Physical characterization of a nucleic acid junction

Normally unstable transient states of DNA, in which the linear duplex branches to form junctions with three or more arms, can be studied at the oligonucleotide level if their sequences are carefully selected. We have designed a series of oligonucleotide complexes with sequences that are restricted to prevent any major overlap among the arms, and chosen to exhibit high equilibrium stabilities, as well. The electrophoretic mobility of these complexes on polyacrylamide gels permits us to demonstrate formation of a stable four-strand complex with 1:1:1:1 stoichiometry. We review here the evidence for formation of a stable stoichiometric junction, and present new circular dichroism data showing that the arms remain in B helix geometry within the complex, and that no significant loss of structure occurs on forming a junction.