The Hairpin Structure of a Topoisomerase II Site DNA Strand Analyzed by Combined NMR and Energy Minimization Methods

Amir-Aslani, Arsia; Mauffret, Olivier; Sourgen, Frédéric; Neplaz, Stéphanie; Maroun, Richard G.; Lescot, Elie; Tevanian, G.; Fermandjian, Serge

doi:10.1006/jmbi.1996.0615

Cited by 16 publications

(14 citation statements)

References 38 publications

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“…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: 94%

“…73 Three-dimensional (3D) structures of r(GAGA), 74 r(GAAA), 75 r(GGAA), 76 and r(GUAA) 24 hairpins cocrystallized with a biological partner are available. NMR data also elucidated GCAA, GAAA, and GAGA r tetraloop 27 and ATC, AT (L) C, 30,77,78 and GAC 79 d triloop structures in solution.…”

Section: Introductionmentioning

confidence: 94%

“…If the A-loadings came from A in stems they should have been similar. Indeed, the 3D structures show high A 1 and A 2 C6N/ N7 accessibility in ATC 30,77,78 and GAC 79 loops, respectively, but A 1 is decisively more reactive in both ATC loci than A 2 in GAC and CAG ( Figures 5 and 6). 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).…”

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

confidence: 99%

“…A reactivity in d hairpins with ATC, AT (L) C, GAC, and CAG loops corroborates the structural results obtained with other spectroscopic techniques (UV, CD, and NMR). 30,[77][78][79]93 The C6N/N7 side of the A residue is solvent exposed and is predictive of high A reactivity. A may be docked without large backbone motions.…”

Section: Hairpin Structuresmentioning

confidence: 99%

“…For example, it is suggested that a dATC loop presents a specific cleavage site for topoisomerase II in pBR322 plasmidic DNA. 30 An A?G single nucleotide polymorphism in a quasipalindromic d locus of the human -globin gene simultaneously transforms a bulged duplex into a triloop stem and B (duplex) into A (stem) secondary structures. 16 This should have dramatic consequences on gene expression.…”

Section: Introductionmentioning

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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