Effects of Unpaired Bases on the Conformation and Stability of Three-Arm DNA Junctions

Min Zhong, Michael S. Rashes, Neville R. Kallenbach, Neocles B. Leontis

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)3660-3667
Number of pages8
Issue number12
StatePublished - Mar 1 1994

ASJC Scopus subject areas

  • Biochemistry


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