Biomolecular NMR Assignments

, Volume 2, Issue 2, pp 167–169 | Cite as

NMR assignments of HIV-2 TAR RNA

  • Teresa Carlomagno
  • Irene Amata
  • James R. Williamson
  • Mirko Hennig


We report nearly complete assignment for all 1H, 13C, 31P, and 15N resonances in the 30-nucleotide stem-loop HIV-2 TAR RNA located at the 5′ end of all viral mRNAs.


HIV-2 TAR RNA synthesis RNA resonance assignment 



The authors thank Lincoln Scott (Cassia LLC, San Diego) and Edit Sperling (TSRI, La Jolla) for preparing nucleotide triphosphates for transcription reactions, Claudia Schwiegk (MPI, Goettingen) for the syntesis of the TAR RNA used in 13C detected experiments and Christophe Fares (UHN, Toronto) for the development of the 13C detected experiments. This work was supported by a grant from the National Institutes of Health (GM-66669, to M.H. and J.R.W), by the Deutsche Forschungsgemeinschaft (SFB416 to T.C.) and by the MPG.


  1. Brodsky AS, Williamson JR (1997) Solution structure of the HIV-2 TAR-argininamide complex. J Mol Biol 267:624–639. doi: 10.1006/jmbi.1996.0879 CrossRefGoogle Scholar
  2. Carlomagno T, Hennig M, Williamson JR (2002) A novel PH-cT-COSY methodology for measuring JPH coupling constants in unlabeled nucleic acids application to HIV-2 TAR RNA. J Biomol NMR 22:65–81. doi: 10.1023/A:1013811631477 CrossRefGoogle Scholar
  3. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) Nmrpipe—a multidimensional spectral processing system based on unix pipes. J Biomol NMR 6:277–293. doi: 10.1007/BF00197809 CrossRefGoogle Scholar
  4. Fares C, Amata I, Carlomagno T (2007) 13C-detection in RNA bases: revealing structure-chemical shift relationships. J Am Chem Soc 129:15814–15823. doi: 10.1021/ja0727417 CrossRefGoogle Scholar
  5. Hennig M, Williamson JR (2000) Detection of N–H…N hydrogen bonding in RNA via scalar couplings in the absence of observable imino proton resonances. Nucleic Acids Res 28:1585–1593. doi: 10.1093/nar/28.7.1585 CrossRefGoogle Scholar
  6. Hennig M, Fohrer J, Carlomagno T (2005) Assignment and NOE analysis of 2′-hydroxyl protons in RNA: implications for stabilization of RNA A-form duplexes. J Am Chem Soc 127:2028–2029. doi: 10.1021/ja043390o CrossRefGoogle Scholar
  7. Milligan JF, Uhlenbeck OC (1989) Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol 180:51–62. doi: 10.1016/0076-6879(89)80091-6 CrossRefGoogle Scholar
  8. Richter S, Cao H, Rana TM (2002) Specific HIV-1 TAR RNA loop sequence and functional groups are required for human cyclin T1-Tat-TAR ternary complex formation. Biochemistry 41:6391–6397. doi: 10.1021/bi0159579 CrossRefGoogle Scholar
  9. Seelamgari A, Maddukuri A, Berro R, De la Fuente C, Kehn K, Deng LW et al (2004) Role of viral regulatory and accessory proteins in HIV-1 replication. Front Biosci 9:2388–2413. doi: 10.2741/1403 CrossRefGoogle Scholar
  10. Wei P, Garber ME, Fang SM, Fischer WH, Jones KA (1998) A novel CDK9-associated C-type cyclin interacts directly with HIV-1 Tat and mediates its high-affinity, loop-specific binding to TAR RNA. Cell 92:451–462. doi: 10.1016/S0092-8674(00)80939-3 CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  1. 1.Structural and Computational Biology UnitEMBL, European Molecular Biology LaboratoryHeidelbergGermany
  2. 2.EMBL, European Molecular Biology LaboratoryHeidelbergGermany
  3. 3.Department of Molecular Biology and The Skaggs Institute for Chemical BiologyThe Scripps Research InstituteLa JollaUSA
  4. 4.Department of Biochemistry and Molecular BiologyMedical University of South CarolinaCharlestonUSA

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