An immobile nucleic acid junction constructed from oligonucleotides

Abstract

Base-paired DNA duplexes involving oligonucleotide model systems have provided the major source of detailed structural and dynamic information about double helical structure¹. Triple- and quadruple-branched ‘junction’ structures of DNA have a transient existence as intermediates in the replication or recombination of DNA molecules^2–5 while cruciforms may be inducible by negatively supercoiling closed circular DNA^6–11. However, it has not been possible to investigate these forms structurally at high resolution in short-chain molecules, where the junction will yield a significant component of the signal, because these naturally occurring intermediates are inherently unstable, due to internal sequence symmetry, which permits their resolution to double helices, via branchpoint migration^12–15. We have recently proposed that migration can be eliminated to yield immobile junctions from oligonucleotides^16–19 by combining sequence symmetry constraints with equilibrium calculations. We present here electrophoretic and UV optical absorbance experiments which indicate that four hexadecadeoxynucleotides (Fig. 1) indeed do form a stable tetrameric junction complex in solution.