Document 0907 DOCN M9650907 TI High resolution 2D-NMR studies indicating complete assignments and conformational characteristics of the NF-kappa B binding enhancer element of HIV-LTR. DT 9605 AU Singh MP; Fregeau NL; Pon RT; Lown JW; Department of Chemistry, University of Alberta, Edmonton, Canada. SO J Biomol Struct Dyn. 1995 Oct;13(2):269-84. Unique Identifier : AIDSLINE MED/96127168 AB 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. DE Base Sequence Chromosome Mapping *Enhancer Elements (Genetics) HIV/*GENETICS Molecular Sequence Data Nuclear Magnetic Resonance/*METHODS Nucleic Acid Conformation NF-kappa B/*GENETICS Protein Binding *Repetitive Sequences, Nucleic Acid Support, Non-U.S. Gov't JOURNAL ARTICLE SOURCE: National Library of Medicine. NOTICE: This material may be protected by Copyright Law (Title 17, U.S.Code).