Effect of T-T Base Mismatches on Three-Arm DNA Junctions

Min Zhong, Michael S. Rashes, Neville R. Kallenbach

Research output: Contribution to journalArticlepeer-review


In contrast to four-arm immobile DNA junctions, three-arm DNA junctions have unique structural and dynamic properties consistent with lack of a single dominant conformation. The effect of T-T base mismatches at the branch in a three-arm model junction has been investigated using a combination of electrophoretic mobility measurements, chemical footprinting experiments, and thermodynamic studies. The results indicate that three-arm junctions are only slightly destabilized by a mismatch flanking the branch, relative to four-arm junctions. The effect of a mismatch varies with the sequence and position of the site of the mismatch. Since a three-arm junction with two mismatches flanking the branch is as stable as two junctions each with a single mismatch, the stability of three-arm junctions is not determined by stacking interactions at the branch in a simple way. The properties of three-arm junctions with one or two mismatches are consistent with a picture in which the conformation is the result of several substrates in which base pairs flanking the branch are transiently open, allowing bases to interact with the remaining duplexes.

Original languageEnglish (US)
Pages (from-to)6898-6907
Number of pages10
Issue number27
StatePublished - 1993

ASJC Scopus subject areas

  • Biochemistry


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