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Gantchev TG, Cecchini S, Hunting DJ. Dynamic conformational states of DNA containing T.T or BrdU.T mispaired bases: wobble H-bond pairing versus cross-strand inter-atomic contacts. J Mol Model 2005; 11:141-59. [PMID: 15719239 DOI: 10.1007/s00894-005-0238-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2004] [Accepted: 12/01/2004] [Indexed: 11/28/2022]
Abstract
The dynamic structure of 11-mer DNA duplexes of different sequences with or without homopyrimidine (T.T, or BrdU.T) mismatches was studied by molecular dynamics (MD) simulations on a time scale from 200 ps to 1 ns. The conformational analysis suggests that in mismatched duplexes the formation of classical T.T wobble H-bonding pairing is nearest-neighbor sequence-dependent and, in most cases, three-centered H-bonds and numerous alternative close cross-strand interatomic contacts exist. Thus, in duplex W1, where the central triplet is 5'd(CTA).d(TTG), two wobble conformations W upward arrow (alphabeta) and W downward arrow (betaalpha) are formed and exchange rapidly at 300 K. In contrast, when the central triplet is 5'd(TTT).d(ATA) (W2 duplex) wobble conformations are rarely observed at 300 K, and the T.T mispair most often adopts a "twisted" conformation with one largely persistent normal H-bond, plus a stable cross-strand contact involving a T flanking base. However, at elevated temperature (400 K) the same W2 duplex shows frequent exchange between the two classical wobble conformations (alphabeta<-->betaalpha), as is in the case when the central triplet is 5'd(TBrdUT).d(ATA) (W3 duplex at 300 K). It is suggested that in the W2 sequence, restrictions due to thymine-methyl/pi interactions prevent the formation of wobble pairing and thermal activation energy, and/or the chemical replacement of T by BrdU are required in order for the T(BrdU).T mismatch to adopt and exchange between wobble conformations. The specific short and/or long-lived (double/triple) cross-strand dynamic interactions in W1, W2 and W3 duplexes are throughout characterized. These frequent atomic encounters exemplify possible inter-strand charge transfer pathways in the studied DNA molecules.
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Affiliation(s)
- Tsvetan G Gantchev
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada.
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Maufrais C, Fazakerley GV, Cadet J, Boulard Y. Structural study of DNA duplex containing an N-(2-deoxy-beta-D-erythro-pentofuranosyl) formamide frameshift by NMR and restrained molecular dynamics. Nucleic Acids Res 2003; 31:5930-40. [PMID: 14530441 PMCID: PMC219481 DOI: 10.1093/nar/gkg803] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The presence of an N-(2-deoxy-beta-D-erythro-pentofuranosyl) formamide (F) residue, a ring fragmentation product of thymine, in a frameshift context in the sequence 5'-d-(AGGACCACG)*d(CGTGGFTCCT) has been studied by 1H and 31P nuclear magnetic resonance (NMR) and molecular dynamics. Two-dimensional NMR studies show that the formamide residue, whether the cis or trans isomer, is rotated out of the helix and that the bases on either side of the formamide residue in the sequence, G14 and T16, are stacked over each other in a way similar to normal B-DNA. The cis and trans isomers were observed in the ratio 3:2 in solution. Information extracted from 31P NMR data reveal a modification of the phosphodiester backbone conformation at the extrahelical site, which is also observed during the molecular dynamics simulations.
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Affiliation(s)
- C Maufrais
- CEA, Département de Biologie Joliot Curie, Service de Biochimie et de Génétique Moléculaire, Bat 144, CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France
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Pakleza C, Cognet JAH. Biopolymer Chain Elasticity: A novel concept and a least deformation energy principle predicts backbone and overall folding of DNA TTT hairpins in agreement with NMR distances. Nucleic Acids Res 2003; 31:1075-85. [PMID: 12560506 PMCID: PMC149214 DOI: 10.1093/nar/gkg194] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A new molecular modelling methodology is presented and shown to apply to all published solution structures of DNA hairpins with TTT in the loop. It is based on the theory of elasticity of thin rods and on the assumption that single-stranded B-DNA behaves as a continuous, unshearable, unstretchable and flexible thin rod. It requires four construction steps: (i) computation of the tri-dimensional trajectory of the elastic line, (ii) global deformation of single-stranded helical DNA onto the elastic line, (iii) optimisation of the nucleoside rotations about the elastic line, (iv) energy minimisation to restore backbone bond lengths and bond angles. This theoretical approach called 'Biopolymer Chain Elasticity' (BCE) is capable of reproducing the tri-dimensional course of the sugar-phosphate chain and, using NMR-derived distances, of reproducing models close to published solution structures. This is shown by computing three different types of distance criteria. The natural description provided by the elastic line and by the new parameter, Omega, which corresponds to the rotation angles of nucleosides about the elastic line, offers a considerable simplification of molecular modelling of hairpin loops. They can be varied independently from each other, since the global shape of the hairpin loop is preserved in all cases.
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Affiliation(s)
- Christophe Pakleza
- Laboratoire de Physico-chimie Biomoléculaire et Cellulaire, UMR 7033 CNRS, T22-12, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris cedex 05, France
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Maufrais C, Boulard Y. Solution structure of a DNA duplex containing a formamide-adenine base pair. Can J Physiol Pharmacol 2002; 80:609-17. [PMID: 12182318 DOI: 10.1139/y02-068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The N-(2-deoxy-beta3-D-erythro-pentofuranosyl) formamide residue results from a ring fragmentation product of thymine or cytosine. The presence of a formamide-adenine base pair in the sequence 5'd(AGGAACCACG).d(CGTGGFTCCT) has been studied by 1H and 31P nuclear magnetic resonance (NMR) and molecular dynamics. There are two possible isomers for the formamide side chain, either cis or trans. For each isomer, we observed an equilibrium in solution between two forms. First, a species where the formamide is intrahelical and paired with the facing adenine. For the cis isomer, the formamide is in a syn conformation and two hydrogen bonds with adenine are formed. The trans isomer is in an anti conformation and a single hydrogen bond is observed. In the second form, whatever the isomer, the formamide is rejected outside the helix, whereas the adenine remains inside.
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Affiliation(s)
- Corinne Maufrais
- CEA Saclay, Service de Biochimie et de Génétique Moléculaire, Gif-sur-Yvette, France
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Abstract
Loss of a base in DNA, i.e., creation of an abasic site leaving a deoxyribose residue in the strand, is a frequent lesion that may occur spontaneously, or under the action of radiations and alkylating agents, or enzymatically as an intermediate in the repair of modified or abnormal bases. The abasic site lesion is mutagenic or lethal if not repaired. From a chemical point of view,the abasic site is an alkali-labile residue that leads to strand breakage through beta- and delta- elimination. Progress in the understanding of the chemistry and enzymology of abasic DNA largely relies upon the study of synthetic abasic duplexes. Several efficient synthetic methods have thus been developed to introduce the lesion (or a stable analogue) at defined position in the sequence. Physicochemical and spectroscopic examination of such duplexes, including calorimetry, melting temperature, high-field nmr and molecular modeling indicate that the lesion strongly destabilizes the duplex, although remaining in the canonical B-form with structural modifications strictly located at the site of the lesion. Probes have been developed to titrate the damage in DNA in vitro. Series of molecules have been devised to recognize specifically the abasic site, exhibiting a cleavage activity and mimicking the AP nucleases. Others have been prepared that bind strongly to the abasic site and show promise in potentiating the cytotoxic and antitumor activity of the clinically used nitrosourea (bis-chloroethylnitrosurea).
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Affiliation(s)
- J Lhomme
- LEDSS, Chimie Bioorganique, UMR CNRS 5616, Université Joseph Fourier, Grenoble Cedex 9, France.
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Abstract
In the years that have passed since the publication of Wolfram Saenger's classic book on nucleic acid structure (Saenger, 1984), a considerable amount of new data has been accumulated on the range of conformations which can be adopted by DNA. Many unusual species have joined the DNA zoo, including new varieties of two, three and four stranded helices. Much has been learnt about intrinsic DNA curvature, dynamics and conformational transitions and many types of damaged or deformed DNA have been investigated. In this article, we will try to summarise this progress, pointing out the scope of the various experimental techniques used to study DNA structure, and, where possible, trying to discern the rules which govern the behaviour of this subtle macromolecule. The article is divided into six major sections which begin with a general discussion of DNA structure and then present successively, B-DNA, DNA deformations, A-DNA, Z-DNA and DNARNA hybrids. An extensive set of references is included and should serve the reader who wishes to delve into greater detai.
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Affiliation(s)
- B Hartmann
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Paris, France
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Gervais V, Cognet JAH, Bret M, Sowers LC, Fazakerley GV. Solution Structure of two Mismatches A . A and T . T in the K-ras Gene Context by Nuclear Magnetic Resonance and Molecular Dynamics. ACTA ACUST UNITED AC 1995. [DOI: 10.1111/j.1432-1033.1995.0279n.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Gervais V, Cognet JAH, Bret M, Sowers LC, Fazakerley GV. Solution Structure of two Mismatches A . A and T . T in the K-ras Gene Context by Nuclear Magnetic Resonance and Molecular Dynamics. ACTA ACUST UNITED AC 1995. [DOI: 10.1111/j.1432-1033.1995.00279.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Piriou JM, Ketterlé C, Gabarro-Arpa J, Cognet JA, Le Bret M. A database of 32 DNA triplets to study triple helices by molecular mechanics and dynamics. Biophys Chem 1994; 50:323-43. [PMID: 8011951 DOI: 10.1016/0301-4622(93)e0103-c] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We present here a database of 32 deoxyribonucleotide triplets, that can be used as building blocks of triple helix forming deoxyribonucleotides on a computer. This database is made of all the pairing schemes of the triplets ATT, GCC+, ATA and GCG where the third base forms two hydrogen bonds with the purine of the first two Watson-Crick strands. The essential features of the known triple helices were preserved in the resulting structures. A triple helix can be easily built from any combination of these basic triplets. Four homogeneous and alternate triple helices thus obtained were studied by molecular mechanics and dynamics in vacuo. The results are in agreement with known experimental observations for ATT and suggest a possible structure for the GCG triple helix. In order to characterize the geometry of the structures obtained, the definitions of nucleic acid structure parameters (R.E. Dickerson et al., EMBO J. 8 (1989) 1-4) have been extended to triple helical polynucleotides.
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Affiliation(s)
- J M Piriou
- Laboratoire de Physicochimie et Pharmacologie des macromolécules biologiques (INSERM U140, CNRS URA 147), Villejuif, France
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Mouscadet JF, Ketterlé C, Goulaouic H, Carteau S, Subra F, Le Bret M, Auclair C. Triple helix formation with short oligonucleotide-intercalator conjugates matching the HIV-1 U3 LTR end sequence. Biochemistry 1994; 33:4187-96. [PMID: 8155634 DOI: 10.1021/bi00180a011] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In an attempt to target short purine sequences in view of pharmacological application, we have synthesized three new TFO (triple-helix-forming oligonucleotide) conjugates in which an intercalating oxazolopyridocarbazole (OPC) chromophore is linked by a pentamethylene linker to a 7-mer oligonucleotide matching the polypurine/polypyrimidine sequence located in the HIV-1 U3 LTR end region. The TFO moiety of conjugates are 5'CCTTCCC, 5'GGGAAGG, and 5'GGGTTGG. Their ability to bind to double-stranded DNA targets was examined. This binding is demonstrated by a footprinting technique using DNase I as a cleaving agent. The complex involved intermolecular pyr-pur*pyr or pur-pur*pyr triple helix. Pyrimidine TFO-OPC binds in a pH-dependent manner, whereas the others do not. The formation of the complex has been investigated at neutral pH and increasing temperature. We observed that the protection due to the purine and mixed TFO-OPC was pH independent and remained identical up to 40 degrees C. To determine the position of the OPC chromophore, molecular modeling was undertaken on the purine-conjugate/target complex. It has been suggested that the complex involved the intercalation of the OPC at the triplex-duplex junction with a small unwinding at the next excluded site.
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Affiliation(s)
- J F Mouscadet
- Laboratoire de Physicochimie et de Pharmacologie des Macromolécules Biologiques, Institut Gustave-Roussy, CNRS URA 147, INSERM, Villejuif, France
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Boulard Y, Cognet JA, Gabarro-Arpa J, Le Bret M, Sowers LC, Fazakerley GV. The pH dependent configurations of the C.A mispair in DNA. Nucleic Acids Res 1992; 20:1933-41. [PMID: 1579495 PMCID: PMC312309 DOI: 10.1093/nar/20.8.1933] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The structure of the cytosine-adenine mispair in a 7 base pair duplex has been investigated by proton NMR spectroscopy. At low pH, the predominant structure is protonated on the A residue and assumes a wobble conformation consistent with previous findings. The C residue of the mispair is found in a C2'-C3' endo equilibrium. This is confirmed by molecular dynamics calculations which suggest that the conformation of the protonated wobble is flexible and not as rigid as a normal base pair. As the solution pH is raised, a structural transition is observed with an apparent pK of 7.54 at 23 degrees C. At higher pH the predominant structure is one in which both the C and A residues are intrahelical. Evidence is presented that this structure corresponds to a reverse wobble in which the two bases are held together by one hydrogen bond. This structure is much less stable than the protonated form and even at low temperature single strands are observed in slow exchange with the neutral duplex form.
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Affiliation(s)
- Y Boulard
- Service de Biochimie et de Génétique Moléculaire, Département de Biologie Cellulaire et Moléculaire, Gif-sur-Yvette, France
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Cognet JA, Gabarro-Arpa J, Le Bret M, van der Marel GA, van Boom JH, Fazakerley GV. Solution conformation of an oligonucleotide containing a G.G mismatch determined by nuclear magnetic resonance and molecular mechanics. Nucleic Acids Res 1991; 19:6771-9. [PMID: 1837078 PMCID: PMC329308 DOI: 10.1093/nar/19.24.6771] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We have determined by two-dimensional nuclear magnetic resonance studies and molecular mechanics calculations the three dimensional solution structure of the non-selfcomplementary oligonucleotide, d(GAGGAGGCACG). d(CGTGCGTCCTC) in which the central base pair is G.G. This is the first structural determination of a G.G mismatch in a oligonucleotide. Two dimensional nuclear magnetic resonance spectra show that the bases of the mismatched pair are stacked into the helix and that the helix adopts a classical B-DNA form. Spectra of the exchangeable protons show that the two guanosines are base paired via their imino protons. For the non-exchangeable protons and for some of the exchangeable protons nuclear Overhauser enhancement build up curves at short mixing times have been measured. These give 84 proton-proton distances which are sensitive to the helix conformation. One of the guanosines adopts a normal anti conformation while the other is syn or close to syn. All non-terminal sugars are C2' endo. These data sets were incorporated into the refinement of the oligonucleotide structure by molecular mechanics calculations. The G.G mismatch shows a symmetrical base pairing structure. Although the mismatch is very bulky many of its features are close to that of normal B-DNA. The mismatch induces a small lateral shift in the helix axis and the sum of the helical twist above and below the mismatch is close to that of B-DNA.
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Affiliation(s)
- J A Cognet
- Laboratoire de Physico-chimie Macromoléculaire, Institut Gustave Roussy, Villejuif, France
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