High Resolution 2D-NMR Studies Including Complete Assignments and Conformational Characteristics of the NF-κB Binding Enhancer Element of HIV-LTR
| Autor: | Singh Mp, Fregeau Nl, J. W. Lown, Richard T. Pon |
|---|---|
| Rok vydání: | 1995 |
| Předmět: |
Magnetic Resonance Spectroscopy
Stereochemistry Molecular Sequence Data Human immunodeficiency virus (HIV) Biology medicine.disease_cause Genome chemistry.chemical_compound Nuclear magnetic resonance Structural Biology medicine Binding site Enhancer Molecular Biology Transcription factor Repetitive Sequences Nucleic Acid Base Sequence NF-kappa B Chromosome Mapping HIV NF-κB General Medicine Enhancer Elements Genetic chemistry Duplex (building) Nucleic Acid Conformation Two-dimensional nuclear magnetic resonance spectroscopy Protein Binding |
| Zdroj: | Journal of Biomolecular Structure and Dynamics. 13:269-284 |
| ISSN: | 1538-0254 0739-1102 |
| DOI: | 10.1080/07391102.1995.10508839 |
| Popis: | The asymmetrical DNA duplex [5'd(AAGGGACTTTCC)].[5'-d(GGAAAGTCCCTT)] has been studied by one- and two-dimensional NMR techniques. The sequence is comprised of the actual 10 base-pair long binding site for the transcription factor NF-kappa B in the enhancer sequence of the long term repeat (LTR) region of HIV and SIV types of retroviruses associated with the AIDS syndrome. Two additional A.T base-pairs are also included on one end for an added interest in the 12-bp duplex sequence with a pseudo dyad-symmetric disposition of the oligopurine and oligopyrimidine segments, as it appears in the HIV-1 genome. Phase-sensitive two-dimensional spectra (NOESY, ROESY, COSY and TOCSY) were obtained at three different temperatures (5, 15 and 25 degrees C) for a complete assignment of the non-exchangeable protons by tracing through sequence specific intra- and internucleotide connectivities. 2D-NOESY spectra were also acquired in aqueous (90% H2O-D2O) solutions, with two different methods of water signal suppression, to assign the exchangeable protons from specific NOE correlations. Adenine H2 protons were assigned by the use of NOE correlations and from T1 relaxation time measurements. The general spectral features and semi-quantitative interproton distance estimates indicate a B-DNA type conformation. However, some distinctly unusual features associated with the nucleotides at and immediately adjacent to both the 5'-and 3'-ends of AAA/TTT and GGG/CCC segments were noted. The complete assignments, and the observed characteristics, will be of significant value in studying the complexes of this transcriptionally active DNA domain with the protein and other rationally designed DNA binding agents. |
| Databáze: | OpenAIRE |
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