title: A dumbbell double nicked duplex dodecamer DNA with a PEG6 tether.
abstract: A hairpin dodecamer DNA motif with a dangling end composed of four bases was studied in order to find conditions which promote a dumbbell structure as the sole form in solution. It could be used as a model of a DNA duplex with two nicks on opposite strands, mimicking a target for topo II poisons. We have established two alternative means of obtaining a dumbbell in solution as the only form present at 0 °C. The first one is to use a relatively high concentration of a hairpin motif, ca. 3.5 mM, at low ionic strength, and second is to use a moderate hairpin motif concentration of ca. 2 mM at high ionic strength, 200 mM and 15% of methanol. An NMR-derived structure in a buffered water solution is presented. A representative structure ensemble of 10 structures was obtained from MD calculations utilizing the AMBER protocol and using NOESY-derived experiment cross peak volumes transferred to experimental restraints by the MARDIGRAS algorithm.
authors.affiliation: Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44, 01-224, Warszawa, Poland.
authors.forename: Karolina
authors.initials: K
authors.lastname: Hyz
authors.forename: Wojciech
authors.initials: W
authors.lastname: Bocian
authors.forename: Robert
authors.initials: R
authors.lastname: Kawęcki
authors.forename: Elżbieta
authors.initials: E
authors.lastname: Bednarek
authors.forename: Jerzy
authors.initials: J
authors.lastname: Sitkowski
authors.forename: Lech
authors.initials: L
authors.lastname: Kozerski
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D053904:DNA Breaks, Single-Stranded; D004250:DNA Topoisomerases, Type II / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D055029:Inverted Repeat Sequences; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D018716:Molecular Mimicry; D009690:Nucleic Acid Conformation; D011092:Polyethylene Glycols / Q000737:chemistry*; D011522:Protons; D012996:Solutions; D013816:Thermodynamics; D059005:Topoisomerase II Inhibitors / Q000737:chemistry / Q000378:metabolism
chemical_list: D011522:Protons; D012996:Solutions; D059005:Topoisomerase II Inhibitors; D011092:Polyethylene Glycols; D004247:DNA; D004250:DNA Topoisomerases, Type II