A DNA hairpin with a single residue loop closed by a strongly distorted watson-crick G·C base-pair

Amri, Chahrazade El; Mauffret, Olivier; Monnot, Monique; Tevanian, G.; Lescot, Elie; Porumb, Horea; Fermandjian, Serge

doi:10.1006/jmbi.1999.3270

Cited by 18 publications

(10 citation statements)

References 67 publications

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“…However, a bottom-strand oligo in which the central triplet (GAA) was shortened to an A or a T (o-11b, o-22b; Figure 3F) still gave full binding. The stability of hairpins formed at the strong topoisomerase II site in pBR322 has been reported to depend strongly on the loop sequence (39,40). These data suggest that the bottom strand of attC has a more stable conformation than the top strand due to the loop sequence.…”

Section: Mutations In the Central Tripletsupporting

confidence: 52%

Integron integrase binds to bulged hairpin DNA

Johansson

Kamali‐Moghaddam

Sundström

2004

Nucleic Acids Research

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Gene cassettes are short, monogenic DNA elements that translocate between integrons through sitespecific excision and integration. These events require that an integron-coded tyrosine recombinase forms a reactive complex with two sites, at least one of which belongs to the attC class. An attC site can be divided into two pairs of short repeats flanking a palindromic central region. The nucleotide sequence of attC among different cassettes varies extensively, implying that the site contains a structural recognition determinant with low sequence constraints. Oligonucleotides representing many different sequence modifications in either strand of the site were examined for integrase binding by using an electrophoresis mobility shift assay. The inner repeats, a central triplet and two single-nucleotide asymmetries in the site had the strongest influence on binding strength and strand choice. Our data show that the recombinase binds to a bulged hairpin in attC and that the hairpin distortion due to bulging could define the appropriate orientation of the otherwise symmetrical site. This is consistent with the strong bias for binding of recombinase to the bottom-strand oligonucleotides in vitro. Moreover, it was observed that the mobility-shifted complexes persisted under protein-denaturing assay conditions, indicating that a covalent link is indeed formed between integrase and DNA. Upon substitution of the presumed DNA-attacking residue, Y312, with a phenylalanine, DNA binding remained but there was no covalent linkage.

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Section: Mutations In the Central Tripletsupporting

confidence: 52%

Integron integrase binds to bulged hairpin DNA

Johansson

Kamali‐Moghaddam

Sundström

2004

Nucleic Acids Research

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“…43 The ATC loop is stabilized by an A Á C sheared base pair 77 while, in GAC, A stands above a strongly distorted Watson-Crick G Á C pair, while G is sandwiched between A (above) and C (below). 79 At any concentration A 1 is slightly more reactive in AT (L) C than in ATC in agreement with lower T m and A Á C mismatch rupture in AT (L) C. 78 At 2 Â 10 À6 and 2 Â 10 À7 M o , reactivity is impressively nearly as efficient for both d(ATC) hairpins and adenine (Table IV, Figure 6B, B 0 , and C). It is likely that structural adjustments associated with A 1 loading in deflecting the stem away from the silver surface suppress most P competitiveness.…”

Section: Exposed a 2 Nucleotide And Impede Its Docking Onto [Ag]supporting

confidence: 56%

“…NMR data proved that, at 2.5 Â 10 À5 M o , the homologous d19-mers with ATC, AT (L) C, 30,77,78 or GAC central triplets 79 adopt a hairpin structure (Figures 1 and 5) but not the d19-mer with CAG central triplet. Computed molecular dynamics (MD) simulations show that CAG bending is disfavored compared to GAC.…”

Section: Exposed a 2 Nucleotide And Impede Its Docking Onto [Ag]mentioning

confidence: 95%

“…79 The heterochiral d19-mer including a central L 2 0 -dT nucleotide (AT (L) C) was synthesized in the Laboratory of Dr B. Rayner at the University of Montpellier (Montpellier, France). 78 Stock solutions of NaCl and MgCl 2 were prepared at 10 À1 and 5 Â 10 À2 M, respectively, and of adenine, pdA, pA, rACC, Spectral Recording and Analysis UV spectra of nucleic acid solutions were recorded between 200 and 400 nm using an Uvikon 941 spectrophotometer equipped with a Bioblock Ministat or a Cary3 spectrophotometer equipped with a Huber Ministat and a PD415 temperature programmer (Bioblock Scientific, Illkirch, France).…”

Section: Compound Origins and Samplingmentioning

confidence: 99%

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Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopy

Grajcar

Amri²,

Ghomi

et al. 2006

Biopolymers

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We rank the reactivity of the adenyl residues (A) of model DNA and RNA molecules with electropositive subnano size [Ag]n+ sites as a function of nucleic acid primary sequences and secondary structures and in the presence of biological amounts of Cl- and Na+ or Mg2+ ions. In these conditions A is markedly more reactive than any other nucleic acid bases. A reactivity is higher in ribo (r) than in deoxyribo (d) species [pA>pdA and (pA)n>>(pdA)n]. Base pairing decreases A reactivity in corresponding duplexes but much less in r than in d. In linear single and paired dCAG or dGAC loci, base stacking inhibits A reactivity even if A is bulged or mispaired (A.A). dA tracts are highly reactive only when dilution prevents self-association and duplex structures. In d hairpins the solvent-exposed A residues are reactive in CAG and GAC triloops and even more in ATC loops. Among the eight rG1N2R3A4 loops, those bearing a single A (A4) are the least reactive. The solvent-exposed A2 is reactive, but synergistic structural transitions make the initially stacked A residues of any rGNAA loop much more reactive. Mg2+ cross-bridging single strands via phosphates may screen A reactivity. In contrast d duplexes cross-bridging enables "A flipping" much more in rA.U pairs than in dA.T. Mg2+ promotes A reactivity in unpaired strands. For hairpins Mg2+ binding stabilizes the stems, but according to A position in the loops, A reactivity may be abolished, reduced, or enhanced. It is emphasized that not only accessibility but also local flexibility, concerted docking, and cation and anion binding control A reactivity.

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“…These interactions, and hence the positioning of the Mg 2+ ions, are stably maintained throughout the MD simulations in all intercalation systems and are independent of the type of incoming dNTPs. (83)(84)(85), and quantum mechanical calculations also reveal that they are feasible (86). The hydrogen bonds between the nascent base pair with occupancy ≥ 10% are listed in Table 1.…”

Section: Sampling Of Near-reaction-ready Pα-o3′distancesmentioning

confidence: 95%

Accommodation of a 1S-(−)-Benzo[c]phenanthrenyl-N⁶-dA Adduct in the Y-Family Dpo4 DNA Polymerase Active Site: Structural Insights through Molecular Dynamics Simulations

Wang

Yan

et al. 2005

Chem. Res. Toxicol.

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Molecular modeling and molecular dynamics simulations have been performed to elucidate feasible structures in the Y-family Dpo4 DNA polymerase for the 1S-(-)-trans-anti-B[c]Ph-N 6 -dA adduct, derived from the fjord region polycyclic aromatic hydrocarbon (PAH) benzo[c]-phenanthrene. Three types of models were delineated as follows: an intercalation model, a model with the aromatic ring system in the polymerase major groove open pocket, and a -1 deletion major groove model. All four 2′-deoxyribonucleoside 5′-triphosphates (dNTPs) were considered in the first two cases, and a normal Watson-Crick partner positioned to have skipped the modified template was employed as the incoming dNTP in the -1 deletion case. The trajectories derived from the dynamics simulations were analyzed in detail to evaluate the extents of distortion for each system. Overall, our results suggest that the major groove model is the least distorted, followed by the -1 deletion model, while the intercalation model is perturbed the most. The syndGTP and syn-dATP mismatches opposite the lesion are well-accommodated in the major groove model, as is the normal Watson-Crick partner dTTP. The intercalation model appears most likely to impede the polymerase. More broadly, these models look reasonable for other PAH metabolitederived adducts to adenine with similar 1S stereochemistry. Furthermore, these models suggest how error-prone translesion synthesis by Y-family polymerases might produce mutations that may play a role in the initiation of cancer.

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A DNA hairpin with a single residue loop closed by a strongly distorted watson-crick G·C base-pair

Cited by 18 publications

References 67 publications

Integron integrase binds to bulged hairpin DNA

Integron integrase binds to bulged hairpin DNA

Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopy

Accommodation of a 1S-(−)-Benzo[c]phenanthrenyl-N⁶-dA Adduct in the Y-Family Dpo4 DNA Polymerase Active Site: Structural Insights through Molecular Dynamics Simulations

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A DNA hairpin with a single residue loop closed by a strongly distorted watson-crick G·C base-pair

Cited by 18 publications

References 67 publications

Integron integrase binds to bulged hairpin DNA

Integron integrase binds to bulged hairpin DNA

Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopy

Accommodation of a 1S-(−)-Benzo[c]phenanthrenyl-N6-dA Adduct in the Y-Family Dpo4 DNA Polymerase Active Site: Structural Insights through Molecular Dynamics Simulations

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Accommodation of a 1S-(−)-Benzo[c]phenanthrenyl-N⁶-dA Adduct in the Y-Family Dpo4 DNA Polymerase Active Site: Structural Insights through Molecular Dynamics Simulations