DNA Double-Crossover Molecules

The Holliday junction is a well-known intermediate in recombination, but it is not the only one. Another species is the DNA double-crossover molecule, termed DX. The DX molecule consists of two four-arm branched junctions that have been joined at two adjacent arms, to create a molecule containing two helical domains joined by two crossover points (Fu and Seeman 1993). There are five different motifs of the DX molecule these are illustrated in Figure 14, with a modification of one of them. The names of the DX molecules all begin with D, for double crossover . Those in the top row have P for their second letter, indicating that their helix axes are parallel hence, there is a dyad axis, vertical in the plane of the page and parallel to the helix axes, relating each helical domain of the DP molecules to the other domain. 

Fu, T.-J., Kemper, B., Seeman, N.C. (1994a) Endonuclease VII cleavage of DNA double crossover molecules. Biochemistry 33, 3896-3905. 

Of course, the use of AFM is not restricted to the investigation of supramolecular structures in the material sciences. Xrtificial" biomaterials were also recently probed by AFM. For instance, two-dimensional crystalline forms of DNA that self-assemble from synthetic DNA double-crossover molecules were assembled, and their patterned crystals were visualized by AFM. Intermolecular interactions between the structural units are programmed by the design of sticky ends that associate according to Watson-Crick complementarity.Recently, biohybrids, formed by the association of two biotinylated polystyrene... 

FIGURE 3 DNA double-crossover molecules can implement abstract Wang tiles, producing a two-dimensional lattice of DNA with binding interactions dictated by the DNA sticky ends. Source Adapted with permission from Winfree, 2000. 

Fonte, R, Nogueira, T., Gehm, C., Ferreira, D., Sarmento, B., 2011. Chitosan-coated sohd hpid nanoparticles enhance the oral absorption of insulin. Drug Dehv. Transl. Res. 1 (4), 299-308. T.J., Seeman, N.C., 1993. DNA double-crossover molecules. Biochemistry 32 (13), 3211-3220. 

FIG. 13 Synthetic DN A motifs for the construction of DNA framework Three- [75] (13) and four-arm (14) DNA junction [8] DNA double-crossover (DX) molecules 15,16 were used for initial studies of enzymatic oligomerization [79]. The DX motif 17, containing four cohesive ends of individual nucleotide sequence, was used for the construction of two-dimensional DNA crystals [80]. 

Figure 14. Motifs of double crossover molecules. The top row contains the three parallel isomers of double crossover (DX) molecules, DPE, DPOW and DPON P in their name indicates their parallel structure. Arrowheads indicate 3 ends of strands. Strands drawn with the same thickness are related by the vertical dyad axis indicated in the plane of the paper. DPE contains crossovers separated by an even number (two) of half-turns of DNA, DPOx by an odd number in DPOW, the extra half turn is a major groove spacing, in DPON, it is a minor groove spacing. The middle row illustrates two other DX isomers, DAE, and DAO. The symmetry axis of DAE is normal to the page (and broken by the nick in the central strand) the symmetry axis of DAO is horizontal within the page in DAO, strands of opposite thickness are related by symmetry. DAE+J, in the second row, is a DAE molecule, in which an extra junction replaces the nick shown in DAE.

Fig. 8 Schematic representation of DNA junctions and crossover tiles. Motif 1 is a branched DNA junction with three arms and motif 2 with four arms. Every terminal in the arm is an unpaired ssDNA. The ssDNA acts as sticky ends , which may pair with another complementary strand. The two motifs 3 and 4 are two different antiparallel double-crossover molecules containing an even number of half-helical turns between branch points (DAE) or an odd number (DAO). They are more stable and thus usually applied. Oligonucleotide strands are individually represented with different colors...

Holliday intermediate. An intermediate in genetic recombination in which two double-stranded DNA molecules are joined by virtue of a reciprocal crossover involving one strand of each molecule. 

A robust rotary device based on this principle has been developed using a new DNA motif, PX DNA, and one of its variants. JX2 DNA. PX DNA consists of two parallel double helices, wherein crossovers occur at aU possible sites two crossovers are absent in the JX2 molecule. 

RecQ helicase and Topo III was then direaly assessed by AFM. Images show complex catenated DNA species involving crossovers between multiple double-stranded DNA molecules that are consistent with full catenanes. ... 

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