Template dimerization

Figure 4.4 OrgeFs template-directed oligomerization. The main process in template-directed oligomerization of mononucleotides acmally occurs at the dimer or trimer level. When an activated mononucleotide is allowed to react in the presence of a complementary polynucleotide template, dimers are first formed in a non-catalyzed phase of the reaction they then bind to the template and are ligated and extended. (Adapted from Schwarz, 1998.)...

The palladium(II) template dimerization of the thiolato ligands in (%) with boron tribromide, which proceeds via internal nucleophilic displacements of bromide from an intermediate bis(benzyl bromide) complex, affords the 14-membered trans-AS2S2 macrocycle (R, R )- 97) (Figure 2) as air-... 

Figure 5 A general mechanism for autocatalysis, in which template dimers catalyze the coupling of reactants to form trimer complexes, which can then dissociate into template dimers and free template monomers.

Amino-5 -deoxy-2, 3 -0-isopropylideneadenosine was acylated at N-5 with an activated derivative of the 6-carboxy-2-naphthyl ester of Kemp s acid imide. The resulting molecule possesses self-complementary binding sites, the key feature of replicating molecules that act as templates for their own reproduction. The dimer of this molecule is, however, not very stable K = 630 L mol ). When the two initially mentioned educts are added, a small proportion of the ternary complex is also formed and undergoes a fast, template-catalysed... 

Fig. 8. Rephcation. The amino adenosine X and the pentafluorophenyl ester Y form a hydrogen-bonded dimer XY, prior to reaction between the amine and the activated ester groups (shown in the circle). The reaction product is a <7 -amide conformer cis-Z that isomeri2es to the more stable trans- acnide Z. The rephcative process is cataly2ed by the reaction product Z (also referred to as the template). First, a termolecular complex XYZ is formed from X, Y, and Z.

The amide formation reaction (highlighted by the circle) leads to the production of a hydrogen-bonded dimer (ZZ) of the reaction product Z with the template Z. The dimer is in thermodynamic equilibrium with free template in the reaction medium. 

Fig. 6-12. Different types of binding sites in polymers eontaining miero- (site B), meso- and maerop-ores (site A) C) Embedded site, D) Site eomplementary to dimer or multimer, E) Indueed binding site, E) Nonseleetive site, G) Residual template.

Simidzu et al.70) carried out template-directed synthesis using various types of templates, e. g neutral ones, 34 (PSt TCT) and PSt TCTC, and cationic ones, such as APVP, 35 (APVP PSt), UPVP PSt, ARPVP, APEI, and 36 (ARPEI). They obtained a large amount of purine-containing oligomers (dimer or trimer) as compared to pyrimidine ones by condensation of nucleotide mixture in the presence of the neutral templates containing pyrimidine bases, such as PSt TCT and PSt TCTC. The authors stated from the results that the existence of the... 

The coupling reaction of 1 (M=Zn) affords CPO 3 (M=Zn) in 55% yield in the presence of template 2 however, the absence of 2 decreases the yield to 34% [22]. With the increase of yield of 3, template 2 induces the selectivity of the reaction the yield of the by-product (cychc dimer 4 (M=Zn)) was changed from 23% (with no template) to 6% (in the presence of template). A similar CPO formation reaction was reported for the corresponding ruthenium porphyrins (3, M=Ru(CO)), in which the stability constant of the Ru-N coordination bond is 10 larger than that of the Zn-N coordination bond [23]. Although the transition state of the CPO produced by the ruthenium-based substrate is expected to be more stable than that produced by ZnPor, the yield of 3 (M=Ru(CO)) is only... 

The ligation product is a copy of the template, so this represents a self-replication procedure for Pl-Cys-P2. Initial rates depend on the square root of the template concentration (a common observation, readily explained where the template is active as the monomer but present mostly as the dimer), but rates fall off, as expected, as the product accumulates. 

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