Self-complementarity

The tertiary structure of DNA is the structural level that is most relevant to 3-D reality. Traditionally, ODNs in a physiologically relevant aqueous solution are considered to be in a random-coiled ssDNA state or in the form of dsDNA helix in the presence of a complementary DNA, including the case of self-complementarity. The double helix is the dominant tertiary structure for biological DNA that can be in one of the three DNA conformations found in nature, A-DNA, B-DNA, and Z-DNA. The B-conformation described by Watson and Crick (11) is believed to predominate in cells (12). However other types of nucleic acid tertiary structures different from random or classical double-stranded helix forms can also be observed. Among them are triplexes, quadruplexes, and several other nucleic acid structures (13, 14). 

Beijer FH, Kooijman H, Spek AL, Sijbesma RP, Meijer EW. Self-complementarity achieved through quadruple hydrogen bonding. Angew Chem Int Ed 1998 37 75-78. 

Fig. 14 Assembly of adenine-bearing polymers by self-complementarity. Reprinted with permission from [79]...

Several extensions of the above study have now been reported leading to the synthesis of other pseudo-spherical softballs of the above type. For example, two (identical) self-complementarity subunits of type 33, also assemble to form a large. 

In the experiment, the components of the new replicator were mixed with the components of our biphenyl replicator [42], and we expected to generate four self-complementary, replicating systems. We assumed that self-complementarity of structure was sufficient for replication after all, had not all our replicators (and those of others [43]) shared this feature All possible combinations of (4), (8), (41) and (40) were duly synthesized (Figure 25), and their behavior taught us a lesson concerning molecular shape. One of the shuffled replicators, the adenine-thymine product (43), resembles DNA, but with an amide backbone. It turned out to be the most effective synthetic replicator we have encountered to date (perhaps this is not mere coincidence). The other shuffled replicator (44) was unable to catalyze its own formation. 

Isoaromatization of dienone macrocycles afforded Horning-crown macro-cycles - flexible macrocycles bearing structural elements reminiscent of those found in both calixarenes and crown ethers. In some cases the Horning-crown macrocycles exhibited solvent-dependent and switchable conformations. For macrocycles with the same short linker, self-complementarity was observed, and dimers tended to crystallize as solvates or inclusion compounds. This tendency was suppressed with longer linkers and in some Horning-crowns derived from trapezoidal macrocycles. These properties suggest potential applications in analysis, separation and detection (Figure 6.8). ... 

Use of conformational analysis self-complementarity of cyclotriveratrylene-molecular capsules... 

Figure 4.27 How self-complementarity dictates the tertiary structure of tRNA. 

A particularly intriguing kind of supramolecular self-assembly by axial coordination to metaUoporphyrins, namely self-complementary coordination, is reviewed in the second chapter by Yoshiaki Kobuke. Self-complementarity affords large stability constants. The fascinating systems described in Kobuke s contribution were prepared and investigated as models for components of photosynthetic natural systems self-complementary dimers of porphyrins mimic the special pair of the photosynthetic reaction centers, while macrocychc and three-dimensional porphyrin supramolecules were prepared as photosynthetic antenna models. 

Fig. 1.1. Schematic illustration of geometric self-complementarity leading to formation of dimeric supeimolecules and polymeric supramolecular arrays.

---