Nucleic acid junctions and lattices

Abstract It is possible to generate sequences of oligomeric nucleic acids which will preferentially associate to form migrationally immobile junctions, rather than linear duplexes, as they usually do. These structures are predicated on the maximization of Watson-Crick base pairing and the lack of sequence symmetry customarily found in their analogs in living systems. Criteria are presented which oligonucleotide sequences must fulfill in order to yield these junction structures. The generable junctions are nexi, from which 3 to 8 double helices may emanate. Each junction may be treated as a macromolecular “valence cluster”, and the individual clusters may be linked together directly, or with pieces of linear DNA interspersed between them. This covalent linkage can be done with enormous specificity, using the sticky-ended ligation techniques currently employed in genetic engineering studies. It appears to be possible to generate covalently joined three-dimensional networks of nucleic acids which are periodic in connectivity and perhaps in space.