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Téletchéa S, Skauge T, Sletten E, Kozelka J. Cisplatin Adducts on a GGG Sequence within a DNA Duplex Studied by NMR Spectroscopy and Molecular Dynamics Simulations. Chemistry 2009; 15:12320-37. [DOI: 10.1002/chem.200901158] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Abstract
This unit provides an overview of the use of NMR to determine oligonucleotide structure. It covers basic NMR spectral properties, acquisition of interproton distance restraints and torsion angle restraints, structure refinement, assessment of the quality of the structure obtained. Software programs used in the process are also described.
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Affiliation(s)
- T L James
- University of California, San Francisco, California, USA
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3
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von Feilitzsch T, Tuma J, Neubauer H, Verdier L, Haselsberger R, Feick R, Gurzadyan G, Voityuk AA, Griesinger C, Michel-Beyerle ME. Chromophore/DNA Interactions: Femto- to Nanosecond Spectroscopy, NMR Structure, and Electron Transfer Theory. J Phys Chem B 2007; 112:973-89. [DOI: 10.1021/jp076405o] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Till von Feilitzsch
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
| | - Jennifer Tuma
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
| | - Heike Neubauer
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
| | - Laurent Verdier
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
| | - Reinhard Haselsberger
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
| | - Reiner Feick
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
| | - Gagik Gurzadyan
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
| | - Alexander A. Voityuk
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
| | - Christian Griesinger
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
| | - Maria E. Michel-Beyerle
- Physikalische Chemie, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany, Centre d'Études du Bouchet BP 391710, 91710 Vert Le Petit, France, and Institució Catalana de Recerca i Estudis Avancats (ICREA), Institute of Computational Chemistry, Universitat de Girona, Spain
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Lakshman MK, Keeler JC, Ngassa FN, Hilmer JH, Pradhan P, Zajc B, Thomasson KA. Highly diastereoselective synthesis of nucleoside adducts from the carcinogenic benzo[a]pyrene diol epoxide and a computational analysis. J Am Chem Soc 2007; 129:68-76. [PMID: 17199284 PMCID: PMC2659345 DOI: 10.1021/ja063902u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A diastereoselective synthesis of the nucleoside adducts corresponding to a cis ring-opening of the carcinogen (+/-)-7 beta, 8 alpha-dihydroxy-9 alpha,10 alpha-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BaP DE-2) by 2'-deoxyadenosine and 2'-deoxyguanosine is described. The key intermediate (+/-)-10alpha-amino-7beta,8alpha,9alpha-trihydroxy-7,8,9,10-tetrahydrobenzo[a]pyrene was synthesized by a highly diastereoselective dihydroxylation wherein phenylboronic acid was a water surrogate. The resulting boronate ester was converted to a tetraol derivative in which two of the four hydroxyl groups (trans 7, 8) were protected as benzoate esters while the remaining two (cis 9, 10) were free. The cis glycol entity was then subjected to a reaction with 1-chlorocarbonyl-1-methylethylacetate to yield an intermediate chloro monoacetoxy dibenzoate. Displacement of the halide with azide, complete cleavage of the esters, and catalytic reduction of the azide yielded the requisite amino triol. Fluoride displacement from appropriately protected nucleoside derivatives, 6-fluoropurine 2'-deoxyribonucleoside and 2-fluoro-2'-deoxyinosine, by the amino triol then yielded diastereomeric pairs of diol epoxide-adducted 2'-deoxyadenosine (dA) and 2'-deoxyguanosine (dG) nucleosides. Small aliquots of these adducts were separated for characterization purposes. The present approach provides the first diastereoselective synthesis of the cis adducts of BaP DE-2 with 2'-deoxyguanosine as well as the first synthesis of both dA and dG adducts from a common intermediate. An informative analysis of the 1H NMR spectra of the cis adducts synthesized and comparisons to the trans adducts are reported. To gain insight into the diastereoselectivity in the key dihydroxylation step, a computational analysis, including molecular mechanics (MMFF94) and semiempirical AM1 geometry optimizations, yielded results that are in fairly good agreement with the experimental observations.
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Wecker K, Bonnet MC, Meurs EF, Delepierre M. The role of the phosphorus BI-BII transition in protein-DNA recognition: the NF-kappaB complex. Nucleic Acids Res 2002; 30:4452-9. [PMID: 12384592 PMCID: PMC137123 DOI: 10.1093/nar/gkf559] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2002] [Revised: 08/14/2002] [Accepted: 08/14/2002] [Indexed: 11/12/2022] Open
Abstract
We examined, by 1H and 31P NMR, the solution structure of a 16 bp non-palindromic DNA fragment (16M2) containing the HIV-1 NF-kappaB-binding site, in which the sequences flanking the kappaB site had been mutated. 31P NMR was particularly useful for obtaining structural information on the phosphodiester backbone conformation. Structural features were then compared with those of the two previously studied DNA fragments corresponding, respectively, to the native kappaB fragment (16N) and a fragment in which mutations have been introduced at the 5' end of the kappaB site (16M1). For the mutated 16M2 duplex, NMR data showed that the BI-BII equilibrium, previously reported for the native fragment (16N) at the kappaB flanking steps, was lost. The role of the BI-BII equilibrium in NF-kappaB recognition by DNA was then investigated by electrophoretic mobility shift assay. We found that the isolated kappaB site has the potential to bind efficiently due to the BI-BII equilibrium of the kappaB flanking sequences.
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Affiliation(s)
- K Wecker
- Unité de RMN des Biomolécules, URA 2185 CNRS, Institut Pasteur, 28 rue du Docteur Roux, 75015 Paris, France
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6
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Elizondo-Riojas MA, Kozelka J. Unrestrained 5 ns molecular dynamics simulation of a cisplatin-DNA 1,2-GG adduct provides a rationale for the NMR features and reveals increased conformational flexibility at the platinum binding site. J Mol Biol 2001; 314:1227-43. [PMID: 11743736 DOI: 10.1006/jmbi.2000.5216] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A 5 ns unrestrained molecular dynamics (MD) simulation of the DNA duplex d(GCCG*G*ATCGC)-d(GCGATCCGGC), bearing a cis-Pt(NH(3))(2)(2+) unit crosslinking the two G* guanine bases, is reported. The MD trajectory was a posteriori correlated with NMR data determined for the same adduct, and it is shown that interproton distances and the characteristic chemical shifts are accounted for by the simulation. The simulation and its confrontation with the NMR data have confirmed the finding derived early from static models that the cytosine complementary to the 5' G*, C17, is mobile with respect to its adjacent bases. However, in contrast to our previous description of this mobility, which included rupture of the Watson-Crick hydrogen bonds and formation of non-Watson-Crick hydrogen bonds, the MD simulation indicated that the G*4-C17 pair moves continuously along a trajectory roughly perpendicular to the local helix axis, with retention of all three Watson-Crick hydrogen bonds. The simulation indicated the reversible formation of a hydrogen bond between the 5' oriented NH(3) ligand of platinum and the C3pG*4 phosphate group, in accord with our former prediction. Furthermore, the simulation has disclosed previously undetected BI <=> BII transitions at the G*5pA6 and A6pT7 steps, connected to formation/rupture of a hydrogen bond between the 3' oriented NH(3) ligand of platinum and the N7 atom of A6. All these conformational equilibria affect the form of the minor groove and increase the conformational flexibility at the platination site, and are thus likely to facilitate recognition by cellular proteins.
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Affiliation(s)
- M A Elizondo-Riojas
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université René Descartes, UMR 8601 CNRS, 45 rue des Saints-Pères, 75270, Paris 06, France
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7
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Cromsigt JA, Hilbers CW, Wijmenga SS. Prediction of proton chemical shifts in RNA. Their use in structure refinement and validation. JOURNAL OF BIOMOLECULAR NMR 2001; 21:11-29. [PMID: 11693565 DOI: 10.1023/a:1011914132531] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
An analysis is presented of experimental versus calculated chemical shifts of the non-exchangeable protons for 28 RNA structures deposited in the Protein Data Bank, covering a wide range of structural building blocks. We have used existing models for ring-current and magnetic-anisotropy contributions to calculate the proton chemical shifts from the structures. Two different parameter sets were tried: (i) parameters derived by Ribas-Prado and Giessner-Prettre (GP set) [(1981) J. Mol. Struct., 76, 81-92.]; (ii) parameters derived by Case [(1995) J. Biomol. NMR, 6, 341-346]. Both sets lead to similar results. The detailed analysis was carried using the GP set. The root-mean-square-deviation between the predicted and observed chemical shifts of the complete database is 0.16 ppm with a Pearson correlation coefficient of 0.79. For protons in the usually well-defined A-helix environment these numbers are, 0.08 ppm and 0.96, respectively. As a result of this good correspondence, a reliable analysis could be made of the structural dependencies of the 1H chemical shifts revealing their physical origin. For example, a down-field shift of either H2' or H3' or both indicates a high-syn/syn chi-angle. In an A-helix it is essentially the 5'-neighbor that affects the chemical shifts of H5, H6 and H8 protons. The H5, H6 and H8 resonances can therefore be assigned in an A-helix on the basis of their observed chemical shifts. In general, the chemical shifts were found to be quite sensitive to structural changes. We therefore propose that a comparison between calculated and observed 1H chemical shifts is a good tool for validation and refinement of structures derived from NOEs and J-couplings.
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Affiliation(s)
- J A Cromsigt
- Department of Medical Biosciences, Medical Biophysics, Umeå University, Sweden
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Marcourt L, Cordier C, Couesnon T, Dodin G. Impact of C5-cytosine methylation on the solution structure of d(GAAAACGTTTTC)2. An NMR and molecular modelling investigation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 265:1032-42. [PMID: 10518799 DOI: 10.1046/j.1432-1327.1999.00819.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The solution structures of d(GAAAACGTTTTC)2 and of its methylated derivative d(GAAAAMe5CGTTTTC)2 have been determined by NMR and molecular modelling in order to examine the impact of cytosine methylation on the central CpG conformation. Detailed 1H NMR and 31P NMR investigation of the two oligomers includes quantitative NOESY, 2D homonuclear Hartmann-Hahn spectroscopy, double-quantum-filtered COSY and heteronuclear 1H-31P correlation. Back-calculations of NOESY spectra and simulations of double-quantum-filtered COSY patterns were performed to gain accurate information on interproton distances and sugar phase angles. Molecular models under experimental constraints were generated by energy minimization by means of the molecular mechanics program JUMNA. The MORASS software was used to iteratively refine the structures obtained. After methylation, the oligomer still has a B-DNA conformation. However, there are differences in the structural parameters and the thermal stability as compared to the unmethylated molecule. Careful structural analysis shows that after methylation CpG departs from the usual conformation observed in other ACGT tetramers with different surroundings. Subtle displacements of bases, sugars and backbone imposed by the steric interaction of the two methyl groups inside the major groove are accompanied by severe pinching of the minor groove at the C-G residues.
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Affiliation(s)
- L Marcourt
- Institut de Topologie et de Dynamique des Systèmes, associé au CNRS, Université D. Diderot (Paris 7), Paris, France
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Cordier C, Marcourt L, Petitjean M, Dodin G. Conformational variation of the central CG site in d(ATGACGTCAT)2 and d(GAAAACGTTTTC)2. An NMR, molecular modelling and 3D-homology investigation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 261:722-33. [PMID: 10215889 DOI: 10.1046/j.1432-1327.1999.00314.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The determination of the solution structure of two self-complementary oligomers d(ATGACGTCAT)2 (CG10) and d(GAAAACGTTTTC)2 (CG12), both containing the 5'-pur-ACGT-pyr-3' sequence, is reported. The impact of the base context on the conformation of the central CpG site has been examined by a combined approach of: (a) 2D 1H-NMR and 31P-NMR; (b) molecular mechanics under experimental constraints; (c) back-calculations of NOESY spectra and iterative refinements of distances; and (d) 3D-homology search of the central tetrad ACGT within the complete oligonucleotides. A full NMR study of each fragment is achieved by means of standard 2D experiments: NOESY, 2D homonuclear Hartmann-Hahn spectroscopy, double-quantum-filtered COSY and heteronuclear 1H-31P correlation. Sugar phase angle, epsilon-zeta difference angle and NOE-derived distances are input as experimental constraints to generate molecular models by energy minimization with the help of jumna. The morass program is used to iteratively refine the structures obtained. The similarity of the two ACGTs within the whole oligonucleotides is investigated. Both the decamer and the dodecamer adopt a B-like DNA conformation. However, the helical parameters within this conformational type are significantly different in CG12 and CG10. The central CpG step conformation is not locked by its nearest environment (5'A and 3'T) as seen from the structural analysis of ACGT in the two molecules. In CG12, despite the presence of runs of A-T pairs, CpG presents a high twist of 43 degrees and a sugar phase at the guanine of about 180 degrees, previously observed in other ACGT-containing-oligomers. Conversely, ACGT in CG10 exhibits strong inclinations, positive rolls, a flat profile of sugar phase, twist and glycosidic angles, as a result of the nucleotide sequence extending beyond the tetrad. The structural specificity of CG10 and its flexibility (as reflected by its energy) are tentatively related to the process of recognition of the cyclic AMP response element by its cognate protein.
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Affiliation(s)
- C Cordier
- Institut de Topologie et de Dynamique des Systèmes, associé au CNRS, Université D. Diderot (Paris 7), France
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Leporc S, Mauffret O, El Antri S, Convert O, Lescot E, Tevanian G, Fermandjian S. An NMR study of d(CTACTGCTTTAG).d(CTAAAGCAGTAG) showing hydration water molecules in the minor groove of a TpA step. J Biomol Struct Dyn 1998; 16:639-49. [PMID: 10052620 DOI: 10.1080/07391102.1998.10508276] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The hydration properties of the non-palindromic duplex d(CTACTGCTTTAG). d(CTAAAGCAGTAG) were investigated by NMR spectroscopy. The oligonucleotide possesses a heterogeneous B-DNA structure. The H2(n)-H1'(m+1) distances reflect a minor groove narrowing within the TTT/AAA segment (approximately 3.9A) and a sudden widening at the T10:A15 base-pair (approximately 5.3A), the standard B-DNA distance being approximately 5A. The facing T10pA11 and T14pA15 steps at the end of the TTTA/AAAT segment have completely different behaviors. Only A15 ending the AAA run displays NMR features comparable to those shown by adenines of TpA steps occupying the central position of TnAn (n> or =2) segments. These involve particular chemical shifts and line broadening of the H2 and H8 protons. Positive NOESY cross-peaks were measured between the water protons and the H2 protons of A15, A16 and A17 reflecting the occurrence of hydration water molecules with residence times longer than 500 picoseconds along the minor groove of the TTT/AAA segment. In contrast no water molecules with long residence times were observed neither for A3, A20 and A23 nor for A11 ending the 5'TTTA run. We confirm thus that the binding of water molecules with long residence time to adenine residues correlates with the minor groove narrowing. In contrast, the widening of the minor groove at the A11:T14 base-pair ending the TTTA/TAAA segment, likely associated to a high negative propeller twist value at this base-pair, prevents the binding of a water molecule with long residence time to A11 but not to A15 of the preceding T10:A15 base-pair. Thus, in our non-palindromic oligonucleotide the water molecules bind differently to A11 and A15 although both adenines are part of a TpA step. The slower motions occurring at A15 compared to A11 are also well explained by the present results.
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Affiliation(s)
- S Leporc
- Département de Biologie Structurale UMR 1772 CNRS, Institut Gustave Roussy, Villejuif, France
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11
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Dejaegere AP, Case DA. Density Functional Study of Ribose and Deoxyribose Chemical Shifts. J Phys Chem A 1998. [DOI: 10.1021/jp980926h] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Annick P. Dejaegere
- Groupe RMN-UPR 9003, Ecole Supérieure de Biotechnologie de Strasbourg, 67400 Illkirch, France, and Lab. de Chimie Biophysique, ISIS-UPRESA-7006 CNRS, rue B. Pascal, 67000 Strasbourg, France
| | - David A. Case
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92307
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Tisné C, Hantz E, Hartmann B, Delepierre M. Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 kappa B site: evidence for BI-BII equilibrium inducing a global dynamic curvature of the duplex. J Mol Biol 1998; 279:127-42. [PMID: 9636705 DOI: 10.1006/jmbi.1998.1757] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
1H and 31P NMR spectroscopy have been used together with molecular modelling to determine the fine structure of a non-palindromic 16 bp DNA containing the NF-kappa B binding site. Much emphasis has been placed upon NMR optimization of both two-dimensional 31P NMR techniques to extract structural information defining the phosphodiester backbone conformation and selective homonuclear 2D COSY experiments to determine sugar conformations. NMR data show evidence for a dynamic behaviour of steps flanking the ten base-pairs of the NF-kappa B binding site. A BI-BII equilibrium at these steps is demonstrated and two models for each extreme conformation are proposed in agreement with NMR data. In the refined BII structures, the NF-kappa B binding site exhibits an intrinsic curvature towards the major groove that is magnified by the four flanking steps in the BII conformation. Furthermore, the base-pairs are translated into the major groove. Thus, we present a novel mode of dynamic intrinsic curvature compatible with the DNA curvature observed in the X-ray structure of the p50-DNA complex.
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Affiliation(s)
- C Tisné
- Laboratoire de RMN, Institut Pasteur, CNRS URA, Paris, France
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13
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Wijmenga SS, Kruithof M, Hilbers CW. Analysis of (1)H chemical shifts in DNA: Assessment of the reliability of (1)H chemical shift calculations for use in structure refinement. JOURNAL OF BIOMOLECULAR NMR 1997; 10:337-50. [PMID: 20859781 DOI: 10.1023/a:1018348123074] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The reliability of (1)H chemical shift calculations for DNA is assessed by comparing the experimentally and calculated chemical shifts of a reasonably large number of independently determined DNA structures. The calculated chemical shifts are based on semiempirical relations derived by Giessner-Prettre and Pullman [(1987) Q. Rev. Biophys., 20, 113-172]. The standard deviation between calculated and observed chemical shifts is found to be quite small, i.e. 0.17 ppm. This high accuracy, which is achieved without parameter adjustment, makes it possible to analyze the structural dependencies of chemical shifts in a reliable fashion. The conformation-dependent (1)H chemical shift is mainly determined by the ring current effect and the local magnetic anisotropy, while the third possible effect, that of the electric field, is surprisingly small. It was further found that for a double helical environment, the chemical shift of the sugar protons, H2' to H5'', is mainly affected by the ring current and magnetic anisotropy of their own base. Consequently, the chemical shift of these sugar protons is determined by two factors, namely the type of base to which the sugar ring is attached, C, T, A, or G, and secondly by the χ-angle. In particular, the H2' shift varies strongly with the χ-angle, and strong upfield H2' shifts directly indicate that the χ-angle is in the syn domain. The H1' shift is not only strongly affected by its own base, but also by its 3'-neighboring base. On the other hand, base protons, in particular H5 of cytosine and methyl protons of thymine, are affected mainly by the 5'-neighboring bases, although some effect (0.2 ppm) stems from the 3'-neighboring base. The H2 protons are mainly affected by the 3'-neighboring base. As a result of these findings a simple scheme is proposed for sequential assignment of resonances from B-helices based on chemical shifts.
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Affiliation(s)
- S S Wijmenga
- Department of Medical Biochemistry and Biophysics, Umeå University, S-901 87, Umeå, Sweden
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Overmars FJ, Lanzotti V, Galeone A, Pepe A, Mayol L, Pikkemaat JA, Altona C. Design and NMR study of an immobile DNA four-way junction containing 38 nucleotides. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 249:576-83. [PMID: 9370369 DOI: 10.1111/j.1432-1033.1997.00576.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The DNA Holliday junction is a central intermediate in genetic recombination. We have designed and synthesized a DNA oligomer, J1a, as a model compound for the Holliday junction suitable to be studied by NMR spectroscopy and future molecular modelling. The design was based on a 46-base oligomer, J4, previously studied by Pikkemaat, J. A., van den Elst, H., van Boom, J. H. & Altona, C. [Biochemistry 33, 14896-14907 (1994)], including the propensity to undergo a self-folding process to give a four-way junction in which three of the four arms are capped with a hairpin loop. J1a, however, is considerably shortened by eight bases and thus contains only 38 residues which significantly facilitates the proton resonance assignments. The base sequence at the branch point is identical to that in J4. 1H-NMR data clearly point to the presence of three hairpin loops in J1a and show that the double-helical arms adopt the B-DNA form. Quasicontinuous pairwise stacking between helical arms to give a single preferred stacked X-conformation is evident. The extent of folding into this stacked conformation is strongly dependent upon the magnesium concentration. Full Watson-Crick base pairing at the branch point is completely preserved. The A/D-stacking preference of the small junction is the same as that exhibited by J4.
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Affiliation(s)
- F J Overmars
- Leiden Institute of Chemistry, Gorlaeus Laboratories, The Netherlands
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Evans PD, Jaseja M, Jeeves M, Hyde EI. NMR studies of the Escherichia coli Trp repressor.trpRs operator complex. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 242:567-75. [PMID: 9022683 DOI: 10.1111/j.1432-1033.1996.0567r.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
To understand the specificity of the Escherichia coli Trp repressor for its operators, we have begun to study complexes of the protein with alternative DNA sequences, using 1H-NMR spectroscopy. We report here the 1H-NMR chemical shifts of a 20-bp oligodeoxynucleotide containing the sequence of a symmetrised form of the trpR operator in the presence and absence of the holorepressor. Deuterated protein was used to assign the spectrum of the oligodeoxynucleotide in a 37-kDa complex with the Trp holorepressor. Many of the resonances of the DNA shift on binding to the protein, which suggests changes in conformation throughout the sequence. The largest changes in shifts for the aromatic protons in the major groove are for A15 and G16, which are thought to hydrogen bond to the protein, possibly via water molecules. We have also examined the effect of DNA binding on the corepressor, tryptophan, in this complex. The indole proton resonance of the tryptophan undergoes a downfield shift of 1.2 ppm upon binding of DNA. This large shift is consistent with hydrogen bonding of the tryptophan to the phosphate backbone of the trpR operator DNA, as in the crystal structure of the holoprotein with the trp operator.
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Affiliation(s)
- P D Evans
- School of Biochemistry, University of Birmingham, Edgbaston, UK
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Case DA. Calibration of ring-current effects in proteins and nucleic acids. JOURNAL OF BIOMOLECULAR NMR 1995; 6:341-6. [PMID: 8563464 DOI: 10.1007/bf00197633] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Density functional chemical shielding calculations are reported for methane molecules placed in a variety of positions near aromatic rings of the type found in proteins and nucleic acids. The results are compared to empirical formulas that relate these intermolecular shielding effects to magnetic anisotropy ('ring-current') effects and to electrostatic polarization of the C-H bonds. Good agreement is found between the empirical formulas and the quantum chemistry results, allowing a reassessment of the ring-current intensity factors for aromatic amino acids and nucleic acid bases. Electrostatic interactions contribute significantly to the computed chemical shift dispersion. Prospects for using this information in the analysis of chemical shifts in proteins and nucleic acids are discussed.
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Affiliation(s)
- D A Case
- Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
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Lefebvre A, Mauffret O, el Antri S, Monnot M, Lescot E, Fermandjian S. Sequence dependent effects of CpG cytosine methylation. A joint 1H-NMR and 31P-NMR study. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 229:445-54. [PMID: 7744067 DOI: 10.1111/j.1432-1033.1995.0445k.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The impact of cytosine methylation in the central CpG step of two closely related octanucleotide duplexes d(CATCGATG)2 and d(CTTCGAAG)2 was examined by 1H-NMR and 31P-NMR experiments, and a quantitative structural analysis was performed using the NOE-derived distances, the sugar puckers and the epsilon torsion angles. The two starting oligonucleotides displayed a B-DNA conformation with, however, significant local structure differences. Although the methylated oligonucleotides retained their B-DNA conformation, different structural and thermal stability effects were observed. The magnitude of the methylation effects was to depend on the initial conformation of the CpG site, which is governed by the nature of the dinucleotide AT or TT located on the CpG flanks. As an example of sequence dependence, the methylation of CpG entailed larger conformational variation in d(CATCGATG)2 than in d(CTTCGAAG)2. In this study, the 1H and 31P chemical-shift parameters averred as extremely sensitive probes for detecting subtle conformational changes. Finally, our comparative results may aid our understanding of the structural and related biological effects produced by cytosine methylation in DNA.
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Affiliation(s)
- A Lefebvre
- Laboratoire de Biologie Structurale, URA 147 CNRS, Institut Gustave Roussy, Villejuif, France
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18
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Lane A, Martin SR, Ebel S, Brown T. Solution conformation of a deoxynucleotide containing tandem G.A mismatched base pairs and 3'-overhanging ends in d(GTGAACTT)2. Biochemistry 1992; 31:12087-95. [PMID: 1333792 DOI: 10.1021/bi00163a018] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have used 31P and 1H NMR spectroscopy and circular dichroism to define the solution conformation of d(GTGAACTT)2 which contains tandem G.A mismatched base pairs and 3'-overhanging TT ends. Measurements of coupling constants and NOE intensities show that the sugar puckers of the nucleotides are predominantly in the south domain (i.e., near C2'-endo) and that the glycosidic torsion angles are anti. The sequential NOE intensities indicate the presence of a right-handed helix. Analysis of the 31P and 1H NMR spectra of the duplex shows that the tandem mismatch forms a block in which there are unusual backbone torsion angles (i.e., in the BII state), within an otherwise B-like structure. The chemical shift of the N1H of the mismatched guanosine and NOEs between the mismatched base pairs and their nearest neighbors are inconsistent with the imino pairing present in single A.G mismatches or in the X-ray structure of a tandem mismatch [Privé, G. G., et al. (1987) Science 238, 498-503] but the data are consistent with the amino pairing found by Li et al. (1991) [Li, Y., et al. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 26-30]. The strong base-base stacking both within the tandem G.A block and between the G.A mismatches and their other nearest neighbors offsets the intrinsic destabilizing effects of the mismatch. Further, the 3'-TT overhangs stack onto the ends of the helix and stabilize the duplex against fraying, which accounts for the observed increase in the melting temperature compared with the flush-ended duplex.
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Affiliation(s)
- A Lane
- Laboratory for Molecular Structure, National Institute for Medical Research, London, U.K
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Lane AN. N.m.r. assignments and temperature-dependent conformational transitions of a mutant trp operator-promoter in solution. Biochem J 1989; 259:715-24. [PMID: 2730583 PMCID: PMC1138577 DOI: 10.1042/bj2590715] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A total of 145 protons in the mutant trp operator-promoter sequence CGTACTGATTAATCAGTACG were assigned by one-dimensional and two-dimensional n.m.r. methods. Except at the sites of mutation (underlined), the chemical shifts and other n.m.r. parameters are very similar to those observed in the symmetrized wild-type sequence [Lefèvre, Lane & Jardetzky (1987) Biochemistry 26, 5076-5090]. Spin-spin-relaxation rate constants of the resolved base protons and intra- and inter-nucleotide nuclear-Overhauser-enhancement intensities argue for a sequence-dependent structure similar to that of the wild-type, except at and close to the sites of the mutation. The overall tumbling time as a function of temperature was determined from cross-relaxation rate constants for the H-6-H-5 vectors of the four cytosine residues. The values are consistent with the oligonucleotide maintaining a double-helical conformation over the entire temperature range 5-45 degrees C, and that internal motions of the bases are of small amplitude on the subnanosecond time scale. The temperature-dependence of chemical shifts, spin-spin-relaxation rate constants and cross-relaxation rate constants show the occurrence of two conformational transitions localized to the TTAA sequence in the centre of the molecule. The thermodynamics of the transition at the lower temperature (tm = 16 degrees C) were analysed according to a two-state process. The mid-point temperature is about 6 degrees C higher than in the wild-type sequence. The conformational transition does not lead to rupture of the Watson-Crick hydrogen bonds, but probably involves changes in the propellor twists of T.A-9 and T.A-10. The second transition occurs at about 40 degrees C, but cannot be fully characterized. This conformational variability seems to be a property of the sequence TTAA, and may have functional significance in bacterial promoters.
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Affiliation(s)
- A N Lane
- National Institute for Medical Research, London, U.K
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Van de Ven FJ, Hilbers CW. Nucleic acids and nuclear magnetic resonance. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 178:1-38. [PMID: 3060357 DOI: 10.1111/j.1432-1033.1988.tb14425.x] [Citation(s) in RCA: 209] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- F J Van de Ven
- Department of Biophysical Chemistry, University of Nijmegen, The Netherlands
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