title: Effects of unpaired bases on the conformation and stability of three-arm DNA junctions.
abstract: Three-arm DNA junctions, in which three double helices intersect at a branch, have unique structure and reactivity of bases at and near the branch. Their solution conformation is asymmetric in the presence of Mg2+, while bases at the branch are sensitive to single-strand-specific agents. Following the surprising report that unpaired bases at the branch stabilize three-arm junctions, we have investigated the geometry and thermodynamics of three-arm junctions containing pendant T and A bases. The results are consistent with additional structure formation in junctions containing up to four pendant bases at the branch: relative to the tight junction, the thermal stability of junctions with two T's or A's at the branch increases; bases near the branch become less reactive to single-strand-reactive probes; and the enthalpy of formation is more negative. The interaction of ethidium observed at the branch in three-arm junctions is enhanced in junctions with unpaired bases at the branch. The geometry of three-arm junctions is perturbed by the presence of pendant bases, as seen by measuring the electrophoretic mobility of junctions to which long duplex arms are appended pairwise.
authors.affiliation: Department of Chemistry, New York University, New York 10003.
authors.forename: M
authors.initials: M
authors.lastname: Zhong
authors.forename: M S
authors.initials: MS
authors.lastname: Rashes
authors.forename: N B
authors.initials: NB
authors.lastname: Leontis
authors.forename: N R
authors.initials: NR
authors.lastname: Kallenbach
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D002152:Calorimetry, Differential Scanning; D004247:DNA / Q000737:chemistry*; D015246:Deoxyribonuclease EcoRI; D004047:Diethyl Pyrocarbonate / Q000494:pharmacology; D004591:Electrophoresis, Polyacrylamide Gel; D008274:Magnesium / Q000494:pharmacology; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
chemical_list: D004247:DNA; D015246:Deoxyribonuclease EcoRI; D008274:Magnesium; D004047:Diethyl Pyrocarbonate