, Frankel AD. Recognition of RNA branch point sequences by the KH domain of splicing factor 1 (mammalian branch point binding protein) in a splicing factor complex. Mol Cell Biol. 2001 Aug; 21(15):5232-41.
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      33. Branscombe TL, Frankel A, Lee JH, Cook JR, Yang Z, Pestka S, Clarke S. PRMT5 (Janus kinase-binding protein 1) catalyzes the formation of symmetric dimethylarginine residues in proteins. J Biol Chem. 2001 Aug 31; 276(35):32971-6.
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      34. Reyes CM, Nifosì R, Frankel AD, Kollman PA. Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex. Biophys J. 2001 Jun; 80(6):2833-42.
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      35. Zhang Q, Harada K, Cho HS, Frankel AD, Wemmer DE. Structural characterization of the complex of the Rev response element RNA with a selected peptide. Chem Biol. 2001 May; 8(5):511-20.
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      36. Campisi DM, Calabro V, Frankel AD. Structure-based design of a dimeric RNA-peptide complex. EMBO J. 2001 Jan 15; 20(1-2):178-86.
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      37. Smith CA, Calabro V, Frankel AD. An RNA-binding chameleon. Mol Cell. 2000 Nov; 6(5):1067-76.
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      38. Frankel A, Clarke S. PRMT3 is a distinct member of the protein arginine N-methyltransferase family. Conferral of substrate specificity by a zinc-finger domain. J Biol Chem. 2000 Oct 20; 275(42):32974-82.
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      39. Frankel AD. Fitting peptides into the RNA world. Curr Opin Struct Biol. 2000 Jun; 10(3):332-40.
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      40. Bedford MT, Frankel A, Yaffe MB, Clarke S, Leder P, Richard S. Arginine methylation inhibits the binding of proline-rich ligands to Src homology 3, but not WW, domains. J Biol Chem. 2000 May 26; 275(21):16030-6.
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      41. Tang J, Frankel A, Cook RJ, Kim S, Paik WK, Williams KR, Clarke S, Herschman HR. PRMT1 is the predominant type I protein arginine methyltransferase in mammalian cells. J Biol Chem. 2000 Mar 17; 275(11):7723-30.
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      42. Robertson SA, Harada K, Frankel AD, Wemmer DE. Structure determination and binding kinetics of a DNA aptamer-argininamide complex. Biochemistry. 2000 Feb 8; 39(5):946-54.
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      43. Peled-Zehavi H, Smith CA, Harada K, Frankel AD. Screening RNA-binding libraries by transcriptional antitermination in bacteria. Methods Enzymol. 2000; 318:297-308.
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      44. Landt SG, Tan R, Frankel AD. Screening RNA-binding libraries using Tat-fusion system in mammalian cells. Methods Enzymol. 2000; 318:350-63.
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      45. Smith CA, Chen L, Frankel AD. Using peptides as models of RNA-protein interactions. Methods Enzymol. 2000; 318:423-38.
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      46. Harada K, Horiya S, Zehavi H, Frankel AD. Screening in vivo for RNA-binding peptides from combinatorial libraries. Nucleic Acids Symp Ser. 2000; (44):269-70.
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      47. Frankel AD. If the loop fits... Nat Struct Biol. 1999 Dec; 6(12):1081-3.
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      48. McColl DJ, Honchell CD, Frankel AD. Structure-based design of an RNA-binding zinc finger. Proc Natl Acad Sci U S A. 1999 Aug 17; 96(17):9521-6.
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      49. Frankel A, Clarke S. RNase treatment of yeast and mammalian cell extracts affects in vitro substrate methylation by type I protein arginine N-methyltransferases. Biochem Biophys Res Commun. 1999 Jun 7; 259(2):391-400.
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      50. Harada K, Frankel AD. Screening RNA-binding libraries using a bacterial transcription antitermination assay. Methods Mol Biol. 1999; 118:177-87.
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      51. Harada K, Martin SS, Frankel AD. In vivo selection of RNA-binding peptides from combinatorial libraries. Nucleic Acids Symp Ser. 1999; (42):213-4.
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      52. Smith CA, Crotty S, Harada Y, Frankel AD. Altering the context of an RNA bulge switches the binding specificities of two viral Tat proteins. Biochemistry. 1998 Jul 28; 37(30):10808-14.
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      53. Tan R, Frankel AD. A novel glutamine-RNA interaction identified by screening libraries in mammalian cells. Proc Natl Acad Sci U S A. 1998 Apr 14; 95(8):4247-52.
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      54. Frankel AD, Smith CA. Induced folding in RNA-protein recognition: more than a simple molecular handshake. Cell. 1998 Jan 23; 92(2):149-51.
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      55. Frankel AD, Young JA. HIV-1: fifteen proteins and an RNA. Annu Rev Biochem. 1998; 67:1-25.
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      56. Harada K, Martin SS, Tan R, Frankel AD. Molding a peptide into an RNA site by in vivo peptide evolution. Proc Natl Acad Sci U S A. 1997 Oct 28; 94(22):11887-92.
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      57. Tao J, Chen L, Frankel AD. Dissection of the proposed base triple in human immunodeficiency virus TAR RNA indicates the importance of the Hoogsteen interaction. Biochemistry. 1997 Mar 25; 36(12):3491-5.
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      58. Battiste JL, Mao H, Rao NS, Tan R, Muhandiram DR, Kay LE, Frankel AD, Williamson JR. Alpha helix-RNA major groove recognition in an HIV-1 rev peptide-RRE RNA complex. Science. 1996 Sep 13; 273(5281):1547-51.
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      59. Harada K, Martin SS, Frankel AD. Selection of RNA-binding peptides in vivo. Nature. 1996 Mar 14; 380(6570):175-9.
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      60. Tao J, Frankel AD. Arginine-binding RNAs resembling TAR identified by in vitro selection. Biochemistry. 1996 Feb 20; 35(7):2229-38.
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      61. Battiste JL, Tan R, Frankel AD, Williamson JR. Assignment and modeling of the Rev Response Element RNA bound to a Rev peptide using 13C-heteronuclear NMR. J Biomol NMR. 1995 Dec; 6(4):375-89.
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      62. Harada K, Frankel AD. Identification of two novel arginine binding DNAs. EMBO J. 1995 Dec 1; 14(23):5798-811.
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      63. Puglisi JD, Chen L, Blanchard S, Frankel AD. Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex. Science. 1995 Nov 17; 270(5239):1200-3.
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      64. Tan R, Frankel AD. Structural variety of arginine-rich RNA-binding peptides. Proc Natl Acad Sci U S A. 1995 Jun 6; 92(12):5282-6.
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      65. Chen L, Frankel AD. A peptide interaction in the major groove of RNA resembles protein interactions in the minor groove of DNA. Proc Natl Acad Sci U S A. 1995 May 23; 92(11):5077-81.
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      66. Chen LL, Frankel AD, Harder JL, Fawell S, Barsoum J, Pepinsky B. Increased cellular uptake of the human immunodeficiency virus-1 Tat protein after modification with biotin. Anal Biochem. 1995 May 1; 227(1):168-75.
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      67. Williamson JR, Battiste JL, Mao H, Frankel AD. Interaction of HIV Rev peptides with the Rev response element RNA. Nucleic Acids Symp Ser. 1995; (33):46-8.
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      68. Tan R, Frankel AD. Costabilization of peptide and RNA structure in an HIV Rev peptide-RRE complex. Biochemistry. 1994 Dec 6; 33(48):14579-85.
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      69. Battiste JL, Tan R, Frankel AD, Williamson JR. Binding of an HIV Rev peptide to Rev responsive element RNA induces formation of purine-purine base pairs. Biochemistry. 1994 Mar 15; 33(10):2741-7.
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      70. Chen L, Frankel AD. An RNA-binding peptide from bovine immunodeficiency virus Tat protein recognizes an unusual RNA structure. Biochemistry. 1994 Mar 8; 33(9):2708-15.
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      71. Tan R, Chen L, Buettner JA, Hudson D, Frankel AD. RNA recognition by an isolated alpha helix. Cell. 1993 Jun 4; 73(5):1031-40.
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      72. Puglisi JD, Chen L, Frankel AD, Williamson JR. Role of RNA structure in arginine recognition of TAR RNA. Proc Natl Acad Sci U S A. 1993 Apr 15; 90(8):3680-4.
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      73. Tao J, Frankel AD. Electrostatic interactions modulate the RNA-binding and transactivation specificities of the human immunodeficiency virus and simian immunodeficiency virus Tat proteins. Proc Natl Acad Sci U S A. 1993 Feb 15; 90(4):1571-5.
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      74. Frankel AD. The importance of being flexible. Proc Natl Acad Sci U S A. 1992 Dec 15; 89(24):11653.
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      75. Frankel AD. Peptide models of the Tat-TAR protein-RNA interaction. Protein Sci. 1992 Dec; 1(12):1539-42.
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      76. Tan R, Frankel AD. Circular dichroism studies suggest that TAR RNA changes conformation upon specific binding of arginine or guanidine. Biochemistry. 1992 Oct 27; 31(42):10288-94.
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      77. Puglisi JD, Tan R, Calnan BJ, Frankel AD, Williamson JR. Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science. 1992 Jul 3; 257(5066):76-80.
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      78. Frankel AD. Activation of HIV transcription by Tat. Curr Opin Genet Dev. 1992 Apr; 2(2):293-8.
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      79. Tao J, Frankel AD. Specific binding of arginine to TAR RNA. Proc Natl Acad Sci U S A. 1992 Apr 1; 89(7):2723-6.
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      80. Kim Y, Mlsna D, Monzingo AF, Ready MP, Frankel A, Robertus JD. Structure of a ricin mutant showing rescue of activity by a noncatalytic residue. Biochemistry. 1992 Mar 31; 31(12):3294-6.
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      81. Kjems J, Calnan BJ, Frankel AD, Sharp PA. Specific binding of a basic peptide from HIV-1 Rev. EMBO J. 1992 Mar; 11(3):1119-29.
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      82. Frankel AD, Mattaj IW, Rio DC. RNA-protein interactions. Cell. 1991 Dec 20; 67(6):1041-6.
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      83. Kjems J, Frankel AD, Sharp PA. Specific regulation of mRNA splicing in vitro by a peptide from HIV-1 Rev. Cell. 1991 Oct 4; 67(1):169-78.
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      84. Mann DA, Frankel AD. Endocytosis and targeting of exogenous HIV-1 Tat protein. EMBO J. 1991 Jul; 10(7):1733-9.
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      85. Calnan BJ, Tidor B, Biancalana S, Hudson D, Frankel AD. Arginine-mediated RNA recognition: the arginine fork. Science. 1991 May 24; 252(5009):1167-71.
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      86. Feinberg MB, Baltimore D, Frankel AD. The role of Tat in the human immunodeficiency virus life cycle indicates a primary effect on transcriptional elongation. Proc Natl Acad Sci U S A. 1991 May 1; 88(9):4045-9.
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      87. Calnan BJ, Biancalana S, Hudson D, Frankel AD. Analysis of arginine-rich peptides from the HIV Tat protein reveals unusual features of RNA-protein recognition. Genes Dev. 1991 Feb; 5(2):201-10.
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      88. Frankel A, Welsh P, Richardson J, Robertus JD. Role of arginine 180 and glutamic acid 177 of ricin toxin A chain in enzymatic inactivation of ribosomes. Mol Cell Biol. 1990 Dec; 10(12):6257-63.
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      89. Marciniak RA, Calnan BJ, Frankel AD, Sharp PA. HIV-1 Tat protein trans-activates transcription in vitro. Cell. 1990 Nov 16; 63(4):791-802.
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      90. Daly TJ, Rusche JR, Maione TE, Frankel AD. Circular dichroism studies of the HIV-1 Rev protein and its specific RNA binding site. Biochemistry. 1990 Oct 23; 29(42):9791-5.
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      91. Viscidi RP, Mayur K, Lederman HM, Frankel AD. Inhibition of antigen-induced lymphocyte proliferation by Tat protein from HIV-1. Science. 1989 Dec 22; 246(4937):1606-8.
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      92. Frankel AD, Biancalana S, Hudson D. Activity of synthetic peptides from the Tat protein of human immunodeficiency virus type 1. Proc Natl Acad Sci U S A. 1989 Oct; 86(19):7397-401.
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      93. Frankel A, Schlossman D, Welsh P, Hertler A, Withers D, Johnston S. Selection and characterization of ricin toxin A-chain mutations in Saccharomyces cerevisiae. Mol Cell Biol. 1989 Feb; 9(2):415-20.
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      94. Frankel AD, Pabo CO. Cellular uptake of the tat protein from human immunodeficiency virus. Cell. 1988 Dec 23; 55(6):1189-93.
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      95. Stearman RS, Frankel AD, Freire E, Liu BS, Pabo CO. Combining thermostable mutations increases the stability of lambda repressor. Biochemistry. 1988 Sep 20; 27(19):7571-4.
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      96. Frankel AD, Chen L, Cotter RJ, Pabo CO. Dimerization of the tat protein from human immunodeficiency virus: a cysteine-rich peptide mimics the normal metal-linked dimer interface. Proc Natl Acad Sci U S A. 1988 Sep; 85(17):6297-300.
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      97. Frankel AD, Bredt DS, Pabo CO. Tat protein from human immunodeficiency virus forms a metal-linked dimer. Science. 1988 Apr 1; 240(4848):70-3.
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      98. Pabo CO, Jordan SR, Frankel AD. Systematic analysis of possible hydrogen bonds between amino acid side chains and B-form DNA. J Biomol Struct Dyn. 1983 Dec; 1(4):1039-49.
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      99. Frankel AD, Smith HO. Restriction and modification enzymes detect no allosteric changes in DNA with bound lac repressor or RNA polymerase. J Mol Biol. 1981 Mar 15; 146(4):611-9.
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