Conformational Studies by1H NMR of the HIV Enhancer: the Transcription Factors NF-κB and Sp1 Binding Domains

Delepierre, Muriel; Sodano, P.; Gouyette, Catherine; Namane, Abdelkader; Igolen, J.; Virelizier, Jean-Louis

doi:10.1002/(sici)1097-458x(199612)34:13<s67::aid-omr45>3.0.co;2-f

Cited by 4 publications

(1 citation statement)

References 53 publications

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“…The AH2-H1′ interstrand interactions are however quite similar in the case of the 3′-end adenines of both duplexes. These differences between 16N and 16M in interstrand NOE interactions were previously observed for the larger 24 bp fragments encompassing the κB site and one of the Sp1 sites (36). They suggest a wider minor groove for 16M that could induce changes in the major groove geometry where NF-κB binds.…”

Section: Analysis Of Nmr Datasupporting

confidence: 61%

NF-κB Binding Mechanism: A Nuclear Magnetic Resonance and Modeling Study of a GGG → CTC Mutation

1999

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We present the solution structure of the nonpalindromic 16 bp DNA 5'd(CTGCTCACTTTCCAGG)3'. 5'd(CCTGGAAAGTGAGCAG)3' containing a mutated kappaB site for which the mutation of a highly conserved GGG tract of the native kappaB HIV-1 site to CTC abolishes NF-kappaB binding. 1H and 31P NMR spectroscopies have been used together with molecular modeling to determine the fine structure of the duplex. NMR data show evidence for a BI-BII equilibrium of the CpA.TpG steps at the 3'-end of the oligomer. Models for the extreme conformations reached by the mutated duplex (denoted 16M) are proposed in agreement with the NMR data. Since the distribution of BII sites is changed in the mutated duplex compared to that of the native duplex (denoted 16N), large differences are induced in the intrinsic structural properties of both duplexes. In particular, in BII structures, 16M shows a kink located at the 3'-end of the duplex, and in contrast, 16N exhibits an intrinsic global curvature toward the major groove. Whereas 16N can reach a conformation very favorable for the interaction with NF-kappaB, 16M cannot mimic such a conformation and, moreover, its deeper and narrower major groove could hinder the DNA-protein interactions.

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Section: Analysis Of Nmr Datasupporting

confidence: 61%

NF-κB Binding Mechanism: A Nuclear Magnetic Resonance and Modeling Study of a GGG → CTC Mutation

1999

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DNA fine structure and dynamics in crystals and in solution: The impact of BI/BII backbone conformations

2003

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Sugar-phosphate backbone conformations are an important structural element for a complete understanding of specific recognition in nucleic acid-protein interactions. They can be involved both in early stages of target discrimination and in structural adaptation upon binding. In the first part of this study, we have analyzed high-resolution structures of double-stranded B-DNA either isolated or bound to proteins, and explored the impact of both the standard BI and the unusual BII phosphate backbone conformations on neighboring sugar puckers and on selected helical parameters. Correlations are found to be similar for free and bound DNA, and in both categories, the possible facing backbone conformations (BI.BI, BI.BII, and BII.BII) define well-characterized substates in the B-DNA conformational space. Notably, BII.BII steps are characterized by specific, and sequence-independent, structural effects involving reduced standard deviations for almost all conformational parameters. In the second part of this work, we analyze four 10 ns molecular dynamics simulations in explicit solvent on the DNA targets of NF-kappaB and bovine papillomavirus E2 proteins, highlighting the multiplicity of backbone dynamical behavior. These results show sequence effects on the percentages of BI and BII conformers, the preferential state of facing backbones, the occurrence of coupled transitions. The backbone states can consequently be seen as a mechanism for transmitting information from the bases to the phosphate groups and thus for modulating the overall structural properties of the target DNA.

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Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 κb site: evidence for BI-BII equilibrium inducing a global dynamic curvature of the duplex 1 1Edited by I. Tinoco

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et al. 1998

Journal of Molecular Biology

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Conformational Studies by1H NMR of the HIV Enhancer: the Transcription Factors NF-κB and Sp1 Binding Domains

Cited by 4 publications

References 53 publications

NF-κB Binding Mechanism: A Nuclear Magnetic Resonance and Modeling Study of a GGG → CTC Mutation

NF-κB Binding Mechanism: A Nuclear Magnetic Resonance and Modeling Study of a GGG → CTC Mutation

DNA fine structure and dynamics in crystals and in solution: The impact of BI/BII backbone conformations

Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 κb site: evidence for BI-BII equilibrium inducing a global dynamic curvature of the duplex 1 1Edited by I. Tinoco

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