Antiparallel DNA Double Crossover Molecules As Components for Nanoconstruction

Abstract

Double crossover molecules are DNA structures containing two Holliday junctions connected by two double helical arms. There are several types of double crossover molecules, differentiated by the relative orientations of their helix axes, parallel or antiparallel, and by the number of double helical half-turns (even or odd) between the two crossovers. We have examined these molecules from the viewpoint of their potential utility in nanoconstruction. Whereas the parallel double helical molecules are usually not well behaved, we have focused on the antiparallel molecules; antiparallel molecules with an even number of half turns between crossovers (termed DAE molecules) produce a reporter strand when ligated, so these have been characterized in a ligation cyclization assay. In contrast to other molecules that contain branched junctions, we find that these molecules cyclize rarely or not at all. The double crossover molecules cyclize no more readily than the linear molecule containing the same sequence as the ligation domain. We have tested both a conventional DAE molecule and one containing a bulged three-arm branched junction between the crossovers. The conventional DAE molecule appears to be slightly stiffer, but so few cyclic products are obtained in either case that quantitative comparisons are not possible. Thus, it appears that these molecules may be able to serve as the rigid components that are needed to assemble symmetric molecular structures, such as periodic lattices. We suggest that they be combined with DNA triangles and deltahedra in order to accomplish this goal.

Algorithmic Self-Assembly of DNA

“…There are three points to make. First, the rigidity of double crossover molecules, as demonstrated by Li et al (1996), suggests that the binding events should act together -in particular, the slot-filling event during proper growth should be cooperative. This intuition can be bolstered by estimating the "effective" local concentration of the remaining sticky end after one end has bound -giving an estimate for the additional "loop entropy" Schimmel 1980, p. 1205) 1:68 kcal/mol, which roughly offsets the contribution of a single base-pair bond (;1:4 kcal/mol).…”

“…The generality of the approach used here suggests that the potential for universal computation may be widespread among self-assembly processes in nature. In addition to being interesting in its own right as a universal mechanism, it may be worth considering whether the self-assembly processes described here could be useful technologically, perhaps as part of an approach to nanotechnology (Li et al 1996).…”

“…The ligation products ABC, ABCD, and ABCD' (by which we mean whatever it is we get when we intend to make structures ABC, ABCD, and ABCD' respectively) are examined both in non-denaturing and denaturing gels; in the former we are looking for a single band of approximately the correct apparent molecular weight, while in the latter we are looking for linear strands of the lengths predicted for ligation. Ligation of double crossover molecules has previously been shown to be well-behaved (Li et al 1996). Topologically closed structures, such as ABCD, can be assayed by treating with an exonuclease (Ma et al 1986).…”

Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices

“…These hairpin loops serve as topographic markers, which are observable by AFM. The DX tiles are stable and well behaved (32,33), both in solution and when analyzed on nondenaturing polyacrylamide gels.…”

3D DNA origami designed with caDNAno

“…This is made possible due to DNA's capacity for programmable self-assembly and its high stability. In subsequent works, several authors have used DNA to construct an increasing number of composite structures [3][4][5][6][7][8][9]. After the potential of DNA self-assembly was well established, Rothemund [10] introduced the method of DNA origami which is versatile in constructing pre-defined designs.…”