RELATIVE STABILITIES OF DNA 3-WAY, 4-WAY AND 5-WAY JUNCTIONS (MULTI-HELIX JUNCTION LOOPS) - UNPAIRED NUCLEOTIDES CAN BE STABILIZING OR DESTABILIZING

Competition binding and UV melting studies of a DNA model system consi sting of three, four or five mutually complementary oligonucleotides d emonstrate that unpaired bases at the branch point stabilize three- an d five-way junction loops but destabilize four-way junctions. The incl usion of unpaired nucleotides permits the assembly of five-way DNA jun ction complexes (5WJ) having as few as seven basepairs per arm from fi ve mutually complementary oligonucleotides. Previous work showed that 5WJ, having eight basepairs per arm but lacking unpaired bases, could not be assembled I[Wang,Y.L., Mueller,J.E., Kemper,B. and Seeman,N.C. (1991) Biochemistry, 30, 5667-5674]. Competition binding experiments d emonstrate that four-way junctions (4WJ) are more stable than three-wa y junctions (3WJ), when no unpaired bases are included at the branch p oint, but less stable when unpaired bases are present at the junction. 5WJ complexes are in all cases less stable than 4WJ or 3WJ complexes. UV melting curves confirm the relative stabilities of these junctions . These results provide qualitative guidelines for improving the way i n which multi-helix junction loops are handled in secondary structure prediction programs, especially for single-stranded nucleic acids havi ng primary sequences that can form alternative structures comprising d ifferent types of junctions.