| Holliday junctions are intermediates in genetic recombination. In natural systems, their sequences have 2-fold (homologous) sequence symmetry. This symmetry enables the molecules to undergo an isomerization. Branch migration leads to polydispersity, which makes it difficult to characterize the physical properties of the junction and the effects of the sequence context flanking the branch point. We report an undistorted symmetric immobile junction based on the use of DNA parallelogram structures. We have used a series of these junctions to characterize the junction resolution reaction catalyzed by Vaccinia virus DNA topoisomerase. The resolution reaction entails cleavage and rejoining at CCCTT↓N recognition sites arrayed on opposing sides of the four-arm junction. We find that resolution is optimal when the scissile phosphodiester (Tp↓N) is located two nucleotides 5' to the branch point on the helical strand. Covalent topoisomerase-DNA adducts are precursors to recombinant strands in all reactions, as expected. Kinetic analysis suggests a rate limiting step after the first-strand cleavage.; We developed a DNA nanomechanical device that enables the positional synthesis of products whose sequences are determined by the state of the device. This machine emulates the translational capabilities of the ribosome. The device has been prototyped to make specific DNA sequences. The state of the device is established by the addition of DNA set strands. There is no transcriptional relationship between the set strands and the product strands. The device has potential applications that include designer polymer synthesis, encryption of information, and use as a variable-input device for DNA-based computation. |
