DNA molecules can drive the assembly of other DNA molecules into specific four-stranded structures

Single-stranded DNA molecules containing clustered G-repeats can be assembl ed into various four-stranded structures linked by G-quartets. Here, we rep ort that such molecules can also drive the assembly of other DNA molecules containing G-repeats into specific four-stranded structures. In these assay s, the oligonucleotides 5'-CAGGCTGAGCAGGTACGGGGGAGCTGGGGTAGATTGGAATGTAG-3' (oligo D) and 5'-CGGGGGAGCTGGGGT-3' (oligo B), consisting of sequences foun d in immunoglobulin switch regions, were annealed in a buffer containing K and the annealing products were analyzed by polyacrylamide gel electrophor esis. This analysis revealed that whereas annealing of each oligo alone pro duced four-stranded structures designated D-2 and B-2, annealing of mixture s containing both oligos produced additional complexes designated D-2* and B-2*. D-2* and B-2* were found to contain only D molecules and only B molec ules, respectively. The yield of D-2* increased and the yield of Ed decreas ed, as the concentration ratio oligo B/oligo D was increased. These results indicated that B can drive the assembly of D into D-2* and D can drive the assembly of B into B-2*. Further studies revealed that while the assembly of D, followed a second order kinetics, the B-driven assembly of D-2* follo wed a first order kinetics. Dimethyl sulfate footprinting indicated that bo th D-2 and D-2* are four-stranded structures containing two parallel and tw o antiparallel chains. In addition, annealing of D mixed with various B mut ants showed that only mutants containing two G-clusters can drive the assem bly of D-2*. Based on these data, we propose that in the process of D-2* as sembly, a four-stranded intermediate containing B and D is formed and then dissociates into D-2* and B in a rate-limiting first order reaction. Driver mechanisms of this type may cause formation of specific four-stranded stru ctures at G-rich chromosomal sites, thereby regulating processes such as re combination and telomere synthesis. (C) 1999 Academic Press.