Templating group

A few examples illustrate the interaction between monomer and template groups and the nature of forces operating in the system template-monomer (Table 3.1). 

CLUSTAL X Alignments Template Group Four Templates Five Templates Pairwise... 

The Template Group consists of the sequence for a specific protein from several different... 

Figure 2. Glass Rf oxygen plasma apparatus for removing template groups.

The expression template reaction indicates mostly a reaction in which a complexed me) ion holds reactive groups in the correct orientation to allow selective multi-step reactions. T1 template effect of the metal is twofold (i) polymerization reactions are suppressed, since th local concentration of reactants around the metal ion is very high (ii) multi-step reactions are possible, since the metal holds the reactants together. In the following one-step synthesis eleven molecules (three ethylenediamine — en , six formaldehyde, and two ammonia molecules) react with each other to form one single compound in a reported yield of 95%. It is ob vious that such a reaction is dictated by the organizing power of the metal ion (I.I. Creasei 1977),... 

Synthesis of large heterocycles usually involves condensation reactions of two difunctional molecules. Such molecules tend to polymerize. So far two special techniques have been described above to avoid this important side-reaaion , namely high dilution and use of templates. The general procedure to avoid polymerizations in reactions between difunctional molecules is, of course, the application of protecting groups as described in sections 4.1.2 and 2.6. 

Fig. 25. Schematic representation of imprinting (a) cross-linking polymerization ia the presence of a template (T) to obtain cavities of specific shape and a defined spatial arrangement of functional groups (binding sites. A—C) (b) cross-linked polymer prepared from the template monomer and ethylene...

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.

DNA polymerase enzymes all synthesize DNA by adding deoxynucleotides to the free 3 -OH group of an RNA or DNA primer sequence. The identity of the inserted nucleotide is deterrnined by its abiHty to base-pair with the template nucleic acid. The dependence of synthesis on a primer oligonucleotide means that synthesis of DNA proceeds only in a 5%o V direction if only one primer is available, all newly synthesized DNA sequences begin at the same point. 

The incorporation of acyclovir triphosphate into calf thymus DNA primer template has been shown to be much more rapid and extensive with HSV-1 DNA polymerase than with vero cell DNA polymerase a. This incorporation of acyclovir ceased after 15 min since the template is chain terminated by the acyclovir incorporation, as there is no 3 -hydroxyl group on which to continue elongation. The viral DNA polymerase is also inactivated by tight binding to the terminated template. 

Chelation itself is sometimes useful in directing the course of synthesis. This is called the template effect (37). The presence of a suitable metal ion facihtates the preparation of the crown ethers, porphyrins, and similar heteroatom macrocycHc compounds. Coordination of the heteroatoms about the metal orients the end groups of the reactants for ring closure. The product is the chelate from which the metal may be removed by a suitable method. In other catalytic effects, reactive centers may be brought into close proximity, charge or bond strain effects may be created, or electron transfers may be made possible. 

It is interesting to note that although the first examples of template effects were observed in nitrogen macrocycles (see chapter 2) no template effect appears to operate in the synthesis of 72. Richman and Atkins note this in their original report . The authors replaced the sodium cation with tetramethylammonium cations and still obtained greater than 50% yield of tetra-N-tosyl-72. Shaw considered this problem and suggested that because of the bulky N-tosyl groups, .. . the loss of internal entropy on cyclization is small He offered this as an explanation for the apparent lack of a template effect in the cyclization. 

Because dideoxynucleotides lack 3 -OH groups, these nucleotides cannot serve as acceptors for 5 -nucleotide addition in the polymerization reaction, and thus the chain is terminated where they become incorporated. The concentrations of the four deoxynucleotides and the single dideoxynucleotide in each reaction mixture are adjusted so that the dideoxynucleotide is incorporated infrequently. Therefore, base-specific premature chain termination is only a random, occasional event, and a population of new strands of varying length is synthesized. Four reactions are run, one for each dideoxynucleotide, so that termination, although random, can occur everywhere in the sequence. In each mixture, each newly synthesized strand has a dideoxynucleotide at its 3 -end, and its presence at that position demonstrates that a base of that particular kind was specified by the template. A radioactively labeled dNTP is included in each reaction mixture to provide a tracer for the products of the polymerization process. 

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