Erratum: Click dimers to target HIV TAR RNA conformation (Biochemistry (2012) 51: 11 (2331-2347) DOI: 10.1021/bi201657k);Click dimers to target HIV TAR RNA conformation

Biochemistry

Volumn 51, Issue 11, 2012, Pages 2331-2347

  Kumar, Sunil ^a   Kellish, Patrick ^a   Robinson, W Edward ^b   Wang, Deyun ^c   Appella, Daniel H ^c   Arya, Dev P ^a  

^a CLEMSON UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTICS; BINDING ENERGY; BINDING SITES; DICHROISM; DISEASES; ENERGY TRANSFER; FORSTER RESONANCE ENERGY TRANSFER; RNA; SYNTHESIS (CHEMICAL); TAR; THULIUM COMPOUNDS; VIRUSES;

COMPETITIVE ASSAYS; FRET (FLUORESCENCE RESONANCE ENERGY TRANSFER); HUMAN IMMUNODEFICIENCY VIRUS TYPE-1; MULTIPLE BINDING SITES; SPECTROSCOPIC TECHNIQUE; STEM-LOOP STRUCTURES; THERMAL DENATURATION STUDIES; THERMAL DENATURATIONS;

DIMERS;

ANTI HUMAN IMMUNODEFICIENCY VIRUS AGENT; DIMER; DPA 51; DPA 52; DPA 53; DPA 54; DPA 55; DPA 56; DPA 58; DPA 60; DPA 65; ETHIDIUM BROMIDE; NEOMYCIN; TRANSACTIVATOR PROTEIN; TRIAZOLE DERIVATIVE; UNCLASSIFIED DRUG; VIRUS RNA;

ANTIVIRAL ACTIVITY; ARTICLE; BINDING AFFINITY; CELL LINE; CIRCULAR DICHROISM; CLICK CHEMISTRY; CONCENTRATION RESPONSE; CONTROLLED STUDY; DRUG BINDING; DRUG DESIGN; DRUG SELECTIVITY; DRUG STRUCTURE; DRUG SYNTHESIS; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENT INTERCALATOR DISPLACEMENT SPECTROSCOPY; HUMAN IMMUNODEFICIENCY VIRUS 1; IC 50; MELTING POINT; PRIORITY JOURNAL; RNA CONFORMATION; RNA STRUCTURE; SPECTROSCOPY; TRANS ACTIVATION RESPONSIVE RNA REGION; ULTRAVIOLET SPECTROSCOPY; ULTRAVIOLET THERMAL DENATURATION SPECTROSCOPY;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84863378935     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi401088n     Document Type: Erratum

References (67)

1. Berkhout, B. and Jeang, K. T. (1989) Transactivation of human immunodeficiency virus type 1 is sequence specific for both the single-stranded bulge and loop of the trans-acting-responsive hairpin: A quantitative analysis J. Virol. 63, 5501-5504 (Pubitemid 19278798)
2. Jones, K. A. and Peterlin, B. M. (1994) Control of Rna Initiation and Elongation at the Hiv-1 Promoter Annu. Rev. Biochem. 63, 717-743 (Pubitemid 24218647)
3. Draper, D. E. (1995) Protein-RNA Recognition Annu. Rev. Biochem. 64, 593-620
4. Rosen, C. A., Sodroski, J. G., and Haseltine, W. A. (1985) The location of cis-acting regulatory sequences in the human T cell lymphotropic virus type III (HTLV-III/LAV) long terminal repeat Cell 41, 813-823 (Pubitemid 15243388)
5. Muesing, M. A., Smith, D. H., and Capon, D. J. (1987) Regulation of mRNA accumulation by a human immunodeficiency virus trans-activator protein Cell 48, 691-701 (Pubitemid 18096946)
6. Aboul-ela, F., Karn, J., and Varani, G. (1995) 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
7. Rana, T. M. and Jeang, K. T. (1999) Biochemical and functional interactions between HIV-1 Tat protein and TAR RNA Arch. Biochem. Biophys. 365, 175-185 (Pubitemid 29391624)
8. Hauber, J. and Cullen, B. R. (1988) Mutational analysis of the trans-activation-responsive region of the human immunodeficiency virus type I long terminal repeat J. Virol. 62, 673-679 (Pubitemid 18068620)
9. Feng, S. and Holland, E. C. (1988) HIV-1 tat trans-activation requires the loop sequence within tar Nature 334, 165-167
10. Puglisi, J., Tan, R., Calnan, B., and Frankel, A. (1992) Williamson Conformation of the TAR RNA-arginine complex by NMR spectroscopy Science 257, 76-80
11. Thomas, J. R. and Hergenrother, P. J. (2008) Targeting RNA with Small Molecules Chem. Rev. 108, 1171-1224 (Pubitemid 351638813)
12. Bailly, C., Colson, P., Houssier, C., and Hamy, F. (1996) The Binding Mode of Drugs to the TAR RNA of HIV-1 Studied by Electric Linear Dichroism Nucleic Acids Res. 24, 1460-1464 (Pubitemid 26118978)
13. Ratmeyer, L. S., Vinayak, R., Zon, G., and Wilson, W. D. (1992) An ethidium analog that binds with high specificity to a base-bulged duplex from the TAR RNA region of the HIV-1 genome J. Med. Chem. 35, 966-968
14. Dassonneville, L., Hamy, F., Colson, P., Houssier, C., and Bailly, C. (1997) Binding of Hoechst 33258 to the TAR RNA of HIV-1. Recognition of a pyrimidine bulge-dependent structure Nucleic Acids Res. 25, 4487-4492 (Pubitemid 27500758)
15. Lind, K. E., Du, Z., Fujinaga, K., Peterlin, B. M., and James, T. L. (2002) Structure-Based Computational Database Screening, In Vitro Assay, and NMR Assessment of Compounds that Target TAR RNA Chem. Biol. 9, 185-193 (Pubitemid 34196656)
16. Tao, J. and Frankel, A. D. (1992) Specific binding of arginine to TAR RNA Proc. Natl. Acad. Sci. U.S.A. 89, 2723-2726
17. Hwang, S., Tamilarasu, N., Ryan, K., Huq, I., Richter, S., Still, W. C., and Rana, T. M. (1999) Inhibition of gene expression in human cells through small molecule-RNA interactions Proc. Natl. Acad. Sci. U.S.A. 96, 12997-13002
18. Athanassiou, Z., Patora, K., Dias, R. L. A., Moehle, K., Robinson, J. A., and Varani, G. (2007) Structure-Guided Peptidomimetic Design Leads to Nanomolar β-Hairpin Inhibitors of the Tat-TAR Interaction of Bovine Immunodeficiency Virus Biochemistry 46, 741-751 (Pubitemid 46133590)
19. Mei, H., Mack, D. P., Galan, A. A., Halim, N. S., Heldsinger, A., Loo, J. A., Moreland, D. W., Sannes-Lowery, K. A., Sharmeen, L., Truong, H. N., and Czarnik, A. W. (1997) Discovery of selective, small-molecule inhibitors of RNA complexes. 1. The tat protein/TAR RNA complexes required for HIV-1 transcription Bioorg. Med. Chem. 5, 1173-1184 (Pubitemid 27264844)
20. Raghunathan, D., Sánchez-Pedregal, V. M., Junker, J., Schwiegk, C., Kalesse, M., Kirschning, A., and Carlomagno, T. (2006) TAR-RNA recognition by a novel cyclic aminoglycoside analogue Nucleic Acids Res. 34, 3599-3608
21. Tor, Y. (2006) The ribosomal A-site as an inspiration for the design of RNA binders Biochimie 88, 1045-1051
22. Wang, S., Huber, P. W., Cui, M., Czarnik, A. W., and Mei, H. (1998) Binding of Neomycin to the TAR Element of HIV-1 RNA Induces Dissociation of Tat Protein by an Allosteric Mechanism Biochemistry 37, 5549-5557 (Pubitemid 28241938)
23. Charles, I., Xi, H., and Arya, D. P. (2007) Sequence-specific targeting of RNA with an oligonucleotide-neomycin conjugate Bioconjugate Chem. 18, 160-169
24. Shaw, N. N., Xi, H., and Arya, D. P. (2008) Molecular recognition of a DNA:RNA hybrid: Sub-nanomolar binding by a neomycin-methidium conjugate Bioorg. Med. Chem. Lett. 18, 4142-4145
25. Shaw, N. N. and Arya, D. P. (2008) Recognition of the unique structure of DNA:RNA hybrids Biochimie 90, 1026-1039
26. Xi, H., Gray, D., Kumar, S., and Arya, D. P. (2009) Molecular recognition of single-stranded RNA: Neomycin binding to poly(A) FEBS Lett. 583, 2269-2275
27. Arya, D. P. (2011) New approaches toward recognition of nucleic acid triple helices Acc. Chem. Res. 44, 134-146
28. Xi, H., Davis, E., Ranjan, N., Xue, L., Hyde-Volpe, D., and Arya, D. P. (2011) Thermodynamics of Nucleic Acid "Shape Readout" by an Aminosugar Biochemistry 50, 9088-9113
29. Xue, L., Ranjan, N., and Arya, D. P. (2011) Synthesis and spectroscopic studies of the aminoglycoside (Neomycin)-perylene conjugate binding to human telomeric DNA Biochemistry 50, 2838-2849
30. Ranjan, N., Andreasen, K. F., Kumar, S., Hyde-Volpe, D., and Arya, D. P. (2010) Aminoglycoside Binding to Oxytricha nova Telomeric DNA Biochemistry 49, 9891-9903
31. Willis, B. and Arya, D. P. (2010) Triple recognition of B-DNA by a neomycin-Hoechst 33258-pyrene conjugate Biochemistry 49, 452-469
32. Xi, H., Kumar, S., Dosen-Micovic, L., and Arya, D. P. (2010) Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices Biochimie 92, 514-529
33. Xue, L., Xi, H., Kumar, S., Gray, D., Davis, E., Hamilton, P., Skriba, M., and Arya, D. P. (2010) Probing the recognition surface of a DNA triplex: Binding studies with intercalator-neomycin conjugates Biochemistry 49, 5540-5552
34. Willis, B. and Arya, D. P. (2009) Triple Recognition of B-DNA Bioorg. Med. Chem. Lett. 19, 4974-4979
35. Willis, B. and Arya, D. P. (2006) Major groove recognition of DNA by carbohydrates Curr. Org. Chem. 10, 663-673
36. Willis, B. and Arya, D. P. (2006) Recognition of B-DNA by Neomycin-Hoechst 33258 Conjugates Biochemistry 45, 10217-10232 (Pubitemid 44384797)
37. Willis, B. and Arya, D. P. (2006) An expanding view of aminoglycoside-nucleic acid recognition Adv. Carbohydr. Chem. Biochem. 60, 251-302 (Pubitemid 43783388)
38. Arya, D. P. (2005) Aminoglycoside-Nucleic Acid Interactions: The Case for Neomycin Top. Curr. Chem. 253, 149-178 (Pubitemid 44420842)
39. Xi, H. and Arya, D. P. (2005) Recognition of triple helical nucleic acids by aminoglycosides Curr. Med. Chem.: Anti-Cancer Agents 5, 327-338 (Pubitemid 40974807)
40. Arya, D. P., Xue, L., and Willis, B. (2003) Aminoglycoside (Neomycin) Preference Is for A-Form Nucleic Acids, Not Just RNA: Results from a Competition Dialysis Study J. Am. Chem. Soc. 125, 10148-10149 (Pubitemid 37022207)
41. Arya, D. P., Micovic, L., Charles, I., Coffee, R. L., Jr., Willis, B., and Xue, L. (2003) Neomycin Binding to Watson-Hoogsteen (W-H) DNA Triplex Groove: A Model J. Am. Chem. Soc. 125, 3733-3744 (Pubitemid 36512360)
42. Arya, D. P. and Willis, B. (2003) Reaching into the major groove of B-DNA: Synthesis and nucleic acid binding of a neomycin-Hoechst 33258 conjugate J. Am. Chem. Soc. 125, 12398-12399 (Pubitemid 37254744)
43. Arya, D. P., Xue, L., and Tennant, P. (2003) Combining the best in triplex recognition: Synthesis and nucleic acid binding of a BQQ-neomycin conjugate J. Am. Chem. Soc. 125, 8070-8071 (Pubitemid 36828550)
44. Xue, L., Charles, I., and Arya, D. P. (2002) Pyrene-neomycin conjugate: Dual recognition of a DNA triple helix Chem. Commun. 1, 70-71 (Pubitemid 34081608)
45. Hamilton, P. L. and Arya, D. P. (2012) Natural product DNA major groove binders Nat. Prod. Rep. 29, 134-143
46. Arya, D. P. and Coffee, R. L., Jr. (2000) DNA Triple Helix Stabilization by Aminoglycoside Antibiotics Bioorg. Med. Chem. Lett. 10, 1897-1899 (Pubitemid 30663335)
47. Arya, D. P., Coffee, R. L., Jr., Willis, B., and Abramovitch, A. I. (2001) Aminoglycoside-nucleic acid interactions: Remarkable stabilization of DNA and RNA triple helices by neomycin J. Am. Chem. Soc. 123, 5385-5395 (Pubitemid 32888504)
48. Arya, D. P., Coffee, R. L., Jr., and Charles, I. (2001) Neomycin-Induced Hybrid Triplex Formation J. Am. Chem. Soc. 123, 11093-11094
49. Wang, H. and Tor, Y. (1997) Dimeric aminoglycosides: Design, synthesis and RNA binding Bioorg. Med. Chem. Lett. 7, 1951-1956 (Pubitemid 27317820)
50. Michael, K., Wang, H., and Tor, Y. (1999) Enhanced RNA binding of dimerized aminoglycosides Bioorg. Med. Chem. 7, 1361-1371 (Pubitemid 29292376)
51. Riguet, E., Desire, J., Boden, O., Ludwig, V., Gobel, M., Bailly, C., and Decout, J. L. (2005) Neamine dimers targeting the HIV-1 TAR RNA Bioorg. Med. Chem. Lett. 15, 4651-4655 (Pubitemid 41354785)
52. Sannes-Lowery, K. A., Mei, H., and Loo, J. A. (1999) Studying aminoglycoside antibiotic binding to HIV-1 TAR RNA by electrospray ionization mass spectrometry Int. J. Mass Spectrom. 193, 115-122
53. Matsumoto, C., Hamasaki, K., Mihara, H., and Ueno, A. (2000) A high-throughput screening utilizing intramolecular fluorescence resonance energy transfer for the discovery of the molecules that bind HIV-1 TAR RNA specifically Bioorg. Med. Chem. Lett. 10, 1857-1861 (Pubitemid 30657623)
54. Kolb, H. C. and Sharpless, K. B. (2003) The growing impact of click chemistry on drug discovery Drug Discovery Today 8, 1128-1137 (Pubitemid 37547919)
55. Kolb, H. C., Finn, M. G., and Sharpless, K. B. (2001) Click Chemistry: Diverse Chemical Function from a Few Good Reactions Angew. Chem., Int. Ed. 40, 2004-2021
56. Rostovtsev, V. V., Green, L. G., Fokin, V. V., and Sharpless, K. B. (2002) A stepwise Huisgen cycloaddition process: Copper(I)-catalyzed regioselective ligation of azides and terminal alkynes Angew. Chem., Int. Ed. 41, 2596
57. Kumar, S. and Arya, D. P. (2011) Recognition of HIV TAR RNA by triazole linked neomycin dimers Bioorg. Med. Chem. Lett. 21, 4788-4792
58. Kumar, S., Xue, L., and Arya, D. P. (2011) Neomycin-Neomycin Dimer: An All-Carbohydrate Scaffold with High Affinity for AT-Rich DNA Duplexes J. Am. Chem. Soc. 133, 7361-7375
59. Arya, D. P., Coffee, R. L., and Xue, L. (2004) From triplex to B-form duplex stabilization: Reversal of target selectivity by aminoglycoside dimers Bioorg. Med. Chem. Lett. 14, 4643-4646 (Pubitemid 39490282)
60. Charles, I., Xue, L., and Arya, D. P. (2002) Synthesis of aminoglycoside-DNA conjugates Bioorg. Med. Chem. Lett. 12, 1259-1262 (Pubitemid 34327494)
61. Charles, I. and Arya, D. P. (2005) Synthesis of neomycin-DNA/peptide nucleic acid conjugates J. Carbohydr. Chem. 24, 145-160 (Pubitemid 41659678)
62. Suryawanshi, H., Sabharwal, H., and Maiti, S. (2010) Thermodynamics of Peptide-RNA Recognition: The Binding of a Tat Peptide to TAR RNA J. Phys. Chem. B 114, 11155-11163
63. Boger, D. L., Fink, B. E., Brunette, S. R., Tse, W. C., and Hedrick, M. P. (2001) A Simple, High-Resolution Method for Establishing DNA Binding Affinity and Sequence Selectivity J. Am. Chem. Soc. 123, 5878-5891 (Pubitemid 32888456)
64. Record, M. T., Jr., Anderson, C. F., and Lohman, T. M. (1978) Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: The roles of ion association or release, screening, and ion effects on water activity Q. Rev. Biophys. 11, 103-178 (Pubitemid 8373664)
65. Spolar, R. S., Livingstone, J. R., and Record, M. T. (1992) Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water Biochemistry 31, 3947-3955
66. Leonard, R., Zagury, D., Desportes, I., Bernard, J., Zagury, J. F., and Gallo, R. C. (1988) Cytopathic effect of human immunodeficiency virus in T4 cells is linked to the last stage of virus infection Proc. Natl. Acad. Sci. U.S.A. 85, 3570-3574
67. Robinson, W. E., Montefiori, D. C., Gillespie, D. H., and Mitchell, W. M. (1989) Complement-Mediated, Antibody-Dependent Enhancement of HIV-1 Infection in Vitro Is Characterized by Increased Protein and RNA Syntheses and Infectious Virus Release JAIDS, J. Acquired Immune Defic. Syndr. 2, 33-42 (Pubitemid 19127073)