NMR-STUDIES OF DNA 3-WAY JUNCTIONS CONTAINING 2 UNPAIRED THYMIDINE BASES - THE INFLUENCE OF THE SEQUENCE AT THE JUNCTION ON THE STABILITY OF THE STACKING CONFORMERS

DNA three-way junctions (TWJs) containing unpaired residues at the bra nch point can adopt a conformation in which one helix is stacked upon another, forming a coaxial, quasicontinuous double helix. As in four-w ay junctions (FWJs), two conformers with different stacking arrangemen ts between the arms are possible. However, in both types of structures a markedly strong preference for one conformer has been observed. To investigate the basis for this preference, in particular the influence of the stacking proclivity of the base-pairs at the centre of the jun ction, two linear oligomers (36 nucleotides), TWJ1 and TWJ2, differing only in one base-pair (G . C versus C . G, respectively) at the branc h point, were designed and chemically synthesized. Each one is expecte d to fold into a stable three-way junction, containing two unpaired th ymidine bases at the junction region and two arms capped with a hairpi n loop. The data obtained from H-1 and P-31-NMR spectroscopy confirm t hat both oligomers are present-as stable three-way junctions. In both TWJs two of the helical arms stack preferentially upon each other. How ever, the stacking arrangement is similar in both molecules. From this it is deduced that purine-purine stacking across the junction cannot he considered as a major factor that determines the preferred stacking arrangement. (C) 1996 Academic Press Limited.