Hairpins in a DNA site for topoisomerase II studied by¹H-and³¹P-NMR

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

“…The particular stability exhibited by 22(+) can be explained by both the base-stacking pattern that continues inside the loop and the possible atypical hydrogen bond between the A9 base and the C11 base composing the loop. In comparison, the complementary 22(−) fragment is characterized by a loop with poor stacking interactions and absence of hydrogen bonding (Amir-Aslani et al, 1995;our work in progress). Base-pairings through atypical hydrogen bonds have been characterized in stable loops of RNA hairpins (UUCG, GNRA and CUUG: Varani, 1995;Jucker & Pardi, 1995) and DNA hairpins (Hirao et al, 1994).…”

“…Resonances marked with asterisks have been assigned to the partial duplex. This conformation can be solely observed at NMR concentrations (0mM) and not at lower concentrations (0mM) as used for UV and CD experiments (Amir-Aslani et al, 1995). chemical shifts of the A9 H2' and H2" protons.…”

“…This work, based on both NMR experiments and restrained energy-minimization calculations, describes the folding properties of a 19mer DNA strand, d(AGCTTATC-ATC-GATAAGCT) oligonucleotide (named hereafter 22(+)), which completes a preliminary analysis of the complementary strand d(AGCTTATC-GAT-GATAAGCT) (Amir-Aslani et al, 1995). The 22(+) oligonucleotide presents the optimal sequence for the cleavage of DNA by calf-thymus topoisomerase II coupled to the antitumour drug EPC (2,11-dimethyl-5-ethyl-9-hydroxy-6H-pyrido [4,3-b]carbazolium) (Fossé et al, 1991).…”

Induced‐Fit Recognition of DNA by Small Circular Oligonucleotides

“…Such a recognition process suggests that small cyclic oligonucleotides might be good candidates to target small DNA hairpins, which are known to be present in regulatory regions of the DNA, and are sites of preferential interactions of numerous proteins. [22,30,31] Experimental Section Sample preparation: The cyclic octamers were synthesized as reported by Alazzouzi et al [32] The stoichiometry for complex formation was determined by UV absorbance. Samples for NMR were suspended (in Na Circular dichroism: Circular dichroism spectra were collected on a Jasco J-810 spectropolarimeter fitted with a thermostatted cell holder.…”

Identification of Intrinsic Dynamics in a DNA Sequence Preferentially Cleaved by Topoisomerase II Enzyme

“…It is a symmetrical sequence with a strong potential to adopt a cruciform secondary structure and has been extensively studied in previous works. [31][32][33] Here we focus on the role of the AT-rich regions, located at the 5′ end of both cleavage sites, as determinants for the cleavage activity of topoisomerase II. A modified version of the sequence, in which one of the AT-rich regions is disrupted by mutations, is studied by NMR and molecular dynamics (MD) methods.…”